(v1.6.0.9014) as.rsi() for numeric values

(v1.6.0.9013) website update
2024-12-26 20:06:11 +01:00 · 2021-04-30 13:18:48 +02:00 · 2021-04-29 17:16:30 +02:00
44 changed files with 992 additions and 913 deletions
--- a/4
+++ b/4
@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.6.0.9012
-Date: 2021-04-27
+Version: 1.6.0.9014
+Date: 2021-04-30
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
    person(role = c("aut", "cre"), 
--- a/NEWS.md
+++ b/NEWS.md
@ -1,15 +1,14 @@
-# AMR 1.6.0.9012
-## <small>Last updated: 27 April 2021</small>
+# `AMR` 1.6.0.9014
+## <small>Last updated: 30 April 2021</small>

 ### New
 * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
 * Support for all four methods to determine first isolates as summarised by Hindler *et al* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
-  * Since fungal isolates can also be selected, new functions `key_antimicrobials()` and `all_antimicrobials()` have replaced the now deprecated function `key_antibiotics()`
-  * Using `key_antimicrobials()` still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new `antifungal` argument to set antifungal agents (antimycotics).
-  * The `first_isolate()` function gained the argument `method` that has to be "phenotype-based", "episode-based", "patient-based", or "isolate-based". The old behaviour is equal to "episode-based", while the new default is "phenotype-based".
+  * The `first_isolate()` function gained the argument `method` that has to be "phenotype-based", "episode-based", "patient-based", or "isolate-based". The old behaviour is equal to "episode-based". The new default is "phenotype-based" if antimicrobial test results are available, and "episode-based" otherwise. This new default will yield slightly more isolates for selection (which is a good thing).
+  * Since fungal isolates can also be selected, the functions `key_antibiotics()` and `key_antibiotics_equal()` are now deprecated in favour of the `key_antimicrobials()` and `antimicrobial_equal()` functions. Also, the new `all_antimicrobials()` function works like the old `key_antibiotics()` function, but includes any column with antimicrobial test results. Using `key_antimicrobials()` still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a new `antifungal` argument to set antifungal agents (antimycotics).
  * Using `type == "points"` in the `first_isolate()` function for phenotype-based selection will now consider all antimicrobial drugs in the data set, using the new `all_antimicrobials()`
  * The `first_isolate()` function can now take a vector of values for `col_keyantibiotics` and can have an episode length of `Inf`
-  * The `filter_first_isolate()` function has not changed, as it uses the episode-based method. The `filter_first_weighted_isolate()` may now include more isolates as uses the phenotype-based method.
+  * Since the phenotype-based method is the new default, `filter_first_isolate()` renders the `filter_first_weighted_isolate()` function redundant. For this reason, `filter_first_weighted_isolate()` is now deprecated.
  * The documentation of the `first_isolate()` and `key_antimicrobials()` functions has been completely rewritten.

 ### Changed
@ -32,9 +31,11 @@
 * Fixed an installation error on R-3.0
 * Added `info` argument to `as.mo()` to turn on/off the progress bar
 * Fixed a bug that `col_mo` for some functions (esp. `eucast_rules()` and `mdro()`) could not be column names of the `microorganisms` data set as it would throw an error
+* Fix for transforming numeric values to RSI (`as.rsi()`) when the `vctrs` package is loaded (i.e., when using tidyverse)
+* Colour fix for using `barplot()` on an RSI class


-# AMR 1.6.0
+# `AMR` 1.6.0

 ### New
 * Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
@ -128,7 +129,7 @@
 * Loading the package (i.e., `library(AMR)`) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)


-# AMR 1.5.0
+# `AMR` 1.5.0

 ### New
 * Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
@ -205,7 +206,7 @@
 * Added CodeFactor as a continuous code review to this package: <https://www.codefactor.io/repository/github/msberends/amr/>
 * Added Dr. Rogier Schade as contributor

-# AMR 1.4.0
+# `AMR` 1.4.0

 ### New
 * Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the `eucast_rules()` function can now correct for more than 180 different antibiotics and the `mdro()` function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The `eucast_rules()` function consequently gained the arguments `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2. The `mdro()` function now accepts `guideline == "EUCAST3.1"` and `guideline == "EUCAST3.2"`.
@ -277,7 +278,7 @@
 * Removed unnecessary references to the `base` package
 * Added packages that could be useful for some functions to the `Suggests` field of the `DESCRIPTION` file

-# AMR 1.3.0
+# `AMR` 1.3.0

 ### New
 * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@ -330,7 +331,7 @@
 ### Other
 * Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.

-# AMR 1.2.0
+# `AMR` 1.2.0

 ### Breaking 
 * Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.
@ -368,7 +369,7 @@
 * Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()`
 * Removed function `read.4d()`, that was only useful for reading data from an old test database.

-# AMR 1.1.0
+# `AMR` 1.1.0

 ### New
 * Support for easy principal component analysis for AMR, using the new `pca()` function 
@ -390,7 +391,7 @@
 * Support for the upcoming `dplyr` version 1.0.0
 * More robust assigning for classes `rsi` and `mic`

-# AMR 1.0.1
+# `AMR` 1.0.1

 ### Changed
 * Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
@ -406,7 +407,7 @@
 * Added `uti` (as abbreviation of urinary tract infections) as argument to `as.rsi()`, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
 * Info printing in functions `eucast_rules()`, `first_isolate()`, `mdro()` and `resistance_predict()` will now at default only print when R is in an interactive mode (i.e. not in RMarkdown)

-# AMR 1.0.0
+# `AMR` 1.0.0

 This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.

@ -454,7 +455,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 * Full support for the upcoming R 4.0
 * Removed unnecessary `AMR::` calls

-# AMR 0.9.0
+# `AMR` 0.9.0

 ### Breaking
 * Adopted Adeolu *et al.* (2016), [PMID 27620848](https:/pubmed.ncbi.nlm.nih.gov/27620848/) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
@ -520,7 +521,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 * Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request
 * Added Dr. Sofia Ny as contributor

-# AMR 0.8.0
+# `AMR` 0.8.0

 ### Breaking
 * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new argument `include_unknown`:
@ -649,7 +650,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 * Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
 * Cleaned the coding style of every single syntax line in this package with the help of the `lintr` package

-# AMR 0.7.1
+# `AMR` 0.7.1

 #### New
 * Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
@ -710,7 +711,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 #### Other
 * Fixed a note thrown by CRAN tests

-# AMR 0.7.0
+# `AMR` 0.7.0

 #### New
 * Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
@ -768,13 +769,13 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 #### Other
 * Support for R 3.6.0 and later by providing support for [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html)

-# AMR 0.6.1
+# `AMR` 0.6.1

 #### Changed
 * Fixed a critical bug when using `eucast_rules()` with `verbose = TRUE`
 * Coercion of microbial IDs are now written to the package namespace instead of the user's home folder, to comply with the CRAN policy

-# AMR 0.6.0
+# `AMR` 0.6.0

 **New website!**

@ -967,7 +968,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 #### Other
 * Updated licence text to emphasise GPL 2.0 and that this is an R package.

-# AMR 0.5.0
+# `AMR` 0.5.0

 #### New
 * Repository moved to GitLab
@ -1050,7 +1051,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 * Updated vignettes to comply with README


-# AMR 0.4.0
+# `AMR` 0.4.0

 #### New
 * The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms.
@ -1161,7 +1162,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 #### Other
 * More unit tests to ensure better integrity of functions

-# AMR 0.3.0
+# `AMR` 0.3.0

 #### New
 * **BREAKING**: `rsi_df` was removed in favour of new functions `portion_R`, `portion_IR`, `portion_I`, `portion_SI` and `portion_S` to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old `rsi` function. The old function still works, but is deprecated.
@ -1231,7 +1232,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
  * Windows: https://ci.appveyor.com/project/msberends/amr
 * Added thesis advisors to DESCRIPTION file

-# AMR 0.2.0
+# `AMR` 0.2.0

 #### New
 * Full support for Windows, Linux and macOS
@ -1266,7 +1267,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 * Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
 * Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)

-# AMR 0.1.1
+# `AMR` 0.1.1

 * `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
 * Edited column names to comply with GLIMS, the laboratory information system
@ -1274,6 +1275,6 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 * Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
 * Added barplots for `rsi` and `mic` classes

-# AMR 0.1.0
+# `AMR` 0.1.0

 * First submission to CRAN.
--- a/R/deprecated.R
+++ b/R/deprecated.R
@ -46,6 +46,31 @@ p_symbol <- function(p, emptychar = " ") {
  s
 }

+#' @name AMR-deprecated
+#' @export
+filter_first_weighted_isolate <- function(x = NULL,
+                                          col_date = NULL,
+                                          col_patient_id = NULL,
+                                          col_mo = NULL,
+                                          ...) {
+  
+  .Deprecated(old = "filter_first_weighted_isolate()",
+              new = "filter_first_isolate()",
+              package = "AMR")
+  
+  if (is_null_or_grouped_tbl(x)) {
+    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
+    # is also fix for using a grouped df as input (a dot as first argument)
+    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+  }
+  meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
+  meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
+  meet_criteria(col_patient_id, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
+  meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
+  
+  filter_first_isolate(x = x, col_date = col_date, col_patient_id = col_patient_id, col_mo = col_mo, ...)
+}
+
 #' @name AMR-deprecated
 #' @export
 key_antibiotics <- function(x = NULL,
--- a/R/episode.R
+++ b/R/episode.R
@ -29,13 +29,13 @@
 #' @inheritSection lifecycle Stable Lifecycle
 #' @param x vector of dates (class `Date` or `POSIXt`)
 #' @param episode_days required episode length in days, can also be less than a day or `Inf`, see *Details*
-#' @param ... currently not used
+#' @param ... ignored, only in place to allow future extensions
 #' @details 
 #' Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least `episode_days` days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least `episode_days` days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
 #' 
-#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but is more efficient for data sets containing microorganism codes or names.
+#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but is more efficient for data sets containing microorganism codes or names and allows for different isolate selection methods.
 #' 
-#' The `dplyr` package is not required for these functions to work, but these functions support [variable grouping][dplyr::group_by()] and work conveniently inside `dplyr` verbs such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
+#' The `dplyr` package is not required for these functions to work, but these functions do support [variable grouping][dplyr::group_by()] and work conveniently inside `dplyr` verbs such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
 #' @return 
 #' * [get_episode()]: a [double] vector
 #' * [is_new_episode()]: a [logical] vector
@ -85,8 +85,8 @@
 #'               n_episodes_30  = sum(is_new_episode(date, episode_days = 30)))
 #'     
 #'     
-#'   # grouping on patients and microorganisms leads to the same results
-#'   # as first_isolate():
+#'   # grouping on patients and microorganisms leads to the same
+#'   # results as first_isolate() when using 'episode-based':
 #'   x <- example_isolates %>%
 #'     filter_first_isolate(include_unknown = TRUE,
 #'                          method = "episode-based")
@ -127,7 +127,7 @@ is_new_episode <- function(x, episode_days, ...) {
 }

 exec_episode <- function(type, x, episode_days, ...) {
-  x <- as.double(as.POSIXct(x)) # as.POSIXct() for Date classes
+  x <- as.double(as.POSIXct(x)) # as.POSIXct() required for Date classes
  # since x is now in seconds, get seconds from episode_days as well
  episode_seconds <- episode_days * 60 * 60 * 24
  
--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@ -25,7 +25,7 @@

 #' Determine First (Weighted) Isolates
 #'
-#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package.
+#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler *et al.* in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package.
 #' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [data.frame] containing isolates. Can be left blank for automatic determination, see *Examples*.
 #' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column with a date class
@ -40,15 +40,15 @@
 #' @param icu_exclude logical to indicate whether ICU isolates should be excluded (rows with value `TRUE` in the column set with `col_icu`)
 #' @param specimen_group value in the column set with `col_specimen` to filter on
 #' @param type type to determine weighed isolates; can be `"keyantimicrobials"` or `"points"`, see *Details*
-#' @param method the algorithm to apply, either `"phenotype-based"`, `"episode-based"`, `"patient-based"` or `"isolate-based"` (can be abbreviated), see *Details*
+#' @param method the method to apply, either `"phenotype-based"`, `"episode-based"`, `"patient-based"` or `"isolate-based"` (can be abbreviated), see *Details*. The default is `"phenotype-based"` if antimicrobial test results are present in the data, and `"episode-based"` otherwise.
 #' @param ignore_I logical to indicate whether antibiotic interpretations with `"I"` will be ignored when `type = "keyantimicrobials"`, see *Details*
 #' @param points_threshold minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when `type = "points"`, see *Details*
 #' @param info a [logical] to indicate info should be printed, defaults to `TRUE` only in interactive mode
 #' @param include_unknown logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate.
 #' @param include_untested_rsi logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use `include_untested_rsi = FALSE` to always return `FALSE` for such rows. This checks the data set for columns of class `<rsi>` and consequently requires transforming columns with antibiotic results using [as.rsi()] first.
-#' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], or arguments passed on to [key_antimicrobials()] otherwise (such as `universal`, `gram_negative`, `gram_positive`)
+#' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], otherwise arguments passed on to [key_antimicrobials()] (such as `universal`, `gram_negative`, `gram_positive`)
 #' @details 
-#' To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different algorithms can be used to do so, see below.
+#' To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.
 #' 
 #' These functions are context-aware. This means that then the `x` argument can be left blank, see *Examples*.
 #' 
@ -56,51 +56,51 @@
 #' 
 #' All isolates with a microbial ID of `NA` will be excluded as first isolate.
 #' 
-#' ## Different algorithms
+#' ## Different methods
 #' 
-#' According to Hindler *et al.* (2007, \doi{10.1086/511864}), there are different algorithms to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All algorithms select on a combination of the taxonomic genus and species (not subspecies). 
+#' According to Hindler *et al.* (2007, \doi{10.1086/511864}), there are different methods (algorithms) to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All methods select on a combination of the taxonomic genus and species (not subspecies). 
 #' 
-#' All mentioned algorithms are covered in the [first_isolate()] function:
+#' All mentioned methods are covered in the [first_isolate()] function:
 #' 
 #' 
-#' | **Algorithm**                                    | **Function to apply**                                 |
+#' | **Method**                                       | **Function to apply**                                 |
 #' |--------------------------------------------------|-------------------------------------------------------|
-#' | Isolate-based                                    | `first_isolate(x, method = "isolate-based")`          |
+#' | **Isolate-based**                                | `first_isolate(x, method = "isolate-based")`          |
 #' | *(= all isolates)*                               |                                                       |
 #' |                                                  |                                                       |
 #' |                                                  |                                                       |
-#' | Patient-based                                    | `first_isolate(x, method = "patient-based")`          |
+#' | **Patient-based**                                | `first_isolate(x, method = "patient-based")`          |
 #' | *(= first isolate per patient)*                  |                                                       |
 #' |                                                  |                                                       |
 #' |                                                  |                                                       |
-#' | Episode-based                                    | `first_isolate(x, method = "episode-based")`, or:     |
+#' | **Episode-based**                                | `first_isolate(x, method = "episode-based")`, or:     |
 #' | *(= first isolate per episode)*                  |                                                       |
 #' | - 7-Day interval from initial isolate            | - `first_isolate(x, method = "e", episode_days = 7)`  |
 #' | - 30-Day interval from initial isolate           | - `first_isolate(x, method = "e", episode_days = 30)` |
 #' |                                                  |                                                       |
 #' |                                                  |                                                       |
-#' | Phenotype-based                                  | `first_isolate(x, method = "phenotype-based")`, or:   |
+#' | **Phenotype-based**                              | `first_isolate(x, method = "phenotype-based")`, or:   |
 #' | *(= first isolate per phenotype)*                |                                                       |
 #' | - Major difference in any antimicrobial result   | - `first_isolate(x, type = "points")`                 |
 #' | - Any difference in key antimicrobial results    | - `first_isolate(x, type = "keyantimicrobials")`      |
 #' 
 #' ### Isolate-based
 #' 
-#' This algorithm does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the [first_isolate()] function. For example, the default setting for `include_unknown` (`FALSE`) will omit selection of rows without a microbial ID.
+#' This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the [first_isolate()] function. For example, the default setting for `include_unknown` (`FALSE`) will omit selection of rows without a microbial ID.
 #' 
 #' ### Patient-based
 #' 
-#' To include every genus-species combination per patient once, set the `episode_days` to `Inf`. Although often inappropriate, this algorithm makes sure that no duplicate isolates are selected from the same patient.
+#' To include every genus-species combination per patient once, set the `episode_days` to `Inf`. Although often inappropriate, this method makes sure that no duplicate isolates are selected from the same patient. In a large longitudinal data set, this could mean that isolates are *excluded* that were found years after the initial isolate.
 #' 
 #' ### Episode-based
 #' 
 #' To include every genus-species combination per patient episode once, set the `episode_days` to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data, long episodes are common for analysing regional and national data.
 #' 
-#' This is the most common algorithm to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common algorithm, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant *Staphylococcus aureus* (MRSA) isolate cannot be differentiated from a wildtype *Staphylococcus aureus* isolate.
+#' This is the most common method to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common method, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant *Staphylococcus aureus* (MRSA) isolate cannot be differentiated from a wildtype *Staphylococcus aureus* isolate.
 #' 
 #' ### Phenotype-based
 #' 
-#' This is a more reliable algorithm, since it also *weighs* the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
+#' This is a more reliable method, since it also *weighs* the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
 #' 
 #' 1. Using `type = "points"` and argument `points_threshold`
 #' 
@ -116,14 +116,16 @@
 #'    Key antimicrobials are internally selected using the [key_antimicrobials()] function, but can also be added manually as a variable to the data and set in the `col_keyantimicrobials` argument. Another option is to pass the output of the [key_antimicrobials()] function directly to the `col_keyantimicrobials` argument.
 #'    
 #'    
-#' The default algorithm is phenotype-based (using `type = "points"`) and episode-based (using `episode_days = 365`). This makes sure that every genus-species combination is selected per patient once per year, while taking into account all antimicrobial test results.
+#' The default method is phenotype-based (using `type = "points"`) and episode-based (using `episode_days = 365`). This makes sure that every genus-species combination is selected per patient once per year, while taking into account all antimicrobial test results. If no antimicrobial test results are available in the data set, only the episode-based method is applied at default.
 #' @rdname first_isolate
 #' @seealso [key_antimicrobials()]
 #' @export
 #' @return A [`logical`] vector
 #' @source Methodology of this function is strictly based on:
 #' 
-#' **M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition**, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
+#' - **M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition**, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
+#' 
+#' - Hindler JF and Stelling J (2007). **Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.** Clinical Infectious Diseases, 44(6), 867–873. \doi{10.1086/511864}
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' # `example_isolates` is a data set available in the AMR package.
@ -142,11 +144,9 @@
 #'   example_isolates %>%
 #'     filter(first_isolate())
 #'  
-#'   # short-hand versions:
+#'   # short-hand version:
 #'   example_isolates %>%
 #'     filter_first_isolate()
-#'   example_isolates %>%
-#'     filter_first_weighted_isolate()
 #'     
 #'  # grouped determination of first isolates (also prints group names):
 #'  example_isolates %>%
@ -160,7 +160,7 @@
 #'               resistance = resistance(GEN))  # gentamicin resistance
 #'  
 #'   B <- example_isolates %>%
-#'     filter_first_weighted_isolate() %>%      # the 1st isolate filter
+#'     filter_first_isolate() %>%               # the 1st isolate filter
 #'     group_by(hospital_id) %>%
 #'     summarise(count = n_rsi(GEN),            # gentamicin availability
 #'               resistance = resistance(GEN))  # gentamicin resistance
@ -220,9 +220,7 @@ first_isolate <- function(x = NULL,
  meet_criteria(col_specimen, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
  meet_criteria(col_icu, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
  # method
-  if (missing(method)) {
-    method <- method[1L]
-  }
+  method <- coerce_method(method)
  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based", "p", "e", "i"))
  # key antimicrobials
  if (length(col_keyantimicrobials) > 1) {
@ -233,7 +231,7 @@ first_isolate <- function(x = NULL,
    if (isFALSE(col_keyantimicrobials)) {
      col_keyantimicrobials <- NULL
      # method cannot be phenotype-based anymore
-      if (method %in% c("phenotype-based", "p")) {
+      if (method == "phenotype-based") {
        method <- "episode-based"
      }
    }
@ -250,10 +248,17 @@ first_isolate <- function(x = NULL,
  meet_criteria(include_unknown, allow_class = "logical", has_length = 1)
  meet_criteria(include_untested_rsi, allow_class = "logical", has_length = 1)
  
-  method[method == "p"] <- "phenotype-based"
-  method[method == "e"] <- "episode-based"
-  method[method == "i"] <- "isolate-based"
-  if (info == TRUE) {
+  # remove data.table, grouping from tibbles, etc.
+  x <- as.data.frame(x, stringsAsFactors = FALSE)
+  
+  any_col_contains_rsi <- any(vapply(FUN.VALUE = logical(1), 
+                                     X = x, 
+                                     FUN = function(x) any(as.character(x) %in% c("R", "S", "I"), na.rm = TRUE),
+                                     USE.NAMES = FALSE))
+  if (method == "phenotype-based" & !any_col_contains_rsi) {
+    method <- "episode-based"
+  }
+  if (info == TRUE & message_not_thrown_before("first_isolate.method")) {
    message_(paste0("Determining first isolates using the '", font_bold(method), "' method",
                    ifelse(method %in% c("episode-based", "phenotype-based"),
                           ifelse(is.infinite(episode_days),
@ -262,11 +267,9 @@ first_isolate <- function(x = NULL,
                           "")),
             as_note = FALSE,
             add_fn = font_black)
+    remember_thrown_message("first_isolate.method")
  }
  
-  # remove data.table, grouping from tibbles, etc.
-  x <- as.data.frame(x, stringsAsFactors = FALSE)
-  
  # try to find columns based on type
  # -- mo
  if (is.null(col_mo)) {
@ -360,10 +363,11 @@ first_isolate <- function(x = NULL,
    testcodes_exclude <- NULL
  }
  # remove testcodes
-  if (!is.null(testcodes_exclude) & info == TRUE) {
+  if (!is.null(testcodes_exclude) & info == TRUE & message_not_thrown_before("first_isolate.excludingtestcodes")) {
    message_("Excluding test codes: ", toString(paste0("'", testcodes_exclude, "'")),
             add_fn = font_black,
             as_note = FALSE)
+    remember_thrown_message("first_isolate.excludingtestcodes")
  }
  
  if (is.null(col_specimen)) {
@ -373,10 +377,11 @@ first_isolate <- function(x = NULL,
  # filter on specimen group and keyantibiotics when they are filled in
  if (!is.null(specimen_group)) {
    check_columns_existance(col_specimen, x)
-    if (info == TRUE) {
+    if (info == TRUE & message_not_thrown_before("first_isolate.excludingspecimen")) {
      message_("Excluding other than specimen group '", specimen_group, "'",
               add_fn = font_black,
               as_note = FALSE)
+      remember_thrown_message("first_isolate.excludingspecimen")
    }
  }
  if (!is.null(col_keyantimicrobials)) {
@ -449,18 +454,16 @@ first_isolate <- function(x = NULL,
                              FALSE,
                              TRUE)
  x$episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
-  x$more_than_episode_ago <- unlist(lapply(unique(x$episode_group),
-                                           function(g,
-                                                    df = x,
-                                                    days = episode_days) {
-                                             is_new_episode(x = df[which(df$episode_group == g), ]$newvar_date,
-                                                            episode_days = days)
-                                           }))
+  x$more_than_episode_ago <- unlist(lapply(split(x$newvar_date,
+                                                 x$episode_group), 
+                                           is_new_episode,
+                                           episode_days = episode_days),
+                                    use.names = FALSE)
  
  weighted.notice <- ""
  if (!is.null(col_keyantimicrobials)) {
    weighted.notice <- "weighted "
-    if (info == TRUE) {
+    if (info == TRUE & message_not_thrown_before("first_isolate.type")) {
      if (type == "keyantimicrobials") {
        message_("Basing inclusion on key antimicrobials, ",
                 ifelse(ignore_I == FALSE, "not ", ""),
@ -474,6 +477,7 @@ first_isolate <- function(x = NULL,
                 add_fn = font_black,
                 as_note = FALSE)
      }
+      remember_thrown_message("first_isolate.type")
    }
    type_param <- type
    
@ -481,8 +485,7 @@ first_isolate <- function(x = NULL,
                                            z = pm_lag(x$newvar_key_ab),
                                            type = type_param,
                                            ignore_I = ignore_I,
-                                            points_threshold = points_threshold,
-                                            na.rm = TRUE)
+                                            points_threshold = points_threshold)
    # with key antibiotics
    x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
                                           x$newvar_row_index_sorted <= row.end &
@ -540,7 +543,8 @@ first_isolate <- function(x = NULL,
          }
        })
        message_("\nGroup: ", paste0(names(group), " = ", group, collapse = ", "), "\n",
-                 as_note = FALSE)
+                 as_note = FALSE,
+                 add_fn = font_red)
      }
    }
  }
@ -608,7 +612,8 @@ filter_first_isolate <- function(x = NULL,
                                 col_date = NULL,
                                 col_patient_id = NULL,
                                 col_mo = NULL,
-                                 method = "episode-based",
+                                 episode_days = 365,
+                                 method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
                                 ...) {
  if (is_null_or_grouped_tbl(x)) {
    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
@ -619,39 +624,27 @@ filter_first_isolate <- function(x = NULL,
  meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
  meet_criteria(col_patient_id, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
  meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
-  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based"))
+  meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
+  method <- coerce_method(method)
+  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based", "p", "e", "i"))
  
  subset(x, first_isolate(x = x,
                          col_date = col_date,
                          col_patient_id = col_patient_id,
                          col_mo = col_mo,
+                          episode_days = episode_days,
                          method = method,
                          ...))
 }

-#' @rdname first_isolate
-#' @export
-filter_first_weighted_isolate <- function(x = NULL,
-                                          col_date = NULL,
-                                          col_patient_id = NULL,
-                                          col_mo = NULL,
-                                          method = "phenotype-based",
-                                          ...) {
-  if (is_null_or_grouped_tbl(x)) {
-    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
-    # is also fix for using a grouped df as input (a dot as first argument)
-    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
+coerce_method <- function(method) {
+  if (is.null(method)) {
+    return(method)
  }
-  meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
-  meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
-  meet_criteria(col_patient_id, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
-  meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
-  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based"))
-  
-  subset(x, first_isolate(x = x,
-                          col_date = col_date,
-                          col_patient_id = col_patient_id,
-                          col_mo = col_mo,
-                          method = method,
-                          ...))
+  method <- tolower(as.character(method[1L]))
+  method[method %like% "^(p$|pheno)"] <- "phenotype-based"
+  method[method %like% "^(e$|episode)"] <- "episode-based"
+  method[method %like% "^patient"] <- "patient-based"
+  method[method %like% "^(i$|iso)"] <- "isolate-based"
+  method
 }
--- a/R/ggplot_pca.R
+++ b/R/ggplot_pca.R
@ -47,7 +47,7 @@
 #' @param arrows_textangled a logical whether the text at the end of the arrows should be angled
 #' @param arrows_alpha the alpha (transparency) of the arrows and their text
 #' @param base_textsize the text size for all plot elements except the labels and arrows
-#' @param ... Arguments passed on to functions
+#' @param ... arguments passed on to functions
 #' @source The [ggplot_pca()] function is based on the `ggbiplot()` function from the `ggbiplot` package by Vince Vu, as found on GitHub: <https://github.com/vqv/ggbiplot> (retrieved: 2 March 2020, their latest commit: [`7325e88`](https://github.com/vqv/ggbiplot/commit/7325e880485bea4c07465a0304c470608fffb5d9); 12 February 2015).
 #' 
 #' As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were: 
--- a/R/join_microorganisms.R
+++ b/R/join_microorganisms.R
@ -33,7 +33,7 @@
 #' @param x existing table to join, or character vector
 #' @param by a variable to join by - if left empty will search for a column with class [`mo`] (created with [as.mo()]) or will be `"mo"` if that column name exists in `x`, could otherwise be a column name of `x` with values that exist in `microorganisms$mo` (such as `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("bacteria_id" = "fullname")`)
 #' @param suffix if there are non-joined duplicate variables in `x` and `y`, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.
-#' @param ... ignored
+#' @param ... ignored, only in place to allow future extensions
 #' @details **Note:** As opposed to the `join()` functions of `dplyr`, [character] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix. 
 #' 
 #' If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] function from base R will be used.
--- a/R/key_antimicrobials.R
+++ b/R/key_antimicrobials.R
@ -35,7 +35,7 @@
 #' @param gram_positive names of antibiotic agents for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents.
 #' @param antifungal names of antifungal agents for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents.
 #' @param only_rsi_columns a logical to indicate whether only columns must be included that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
-#' @param ... ignored, allows for future extensions
+#' @param ... ignored, only in place to allow future extensions
 #' @details 
 #' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that then the `x` argument can be left blank, see *Examples*.
 #' 
@ -264,14 +264,12 @@ generate_antimcrobials_string <- function(df) {
 }

 #' @rdname key_antimicrobials
-#' @param info unused - previously used to indicate whether a progress bar should print
 #' @export
 antimicrobials_equal <- function(y,
                                  z,
                                  type = c("points", "keyantimicrobials"),
                                  ignore_I = TRUE,
                                  points_threshold = 2,
-                                  info = FALSE,
                                  ...) {
  meet_criteria(y, allow_class = "character")
  meet_criteria(z, allow_class = "character")
@ -279,7 +277,6 @@ antimicrobials_equal <- function(y,
  meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("points", "keyantimicrobials"))
  meet_criteria(ignore_I, allow_class = "logical", has_length = 1)
  meet_criteria(points_threshold, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
-  meet_criteria(info, allow_class = "logical", has_length = 1)
  stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")

  key2rsi <- function(val) {
--- a/R/plot.R
+++ b/R/plot.R
@ -586,6 +586,8 @@ barplot.rsi <- function(height,
  
  if (length(colours_RSI) == 1) {
    colours_RSI <- rep(colours_RSI, 3)
+  } else {
+    colours_RSI <- c(colours_RSI[2], colours_RSI[3], colours_RSI[1])
  }
  main <- gsub(" +", " ", paste0(main, collapse = " "))
  
--- a/R/random.R
+++ b/R/random.R
@ -31,7 +31,7 @@
 #' @param mo any character that can be coerced to a valid microorganism code with [as.mo()]
 #' @param ab any character that can be coerced to a valid antimicrobial agent code with [as.ab()]
 #' @param prob_RSI a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value)
-#' @param ... extension for future versions, not used at the moment
+#' @param ... ignored, only in place to allow future extensions
 #' @details The base R function [sample()] is used for generating values.
 #' 
 #' Generated values are based on the latest EUCAST guideline implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
--- a/R/rsi.R
+++ b/R/rsi.R
@ -259,9 +259,10 @@ as.rsi.default <- function(x, ...) {
  }
  
  if (inherits(x, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
-    x[x == 1] <- "S"
-    x[x == 2] <- "I"
-    x[x == 3] <- "R"
+    x <- as.character(x) # this is needed to prevent the vctrs pkg to throw an error
+    x[x == "1"] <- "S"
+    x[x == "2"] <- "I"
+    x[x == "3"] <- "R"
    
  } else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !all(x %in% c("R", "S", "I", NA))) {

--- a/R/sysdata.rda
+++ b/R/sysdata.rda
--- a/data-raw/AMR_latest.tar.gz
+++ b/data-raw/AMR_latest.tar.gz
--- a/docs/404.html
+++ b/docs/404.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
      </span>
    </div>

@ -89,14 +89,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -105,77 +105,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -184,21 +184,21 @@
 </li>
 <li>
  <a href="reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -207,14 +207,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
      </span>
    </div>

@ -89,14 +89,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -105,77 +105,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -184,21 +184,21 @@
 </li>
 <li>
  <a href="reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -207,14 +207,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
      </span>
    </div>

@ -89,14 +89,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -105,77 +105,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -184,21 +184,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -207,14 +207,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
--- a/docs/authors.html
+++ b/docs/authors.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
      </span>
    </div>

@ -89,14 +89,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -105,77 +105,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -184,21 +184,21 @@
 </li>
 <li>
  <a href="reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -207,14 +207,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -240,10 +240,11 @@
    <pre>@Article{,
  title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
  author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
+  doi = {1.24720276528394e-05},
  journal = {bioRxiv},
  publisher = {Cold Spring Harbor Laboratory},
  year = {2021},
-  url = {https://doi.org/10.1101/810622},
+  url = {https://www.biorxiv.org/content/10.1101/810622v4},
 }</pre>

    <div class="page-header">
--- a/docs/extra.css
+++ b/docs/extra.css
@ -25,14 +25,18 @@
 # ==================================================================== #
 */

-/* R for Data Science (r4ds) */
-#r4ds a {
-  display: inline-flex;
-  align-items: center;
-  text-align: right;
+/* R for Data Science (r4ds) on vignettes (articles) */
+#r4ds {
+  display: flex;
+  border-bottom: 1px solid #ddd;
+  margin-bottom: 10px;
+  padding-bottom: 10px;
 }
-#r4ds img {
-  margin-left: 10px;
+#r4ds .txt {
+  width: 67%;
+}
+#r4ds .img {
+  width: 33%;
 }

 /* class for footer */
@ -196,16 +200,20 @@ div[id^=last-updated] h2 {
 .table td {
  padding: 4px !important;
 }
-.table thead {
+.table thead,
+.template-reference-topic .table tr:first-child {
+  /* tables in manual are in LaTeX and thus have no thead */
  border-top: 2px solid black;
  border-bottom: 2px solid black;
 }
-.table thead ~ tbody {
+.table thead ~ tbody,
+.template-reference-topic .table tr:last-child {
  /* only when it has a header */
+  /* tables in manual are in LaTeX and thus have no thead */
  border-bottom: 2px solid black;
 }
 .table thead th {
-  text-align: inherit; 
+  /* text-align: inherit; */
 }
 /* all tables, including argument lists */
 table a:not(.btn) {
@ -227,6 +235,8 @@ table a:not(.btn):hover {
 }
 .template-reference-topic h4 {
  font-size: 15px;
+  font-weight: bold;
+  padding-top: 35px;
 }

 .template-home h4 {
--- a/docs/extra.js
+++ b/docs/extra.js
@ -30,12 +30,6 @@ $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" hr

 $(document).ready(function() {

-  // add SurveyMonkey
-  // $('body').append('<script>(function(t,e,s,o){var n,a,c;t.SMCX=t.SMCX||[],e.getElementById(o)||(n=e.getElementsByTagName(s),a=n[n.length-1],c=e.createElement(s),c.type="text/javascript",c.async=!0,c.id=o,c.src=["https:"===location.protocol?"https://":"http://","widget.surveymonkey.com/collect/website/js/tRaiETqnLgj758hTBazgd_2BrwaGaWbg59AiLjNGdPaaJiBHKqgXKIw46VauwBvZ67.js"].join(""),a.parentNode.insertBefore(c,a))})(window,document,"script","smcx-sdk");</script>');
-  // add link to survey at home sidebar
-  // $('.template-home #sidebar .list-unstyled:first').append('<li><strong>Please fill in our survey at</strong> <br><a href="https://www.surveymonkey.com/r/AMR_for_R" target="_blank">https://www.surveymonkey.com/r/AMR_for_R</a></li>');
-
-
  // remove version label from header
  $(".version.label").remove();

@ -45,21 +39,38 @@ $(document).ready(function() {
  if (url_old != url_new) {
    window.location.replace(url_new);
  }
+  
+  // Edit title of manual
+  $('.template-reference-index h1').text('Manual');

-  // Replace 'Value' in manual to 'Returned value'
+  // replace 'Value' in manual with 'Returned value'
  $(".template-reference-topic h2#value").text("Returned value");
+  
+  // replace \donttest and \dontrun texts in Examples
+  if ($("pre.examples").length > 0) {
+    $("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", ""));
+    $("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", ""));
+    $("pre.examples").html($("pre.examples").html().replaceAll("# }", ""));
+  }

  // PR for 'R for Data Science' on How To pages
  if ($(".template-article").length > 0) {
-    $('#sidebar').prepend(
+    $('#pkgdown-sidebar').prepend(
    '<div id="r4ds">' +
-    '  <a target="_blank" href="https://r4ds.had.co.nz/">' +
-    '    Learn R reading this great book: R for Data Science.' +
-    '    <br><br>' +
-    '    Click to read it online - it was published for free.' +
-    '    <img src="https://github.com/msberends/AMR/raw/master/docs/cover_r4ds.png" height="100px">' +
-    '  </a>     ' +
-    '  <hr>' +
+    '  <div class="txt">' +
+    '    <p>' +
+    '      Learn R reading this great book: <i>R for Data Science</i>.' +
+    '      <br><br>' +
+    '      <a target="_blank" href="https://r4ds.had.co.nz/">' +
+    '        Click to read it online - it was published for free.' +
+    '      </a>' +
+    '    </p>' +
+    '  </div>' +
+    '  <div class="img">' +
+    '    <a target="_blank" href="https://r4ds.had.co.nz/">' +
+    '      <img src="https://github.com/msberends/AMR/raw/master/docs/cover_r4ds.png">' +
+    '    </a>' +
+    '  </div>' +
    '</div>');
  }

@ -96,13 +107,10 @@ $(document).ready(function() {
  }
  $(".template-authors").html(doct_tit($(".template-authors").html()));
  $(".template-citation-authors").html(doct_tit($(".template-citation-authors").html()));
-  $('.template-citation-authors h1').eq(0).text('How to cite');
-  $('.template-citation-authors h1').eq(1).text('All contributors');
+  $('.template-citation-authors h1').eq(0).html("How to cite the <code>AMR</code> package");
+  $('.template-citation-authors h1').eq(1).html("All contributors of the <code>AMR</code> package");
  $(".developers").html(doct_tit($(".developers").html()));
  $(".developers a[href='authors.html']").text("All contributors...");
-
-  // Edit title of manual
-  $('.template-reference-index h1').text('Manual');
 });

 $('head').append("<!-- Global site tag (gtag.js) - Google Analytics --> <script async src=\"https://www.googletagmanager.com/gtag/js?id=UA-172114740-1\"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-172114740-1'); </script><!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.github.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);  })();</script><!-- End Matomo Code -->");
--- a/docs/index.html
+++ b/docs/index.html
@ -42,7 +42,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
      </span>
    </div>

@ -50,14 +50,14 @@
      <ul class="nav navbar-nav">
 <li>
  <a href="index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -66,77 +66,77 @@
  <ul class="dropdown-menu" role="menu">
 <li>
      <a href="articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -145,21 +145,21 @@
 </li>
 <li>
  <a href="reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -168,14 +168,14 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -212,8 +212,8 @@
 <div id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="section level5">
 <h5 class="hasAnchor">
 <a href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="anchor"></a>With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!</h5>
-<div class="sourceCode" id="cb1"><pre class="downlit">
-<span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>

@ -227,7 +227,7 @@
 <span class="co">#&gt;       'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020).</span>
 <span class="co">#&gt; Selecting aminoglycosides: columns 'AMK' (amikacin), 'GEN' (gentamicin), </span>
 <span class="co">#&gt;       'KAN' (kanamycin) and 'TOB' (tobramycin)</span>
-<span class="co">#&gt; Selecting carbapenems: columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></pre></div>
+<span class="co">#&gt; Selecting carbapenems: columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></code></pre></div>
 <p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
 <table class="table">
 <thead><tr class="header">
@ -333,18 +333,18 @@
 </tbody>
 </table>
 <p>A base R equivalent would be, giving the exact same results:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit">
-<span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span>
 <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span>
                         <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span>,
-                 <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></pre></div>
+                 <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></code></pre></div>
 </div>
 <div id="partners" class="section level4">
 <h4 class="hasAnchor">
 <a href="#partners" class="anchor"></a>Partners</h4>
 <p>The development of this package is part of, related to, or made possible by:</p>
 <div align="center">
-<a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a>
+<p><a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a></p>
 </div>
 </div>
 </div>
@ -379,8 +379,8 @@
 <a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
 <p><a href="https://cran.r-project.org/package=AMR"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
 <p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
 <p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
 <p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
 </div>
@ -389,9 +389,9 @@
 <a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
 <p><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"><a href="https://www.codefactor.io/repository/github/msberends/amr"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" alt="Codecov"></a></p>
 <p>The latest and unpublished development version can be installed from GitHub using:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
-<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
+<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
 <p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz" class="uri">https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz</a></p>
 </div>
 </div>
--- a/docs/news/index.html
+++ b/docs/news/index.html
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@ -1,4 +1,4 @@
-pandoc: '2.6'
+pandoc: 2.11.2
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
@ -12,7 +12,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-04-27T09:08Z
+last_built: 2021-04-30T08:14Z
 urls:
  reference: https://msberends.github.io/AMR//reference
  article: https://msberends.github.io/AMR//articles
--- a/docs/reference/AMR-deprecated.html
+++ b/docs/reference/AMR-deprecated.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
      </span>
    </div>

@ -244,6 +244,14 @@

    <pre class="usage"><span class='fu'>p_symbol</span><span class='op'>(</span><span class='va'>p</span>, emptychar <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span>

+<span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span>
+  x <span class='op'>=</span> <span class='cn'>NULL</span>,
+  col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
+  col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
+  col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span>
+
 <span class='fu'>key_antibiotics</span><span class='op'>(</span>
  x <span class='op'>=</span> <span class='cn'>NULL</span>,
  col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
--- a/docs/reference/first_isolate.html
+++ b/docs/reference/first_isolate.html
@ -49,7 +49,8 @@
  <script src="../extra.js"></script>

 <meta property="og:title" content="Determine First (Weighted) Isolates — first_isolate" />
-<meta property="og:description" content="Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package." />
+<meta property="og:description" content="Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi: 10.1086/511864
+). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />


@ -82,7 +83,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
      </span>
    </div>

@ -239,7 +240,8 @@
    </div>

    <div class="ref-description">
-    <p>Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use <code><a href='get_episode.html'>is_new_episode()</a></code> that also supports grouping with the <code>dplyr</code> package.</p>
+    <p>Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler <em>et al.</em> in 2007 (doi: <a href='https://doi.org/10.1086/511864'>10.1086/511864</a>
+). To determine patient episodes not necessarily based on microorganisms, use <code><a href='get_episode.html'>is_new_episode()</a></code> that also supports grouping with the <code>dplyr</code> package.</p>
    </div>

    <pre class="usage"><span class='fu'>first_isolate</span><span class='op'>(</span>
@ -270,16 +272,8 @@
  col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
  col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
  col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
-  method <span class='op'>=</span> <span class='st'>"episode-based"</span>,
-  <span class='va'>...</span>
-<span class='op'>)</span>
-
-<span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span>
-  x <span class='op'>=</span> <span class='cn'>NULL</span>,
-  col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
-  col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
-  col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
-  method <span class='op'>=</span> <span class='st'>"phenotype-based"</span>,
+  episode_days <span class='op'>=</span> <span class='fl'>365</span>,
+  method <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"phenotype-based"</span>, <span class='st'>"episode-based"</span>, <span class='st'>"patient-based"</span>, <span class='st'>"isolate-based"</span><span class='op'>)</span>,
  <span class='va'>...</span>
 <span class='op'>)</span></pre>

@ -340,7 +334,7 @@
    </tr>
    <tr>
      <th>method</th>
-      <td><p>the algorithm to apply, either <code>"phenotype-based"</code>, <code>"episode-based"</code>, <code>"patient-based"</code> or <code>"isolate-based"</code> (can be abbreviated), see <em>Details</em></p></td>
+      <td><p>the method to apply, either <code>"phenotype-based"</code>, <code>"episode-based"</code>, <code>"patient-based"</code> or <code>"isolate-based"</code> (can be abbreviated), see <em>Details</em>. The default is <code>"phenotype-based"</code> if antimicrobial test results are present in the data, and <code>"episode-based"</code> otherwise.</p></td>
    </tr>
    <tr>
      <th>ignore_I</th>
@ -364,44 +358,47 @@
    </tr>
    <tr>
      <th>...</th>
-      <td><p>arguments passed on to <code>first_isolate()</code> when using <code>filter_first_isolate()</code>, or arguments passed on to <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code> otherwise (such as <code>universal</code>, <code>gram_negative</code>, <code>gram_positive</code>)</p></td>
+      <td><p>arguments passed on to <code>first_isolate()</code> when using <code>filter_first_isolate()</code>, otherwise arguments passed on to <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code> (such as <code>universal</code>, <code>gram_negative</code>, <code>gram_positive</code>)</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

-    <p>Methodology of this function is strictly based on:</p>
-<p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
+    <p>Methodology of this function is strictly based on:</p><ul>
+<li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
+<li><p>Hindler JF and Stelling J (2007). <strong>Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.</strong> Clinical Infectious Diseases, 44(6), 867–873. doi: <a href='https://doi.org/10.1086/511864'>10.1086/511864</a></p></li>
+</ul>
+
    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>A <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector</p>
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

-    <p>To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different algorithms can be used to do so, see below.</p>
+    <p>To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.</p>
 <p>These functions are context-aware. This means that then the <code>x</code> argument can be left blank, see <em>Examples</em>.</p>
 <p>The <code>first_isolate()</code> function is a wrapper around the <code><a href='get_episode.html'>is_new_episode()</a></code> function, but more efficient for data sets containing microorganism codes or names.</p>
-<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Different algorithms</h3>
+<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Different methods</h3>


 <p>According to Hindler <em>et al.</em> (2007, doi: <a href='https://doi.org/10.1086/511864'>10.1086/511864</a>
-), there are different algorithms to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All algorithms select on a combination of the taxonomic genus and species (not subspecies).</p>
-<p>All mentioned algorithms are covered in the <code>first_isolate()</code> function:</p><table class='table'>
-<tr><td><strong>Algorithm</strong></td><td><strong>Function to apply</strong></td></tr>
-<tr><td>Isolate-based</td><td><code>first_isolate(x, method = "isolate-based")</code></td></tr>
+), there are different methods (algorithms) to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All methods select on a combination of the taxonomic genus and species (not subspecies).</p>
+<p>All mentioned methods are covered in the <code>first_isolate()</code> function:</p><table class='table'>
+<tr><td><strong>Method</strong></td><td><strong>Function to apply</strong></td></tr>
+<tr><td><strong>Isolate-based</strong></td><td><code>first_isolate(x, method = "isolate-based")</code></td></tr>
 <tr><td><em>(= all isolates)</em></td><td></td></tr>
 <tr><td></td><td></td></tr>
 <tr><td></td><td></td></tr>
-<tr><td>Patient-based</td><td><code>first_isolate(x, method = "patient-based")</code></td></tr>
+<tr><td><strong>Patient-based</strong></td><td><code>first_isolate(x, method = "patient-based")</code></td></tr>
 <tr><td><em>(= first isolate per patient)</em></td><td></td></tr>
 <tr><td></td><td></td></tr>
 <tr><td></td><td></td></tr>
-<tr><td>Episode-based</td><td><code>first_isolate(x, method = "episode-based")</code>, or:</td></tr>
+<tr><td><strong>Episode-based</strong></td><td><code>first_isolate(x, method = "episode-based")</code>, or:</td></tr>
 <tr><td><em>(= first isolate per episode)</em></td><td></td></tr>
 <tr><td>- 7-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 7)</code></td></tr>
 <tr><td>- 30-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 30)</code></td></tr>
 <tr><td></td><td></td></tr>
 <tr><td></td><td></td></tr>
-<tr><td>Phenotype-based</td><td><code>first_isolate(x, method = "phenotype-based")</code>, or:</td></tr>
+<tr><td><strong>Phenotype-based</strong></td><td><code>first_isolate(x, method = "phenotype-based")</code>, or:</td></tr>
 <tr><td><em>(= first isolate per phenotype)</em></td><td></td></tr>
 <tr><td>- Major difference in any antimicrobial result</td><td>- <code>first_isolate(x, type = "points")</code></td></tr>
 <tr><td>- Any difference in key antimicrobial results</td><td>- <code>first_isolate(x, type = "keyantimicrobials")</code></td></tr>
@ -411,23 +408,23 @@
 <h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Isolate-based</h4>


-<p>This algorithm does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the <code>first_isolate()</code> function. For example, the default setting for <code>include_unknown</code> (<code>FALSE</code>) will omit selection of rows without a microbial ID.</p>
+<p>This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the <code>first_isolate()</code> function. For example, the default setting for <code>include_unknown</code> (<code>FALSE</code>) will omit selection of rows without a microbial ID.</p>

 <h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Patient-based</h4>


-<p>To include every genus-species combination per patient once, set the <code>episode_days</code> to <code>Inf</code>. Although often inappropriate, this algorithm makes sure that no duplicate isolates are selected from the same patient.</p>
+<p>To include every genus-species combination per patient once, set the <code>episode_days</code> to <code>Inf</code>. Although often inappropriate, this method makes sure that no duplicate isolates are selected from the same patient. In a large longitudinal data set, this could mean that isolates are <em>excluded</em> that were found years after the initial isolate.</p>

 <h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Episode-based</h4>


 <p>To include every genus-species combination per patient episode once, set the <code>episode_days</code> to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data, long episodes are common for analysing regional and national data.</p>
-<p>This is the most common algorithm to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common algorithm, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) isolate cannot be differentiated from a wildtype <em>Staphylococcus aureus</em> isolate.</p>
+<p>This is the most common method to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common method, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) isolate cannot be differentiated from a wildtype <em>Staphylococcus aureus</em> isolate.</p>

 <h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Phenotype-based</h4>


-<p>This is a more reliable algorithm, since it also <em>weighs</em> the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:</p><ol>
+<p>This is a more reliable method, since it also <em>weighs</em> the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:</p><ol>
 <li><p>Using <code>type = "points"</code> and argument <code>points_threshold</code></p>
 <p>This method weighs <em>all</em> antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as 0.5 points, a difference from S to R (or vice versa) counts as 1 point. When the sum of points exceeds <code>points_threshold</code>, which defaults to <code>2</code>, an isolate will be selected as a first weighted isolate.</p>
 <p>All antimicrobials are internally selected using the <code><a href='key_antimicrobials.html'>all_antimicrobials()</a></code> function. The output of this function does not need to be passed to the <code>first_isolate()</code> function.</p></li>
@ -436,7 +433,7 @@
 <p>Key antimicrobials are internally selected using the <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code> function, but can also be added manually as a variable to the data and set in the <code>col_keyantimicrobials</code> argument. Another option is to pass the output of the <code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code> function directly to the <code>col_keyantimicrobials</code> argument.</p></li>
 </ol>

-<p>The default algorithm is phenotype-based (using <code>type = "points"</code>) and episode-based (using <code>episode_days = 365</code>). This makes sure that every genus-species combination is selected per patient once per year, while taking into account all antimicrobial test results.</p>
+<p>The default method is phenotype-based (using <code>type = "points"</code>) and episode-based (using <code>episode_days = 365</code>). This makes sure that every genus-species combination is selected per patient once per year, while taking into account all antimicrobial test results. If no antimicrobial test results are available in the data set, only the episode-based method is applied at default.</p>



@ -473,11 +470,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
 
-  <span class='co'># short-hand versions:</span>
+  <span class='co'># short-hand version:</span>
  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
    <span class='fu'>filter_first_isolate</span><span class='op'>(</span><span class='op'>)</span>
-  <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
-    <span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span><span class='op'>)</span>
    
 <span class='co'># grouped determination of first isolates (also prints group names):</span>
 <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
@ -491,7 +486,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
              resistance <span class='op'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span><span class='op'>)</span>  <span class='co'># gentamicin resistance</span>
 
  <span class='va'>B</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
-    <span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span>      <span class='co'># the 1st isolate filter</span>
+    <span class='fu'>filter_first_isolate</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span>               <span class='co'># the 1st isolate filter</span>
    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
    <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>count <span class='op'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span>,            <span class='co'># gentamicin availability</span>
              resistance <span class='op'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span><span class='op'>)</span>  <span class='co'># gentamicin resistance</span>
--- a/docs/reference/get_episode.html
+++ b/docs/reference/get_episode.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -259,7 +259,7 @@
    </tr>
    <tr>
      <th>...</th>
-      <td><p>currently not used</p></td>
+      <td><p>ignored, only in place to allow future extensions</p></td>
    </tr>
    </table>

@ -274,8 +274,8 @@
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least <code>episode_days</code> days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least <code>episode_days</code> days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.</p>
-<p>The <code><a href='first_isolate.html'>first_isolate()</a></code> function is a wrapper around the <code>is_new_episode()</code> function, but is more efficient for data sets containing microorganism codes or names.</p>
-<p>The <code>dplyr</code> package is not required for these functions to work, but these functions support <a href='https://dplyr.tidyverse.org/reference/group_by.html'>variable grouping</a> and work conveniently inside <code>dplyr</code> verbs such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p>
+<p>The <code><a href='first_isolate.html'>first_isolate()</a></code> function is a wrapper around the <code>is_new_episode()</code> function, but is more efficient for data sets containing microorganism codes or names and allows for different isolate selection methods.</p>
+<p>The <code>dplyr</code> package is not required for these functions to work, but these functions do support <a href='https://dplyr.tidyverse.org/reference/group_by.html'>variable grouping</a> and work conveniently inside <code>dplyr</code> verbs such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p>
    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>

    
@ -334,8 +334,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
              n_episodes_30  <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>30</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
    
    
-  <span class='co'># grouping on patients and microorganisms leads to the same results</span>
-  <span class='co'># as first_isolate():</span>
+  <span class='co'># grouping on patients and microorganisms leads to the same</span>
+  <span class='co'># results as first_isolate() when using 'episode-based':</span>
  <span class='va'>x</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
    <span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span><span class='op'>(</span>include_unknown <span class='op'>=</span> <span class='cn'>TRUE</span>,
                         method <span class='op'>=</span> <span class='st'>"episode-based"</span><span class='op'>)</span>
--- a/docs/reference/ggplot_pca.html
+++ b/docs/reference/ggplot_pca.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -365,7 +365,7 @@
    </tr>
    <tr>
      <th>...</th>
-      <td><p>Arguments passed on to functions</p></td>
+      <td><p>arguments passed on to functions</p></td>
    </tr>
    </table>

@ -410,7 +410,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
  <span class='co'># new </span>
  <span class='fu'>ggplot_pca</span><span class='op'>(</span><span class='va'>pca_model</span><span class='op'>)</span>
  
-  <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
+  <span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
    <span class='fu'>ggplot_pca</span><span class='op'>(</span><span class='va'>pca_model</span><span class='op'>)</span> <span class='op'>+</span>
      <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
      <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span><span class='op'>(</span>title <span class='op'>=</span> <span class='st'>"Title here"</span><span class='op'>)</span>
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
      </span>
    </div>

@ -89,14 +89,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -105,77 +105,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -184,21 +184,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -207,14 +207,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -490,7 +490,7 @@
      </tr><tr>
        
        <td>
-          <p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_weighted_isolate()</a></code> </p>
+          <p><code><a href="first_isolate.html">first_isolate()</a></code> <code><a href="first_isolate.html">filter_first_isolate()</a></code> </p>
        </td>
        <td><p>Determine First (Weighted) Isolates</p></td>
      </tr><tr>
@ -667,7 +667,7 @@
      <tr>
        
        <td>
-          <p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> </p>
+          <p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">filter_first_weighted_isolate()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> </p>
        </td>
        <td><p>Deprecated Functions</p></td>
      </tr>
--- a/docs/reference/join.html
+++ b/docs/reference/join.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -271,7 +271,7 @@
    </tr>
    <tr>
      <th>...</th>
-      <td><p>ignored</p></td>
+      <td><p>ignored, only in place to allow future extensions</p></td>
    </tr>
    </table>

--- a/docs/reference/key_antimicrobials.html
+++ b/docs/reference/key_antimicrobials.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -265,7 +265,6 @@
  type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"points"</span>, <span class='st'>"keyantimicrobials"</span><span class='op'>)</span>,
  ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
  points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
-  info <span class='op'>=</span> <span class='cn'>FALSE</span>,
  <span class='va'>...</span>
 <span class='op'>)</span></pre>

@ -302,7 +301,7 @@
    </tr>
    <tr>
      <th>...</th>
-      <td><p>ignored, allows for future extensions</p></td>
+      <td><p>ignored, only in place to allow future extensions</p></td>
    </tr>
    <tr>
      <th>y, z</th>
@ -320,10 +319,6 @@
      <th>points_threshold</th>
      <td><p>minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></td>
    </tr>
-    <tr>
-      <th>info</th>
-      <td><p>unused - previously used to indicate whether a progress bar should print</p></td>
-    </tr>
    </table>

    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
--- a/docs/reference/random.html
+++ b/docs/reference/random.html
@ -82,7 +82,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9013</span>
      </span>
    </div>

@ -90,14 +90,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -106,77 +106,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -185,21 +185,21 @@
 </li>
 <li>
  <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -208,14 +208,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
@ -265,7 +265,7 @@
    </tr>
    <tr>
      <th>...</th>
-      <td><p>extension for future versions, not used at the moment</p></td>
+      <td><p>ignored, only in place to allow future extensions</p></td>
    </tr>
    <tr>
      <th>prob_RSI</th>
--- a/docs/survey.html
+++ b/docs/survey.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9012</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
      </span>
    </div>

@ -89,14 +89,14 @@
      <ul class="nav navbar-nav">
        <li>
  <a href="index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
     
    Home
  </a>
 </li>
 <li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
     
    How to
     
@ -105,77 +105,77 @@
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
         
        Conduct AMR analysis
      </a>
    </li>
    <li>
      <a href="articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
         
        Predict antimicrobial resistance
      </a>
    </li>
    <li>
      <a href="articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
         
        Data sets for download / own use
      </a>
    </li>
    <li>
      <a href="articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
         
        Conduct principal component analysis for AMR
      </a>
    </li>
    <li>
      <a href="articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
         
        Determine multi-drug resistance (MDR)
      </a>
    </li>
    <li>
      <a href="articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
         
        Work with WHONET data
      </a>
    </li>
    <li>
      <a href="articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
         
        Import data from SPSS/SAS/Stata
      </a>
    </li>
    <li>
      <a href="articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
         
        Apply EUCAST rules
      </a>
    </li>
    <li>
      <a href="reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
         
        Get properties of a microorganism
      </a>
    </li>
    <li>
      <a href="reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
         
        Get properties of an antibiotic
      </a>
    </li>
    <li>
      <a href="articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
         
        Other: benchmarks
      </a>
@ -184,21 +184,21 @@
 </li>
 <li>
  <a href="reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
     
    Manual
  </a>
 </li>
 <li>
  <a href="authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
     
    Authors
  </a>
 </li>
 <li>
  <a href="news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
     
    Changelog
  </a>
@ -207,14 +207,14 @@
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
     
    Source Code
  </a>
 </li>
 <li>
  <a href="survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
     
    Survey
  </a>
--- a/git_premaster.sh
+++ b/git_premaster.sh
@ -99,7 +99,7 @@ else
 fi
 # set version number to DESCRIPTION and NEWS files
 sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
-sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md
+sed -i -- "1s/.*/# \`AMR\` ${new_version}/" NEWS.md
 rm *-- || true
 echo "• First 3 lines of DESCRIPTION:"
 head -3 DESCRIPTION
--- a/inst/CITATION
+++ b/inst/CITATION
@ -4,10 +4,11 @@ citEntry(
  entry        = "Article",
  title        = "AMR - An R Package for Working with Antimicrobial Resistance Data",
  author       = "M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner",
+  doi          = {10.1101/810622},
  journal      = "bioRxiv",
  publisher    = "Cold Spring Harbor Laboratory",
  year         = 2021,
-  url          = "https://doi.org/10.1101/810622",
+  url          = "https://www.biorxiv.org/content/10.1101/810622v4",
  textVersion  = "Berends MS, Luz CF et al. (2021). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622"
 )

--- a/man/AMR-deprecated.Rd
+++ b/man/AMR-deprecated.Rd
@ -3,12 +3,21 @@
 \name{AMR-deprecated}
 \alias{AMR-deprecated}
 \alias{p_symbol}
+\alias{filter_first_weighted_isolate}
 \alias{key_antibiotics}
 \alias{key_antibiotics_equal}
 \title{Deprecated Functions}
 \usage{
 p_symbol(p, emptychar = " ")

+filter_first_weighted_isolate(
+  x = NULL,
+  col_date = NULL,
+  col_patient_id = NULL,
+  col_mo = NULL,
+  ...
+)
+
 key_antibiotics(
  x = NULL,
  col_mo = NULL,
--- a/man/first_isolate.Rd
+++ b/man/first_isolate.Rd
@ -3,12 +3,13 @@
 \name{first_isolate}
 \alias{first_isolate}
 \alias{filter_first_isolate}
-\alias{filter_first_weighted_isolate}
 \title{Determine First (Weighted) Isolates}
 \source{
 Methodology of this function is strictly based on:
-
-\strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
+\itemize{
+\item \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
+\item Hindler JF and Stelling J (2007). \strong{Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.} Clinical Infectious Diseases, 44(6), 867–873. \doi{10.1086/511864}
+}
 }
 \usage{
 first_isolate(
@ -39,16 +40,8 @@ filter_first_isolate(
  col_date = NULL,
  col_patient_id = NULL,
  col_mo = NULL,
-  method = "episode-based",
-  ...
-)
-
-filter_first_weighted_isolate(
-  x = NULL,
-  col_date = NULL,
-  col_patient_id = NULL,
-  col_mo = NULL,
-  method = "phenotype-based",
+  episode_days = 365,
+  method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
  ...
 )
 }
@ -79,7 +72,7 @@ filter_first_weighted_isolate(

 \item{type}{type to determine weighed isolates; can be \code{"keyantimicrobials"} or \code{"points"}, see \emph{Details}}

-\item{method}{the algorithm to apply, either \code{"phenotype-based"}, \code{"episode-based"}, \code{"patient-based"} or \code{"isolate-based"} (can be abbreviated), see \emph{Details}}
+\item{method}{the method to apply, either \code{"phenotype-based"}, \code{"episode-based"}, \code{"patient-based"} or \code{"isolate-based"} (can be abbreviated), see \emph{Details}. The default is \code{"phenotype-based"} if antimicrobial test results are present in the data, and \code{"episode-based"} otherwise.}

 \item{ignore_I}{logical to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}}

@ -91,43 +84,43 @@ filter_first_weighted_isolate(

 \item{include_untested_rsi}{logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use \code{include_untested_rsi = FALSE} to always return \code{FALSE} for such rows. This checks the data set for columns of class \verb{<rsi>} and consequently requires transforming columns with antibiotic results using \code{\link[=as.rsi]{as.rsi()}} first.}

-\item{...}{arguments passed on to \code{\link[=first_isolate]{first_isolate()}} when using \code{\link[=filter_first_isolate]{filter_first_isolate()}}, or arguments passed on to \code{\link[=key_antimicrobials]{key_antimicrobials()}} otherwise (such as \code{universal}, \code{gram_negative}, \code{gram_positive})}
+\item{...}{arguments passed on to \code{\link[=first_isolate]{first_isolate()}} when using \code{\link[=filter_first_isolate]{filter_first_isolate()}}, otherwise arguments passed on to \code{\link[=key_antimicrobials]{key_antimicrobials()}} (such as \code{universal}, \code{gram_negative}, \code{gram_positive})}
 }
 \value{
 A \code{\link{logical}} vector
 }
 \description{
-Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package.
+Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler \emph{et al.} in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package.
 }
 \details{
-To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different algorithms can be used to do so, see below.
+To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.

 These functions are context-aware. This means that then the \code{x} argument can be left blank, see \emph{Examples}.

 The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but more efficient for data sets containing microorganism codes or names.

 All isolates with a microbial ID of \code{NA} will be excluded as first isolate.
-\subsection{Different algorithms}{
+\subsection{Different methods}{

-According to Hindler \emph{et al.} (2007, \doi{10.1086/511864}), there are different algorithms to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All algorithms select on a combination of the taxonomic genus and species (not subspecies).
+According to Hindler \emph{et al.} (2007, \doi{10.1086/511864}), there are different methods (algorithms) to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All methods select on a combination of the taxonomic genus and species (not subspecies).

-All mentioned algorithms are covered in the \code{\link[=first_isolate]{first_isolate()}} function:\tabular{ll}{
-   \strong{Algorithm} \tab \strong{Function to apply} \cr
-   Isolate-based \tab \code{first_isolate(x, method = "isolate-based")} \cr
+All mentioned methods are covered in the \code{\link[=first_isolate]{first_isolate()}} function:\tabular{ll}{
+   \strong{Method} \tab \strong{Function to apply} \cr
+   \strong{Isolate-based} \tab \code{first_isolate(x, method = "isolate-based")} \cr
   \emph{(= all isolates)} \tab  \cr
    \tab  \cr
    \tab  \cr
-   Patient-based \tab \code{first_isolate(x, method = "patient-based")} \cr
+   \strong{Patient-based} \tab \code{first_isolate(x, method = "patient-based")} \cr
   \emph{(= first isolate per patient)} \tab  \cr
    \tab  \cr
    \tab  \cr
-   Episode-based \tab \code{first_isolate(x, method = "episode-based")}, or: \cr
+   \strong{Episode-based} \tab \code{first_isolate(x, method = "episode-based")}, or: \cr
   \emph{(= first isolate per episode)} \tab  \cr
   - 7-Day interval from initial isolate \tab - \code{first_isolate(x, method = "e", episode_days = 7)} \cr
   - 30-Day interval from initial isolate \tab - \code{first_isolate(x, method = "e", episode_days = 30)} \cr
    \tab  \cr
    \tab  \cr
-   Phenotype-based \tab \code{first_isolate(x, method = "phenotype-based")}, or: \cr
+   \strong{Phenotype-based} \tab \code{first_isolate(x, method = "phenotype-based")}, or: \cr
   \emph{(= first isolate per phenotype)} \tab  \cr
   - Major difference in any antimicrobial result \tab - \code{first_isolate(x, type = "points")} \cr
   - Any difference in key antimicrobial results \tab - \code{first_isolate(x, type = "keyantimicrobials")} \cr
@ -135,24 +128,24 @@ All mentioned algorithms are covered in the \code{\link[=first_isolate]{first_is

 \subsection{Isolate-based}{

-This algorithm does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the \code{\link[=first_isolate]{first_isolate()}} function. For example, the default setting for \code{include_unknown} (\code{FALSE}) will omit selection of rows without a microbial ID.
+This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the \code{\link[=first_isolate]{first_isolate()}} function. For example, the default setting for \code{include_unknown} (\code{FALSE}) will omit selection of rows without a microbial ID.
 }

 \subsection{Patient-based}{

-To include every genus-species combination per patient once, set the \code{episode_days} to \code{Inf}. Although often inappropriate, this algorithm makes sure that no duplicate isolates are selected from the same patient.
+To include every genus-species combination per patient once, set the \code{episode_days} to \code{Inf}. Although often inappropriate, this method makes sure that no duplicate isolates are selected from the same patient. In a large longitudinal data set, this could mean that isolates are \emph{excluded} that were found years after the initial isolate.
 }

 \subsection{Episode-based}{

 To include every genus-species combination per patient episode once, set the \code{episode_days} to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data, long episodes are common for analysing regional and national data.

-This is the most common algorithm to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common algorithm, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant \emph{Staphylococcus aureus} (MRSA) isolate cannot be differentiated from a wildtype \emph{Staphylococcus aureus} isolate.
+This is the most common method to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common method, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant \emph{Staphylococcus aureus} (MRSA) isolate cannot be differentiated from a wildtype \emph{Staphylococcus aureus} isolate.
 }

 \subsection{Phenotype-based}{

-This is a more reliable algorithm, since it also \emph{weighs} the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
+This is a more reliable method, since it also \emph{weighs} the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
 \enumerate{
 \item Using \code{type = "points"} and argument \code{points_threshold}

@ -166,7 +159,7 @@ This method only weighs specific antimicrobial agents, called \emph{key antimicr
 Key antimicrobials are internally selected using the \code{\link[=key_antimicrobials]{key_antimicrobials()}} function, but can also be added manually as a variable to the data and set in the \code{col_keyantimicrobials} argument. Another option is to pass the output of the \code{\link[=key_antimicrobials]{key_antimicrobials()}} function directly to the \code{col_keyantimicrobials} argument.
 }

-The default algorithm is phenotype-based (using \code{type = "points"}) and episode-based (using \code{episode_days = 365}). This makes sure that every genus-species combination is selected per patient once per year, while taking into account all antimicrobial test results.
+The default method is phenotype-based (using \code{type = "points"}) and episode-based (using \code{episode_days = 365}). This makes sure that every genus-species combination is selected per patient once per year, while taking into account all antimicrobial test results. If no antimicrobial test results are available in the data set, only the episode-based method is applied at default.
 }

 }
@ -201,11 +194,9 @@ if (require("dplyr")) {
  example_isolates \%>\%
    filter(first_isolate())
 
-  # short-hand versions:
+  # short-hand version:
  example_isolates \%>\%
    filter_first_isolate()
-  example_isolates \%>\%
-    filter_first_weighted_isolate()
    
 # grouped determination of first isolates (also prints group names):
 example_isolates \%>\%
@ -219,7 +210,7 @@ if (require("dplyr")) {
              resistance = resistance(GEN))  # gentamicin resistance
 
  B <- example_isolates \%>\%
-    filter_first_weighted_isolate() \%>\%      # the 1st isolate filter
+    filter_first_isolate() \%>\%               # the 1st isolate filter
    group_by(hospital_id) \%>\%
    summarise(count = n_rsi(GEN),            # gentamicin availability
              resistance = resistance(GEN))  # gentamicin resistance
--- a/man/get_episode.Rd
+++ b/man/get_episode.Rd
@ -14,7 +14,7 @@ is_new_episode(x, episode_days, ...)

 \item{episode_days}{required episode length in days, can also be less than a day or \code{Inf}, see \emph{Details}}

-\item{...}{currently not used}
+\item{...}{ignored, only in place to allow future extensions}
 }
 \value{
 \itemize{
@ -28,9 +28,9 @@ These functions determine which items in a vector can be considered (the start o
 \details{
 Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least \code{episode_days} days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least \code{episode_days} days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.

-The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but is more efficient for data sets containing microorganism codes or names.
+The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but is more efficient for data sets containing microorganism codes or names and allows for different isolate selection methods.

-The \code{dplyr} package is not required for these functions to work, but these functions support \link[dplyr:group_by]{variable grouping} and work conveniently inside \code{dplyr} verbs such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.
+The \code{dplyr} package is not required for these functions to work, but these functions do support \link[dplyr:group_by]{variable grouping} and work conveniently inside \code{dplyr} verbs such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.
 }
 \section{Stable Lifecycle}{

@ -87,8 +87,8 @@ if (require("dplyr")) {
              n_episodes_30  = sum(is_new_episode(date, episode_days = 30)))
    
    
-  # grouping on patients and microorganisms leads to the same results
-  # as first_isolate():
+  # grouping on patients and microorganisms leads to the same
+  # results as first_isolate() when using 'episode-based':
  x <- example_isolates \%>\%
    filter_first_isolate(include_unknown = TRUE,
                         method = "episode-based")
--- a/man/ggplot_pca.Rd
+++ b/man/ggplot_pca.Rd
@ -100,7 +100,7 @@ ggplot_pca(

 \item{base_textsize}{the text size for all plot elements except the labels and arrows}

-\item{...}{Arguments passed on to functions}
+\item{...}{arguments passed on to functions}
 }
 \description{
 Produces a \code{ggplot2} variant of a so-called \href{https://en.wikipedia.org/wiki/Biplot}{biplot} for PCA (principal component analysis), but is more flexible and more appealing than the base \R \code{\link[=biplot]{biplot()}} function.
--- a/man/join.Rd
+++ b/man/join.Rd
@ -30,7 +30,7 @@ anti_join_microorganisms(x, by = NULL, ...)

 \item{suffix}{if there are non-joined duplicate variables in \code{x} and \code{y}, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.}

-\item{...}{ignored}
+\item{...}{ignored, only in place to allow future extensions}
 }
 \description{
 Join the data set \link{microorganisms} easily to an existing table or character vector.
--- a/man/key_antimicrobials.Rd
+++ b/man/key_antimicrobials.Rd
@ -29,7 +29,6 @@ antimicrobials_equal(
  type = c("points", "keyantimicrobials"),
  ignore_I = TRUE,
  points_threshold = 2,
-  info = FALSE,
  ...
 )
 }
@ -48,7 +47,7 @@ antimicrobials_equal(

 \item{only_rsi_columns}{a logical to indicate whether only columns must be included that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}

-\item{...}{ignored, allows for future extensions}
+\item{...}{ignored, only in place to allow future extensions}

 \item{y, z}{character vectors to compare}

@ -57,8 +56,6 @@ antimicrobials_equal(
 \item{ignore_I}{logical to indicate whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantimicrobials"}, see \emph{Details}}

 \item{points_threshold}{minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
-
-\item{info}{unused - previously used to indicate whether a progress bar should print}
 }
 \description{
 These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see \code{\link[=first_isolate]{first_isolate()}}). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.
--- a/man/random.Rd
+++ b/man/random.Rd
@ -20,7 +20,7 @@ random_rsi(size, prob_RSI = c(0.33, 0.33, 0.33), ...)

 \item{ab}{any character that can be coerced to a valid antimicrobial agent code with \code{\link[=as.ab]{as.ab()}}}

-\item{...}{extension for future versions, not used at the moment}
+\item{...}{ignored, only in place to allow future extensions}

 \item{prob_RSI}{a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value)}
 }
--- a/pkgdown/extra.css
+++ b/pkgdown/extra.css
@ -25,14 +25,18 @@
 # ==================================================================== #
 */

-/* R for Data Science (r4ds) */
-#r4ds a {
-  display: inline-flex;
-  align-items: center;
-  text-align: right;
+/* R for Data Science (r4ds) on vignettes (articles) */
+#r4ds {
+  display: flex;
+  border-bottom: 1px solid #ddd;
+  margin-bottom: 10px;
+  padding-bottom: 10px;
 }
-#r4ds img {
-  margin-left: 10px;
+#r4ds .txt {
+  width: 67%;
+}
+#r4ds .img {
+  width: 33%;
 }

 /* class for footer */
@ -196,16 +200,20 @@ div[id^=last-updated] h2 {
 .table td {
  padding: 4px !important;
 }
-.table thead {
+.table thead,
+.template-reference-topic .table tr:first-child {
+  /* tables in manual are in LaTeX and thus have no thead */
  border-top: 2px solid black;
  border-bottom: 2px solid black;
 }
-.table thead ~ tbody {
+.table thead ~ tbody,
+.template-reference-topic .table tr:last-child {
  /* only when it has a header */
+  /* tables in manual are in LaTeX and thus have no thead */
  border-bottom: 2px solid black;
 }
 .table thead th {
-  text-align: inherit; 
+  /* text-align: inherit; */
 }
 /* all tables, including argument lists */
 table a:not(.btn) {
@ -227,6 +235,8 @@ table a:not(.btn):hover {
 }
 .template-reference-topic h4 {
  font-size: 15px;
+  font-weight: bold;
+  padding-top: 35px;
 }

 .template-home h4 {
--- a/pkgdown/extra.js
+++ b/pkgdown/extra.js
@ -30,12 +30,6 @@ $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" hr

 $(document).ready(function() {

-  // add SurveyMonkey
-  // $('body').append('<script>(function(t,e,s,o){var n,a,c;t.SMCX=t.SMCX||[],e.getElementById(o)||(n=e.getElementsByTagName(s),a=n[n.length-1],c=e.createElement(s),c.type="text/javascript",c.async=!0,c.id=o,c.src=["https:"===location.protocol?"https://":"http://","widget.surveymonkey.com/collect/website/js/tRaiETqnLgj758hTBazgd_2BrwaGaWbg59AiLjNGdPaaJiBHKqgXKIw46VauwBvZ67.js"].join(""),a.parentNode.insertBefore(c,a))})(window,document,"script","smcx-sdk");</script>');
-  // add link to survey at home sidebar
-  // $('.template-home #sidebar .list-unstyled:first').append('<li><strong>Please fill in our survey at</strong> <br><a href="https://www.surveymonkey.com/r/AMR_for_R" target="_blank">https://www.surveymonkey.com/r/AMR_for_R</a></li>');
-
-
  // remove version label from header
  $(".version.label").remove();

@ -45,21 +39,38 @@ $(document).ready(function() {
  if (url_old != url_new) {
    window.location.replace(url_new);
  }
+  
+  // Edit title of manual
+  $('.template-reference-index h1').text('Manual');

-  // Replace 'Value' in manual to 'Returned value'
+  // replace 'Value' in manual with 'Returned value'
  $(".template-reference-topic h2#value").text("Returned value");
+  
+  // replace \donttest and \dontrun texts in Examples
+  if ($("pre.examples").length > 0) {
+    $("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", ""));
+    $("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", ""));
+    $("pre.examples").html($("pre.examples").html().replaceAll("# }", ""));
+  }

  // PR for 'R for Data Science' on How To pages
  if ($(".template-article").length > 0) {
-    $('#sidebar').prepend(
+    $('#pkgdown-sidebar').prepend(
    '<div id="r4ds">' +
-    '  <a target="_blank" href="https://r4ds.had.co.nz/">' +
-    '    Learn R reading this great book: R for Data Science.' +
-    '    <br><br>' +
-    '    Click to read it online - it was published for free.' +
-    '    <img src="https://github.com/msberends/AMR/raw/master/docs/cover_r4ds.png" height="100px">' +
-    '  </a>     ' +
-    '  <hr>' +
+    '  <div class="txt">' +
+    '    <p>' +
+    '      Learn R reading this great book: <i>R for Data Science</i>.' +
+    '      <br><br>' +
+    '      <a target="_blank" href="https://r4ds.had.co.nz/">' +
+    '        Click to read it online - it was published for free.' +
+    '      </a>' +
+    '    </p>' +
+    '  </div>' +
+    '  <div class="img">' +
+    '    <a target="_blank" href="https://r4ds.had.co.nz/">' +
+    '      <img src="https://github.com/msberends/AMR/raw/master/docs/cover_r4ds.png">' +
+    '    </a>' +
+    '  </div>' +
    '</div>');
  }

@ -96,13 +107,10 @@ $(document).ready(function() {
  }
  $(".template-authors").html(doct_tit($(".template-authors").html()));
  $(".template-citation-authors").html(doct_tit($(".template-citation-authors").html()));
-  $('.template-citation-authors h1').eq(0).text('How to cite');
-  $('.template-citation-authors h1').eq(1).text('All contributors');
+  $('.template-citation-authors h1').eq(0).html("How to cite the <code>AMR</code> package");
+  $('.template-citation-authors h1').eq(1).html("All contributors of the <code>AMR</code> package");
  $(".developers").html(doct_tit($(".developers").html()));
  $(".developers a[href='authors.html']").text("All contributors...");
-
-  // Edit title of manual
-  $('.template-reference-index h1').text('Manual');
 });

 $('head').append("<!-- Global site tag (gtag.js) - Google Analytics --> <script async src=\"https://www.googletagmanager.com/gtag/js?id=UA-172114740-1\"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-172114740-1'); </script><!-- Matomo --><script type='text/javascript'> var _paq = _paq || []; /* tracker methods like 'setCustomDimension' should be called before 'trackPageView' */ _paq.push(['setDomains', ['*.msberends.github.io/AMR']]); _paq.push(['enableCrossDomainLinking']); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u='https://analyse.uscloud.nl/'; _paq.push(['setTrackerUrl', u+'piwik.php']); _paq.push(['setSiteId', '3']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);  })();</script><!-- End Matomo Code -->");
--- a/tests/testthat/test-_deprecated.R
+++ b/tests/testthat/test-_deprecated.R
@ -29,4 +29,17 @@ test_that("deprecated functions work", {
  skip_on_cran()
  expect_identical(suppressWarnings(p_symbol(c(0.001, 0.01, 0.05, 0.1, 1, NA, 3))),
                   c("***", "**", "*", ".", " ", NA, NA))
+  
+  expect_warning(key_antibiotics(example_isolates))
+  expect_identical(suppressWarnings(key_antibiotics(example_isolates)),
+                   key_antimicrobials(example_isolates, antifungal = NULL))
+  
+  expect_warning(key_antibiotics_equal("S", "S"))
+  expect_identical(suppressWarnings(key_antibiotics_equal("S", "S")),
+                   antimicrobials_equal("S", "S", type = "keyantimicrobials"))
+  
+  expect_warning(filter_first_weighted_isolate(example_isolates))
+  expect_identical(suppressWarnings(filter_first_weighted_isolate(example_isolates)),
+                   filter_first_isolate(example_isolates))
+  
 })
--- a/tests/testthat/test-first_isolate.R
+++ b/tests/testthat/test-first_isolate.R
@ -175,9 +175,8 @@ test_that("first isolates work", {
  
  # shortcuts
  expect_identical(filter_first_isolate(example_isolates),
-                   subset(example_isolates, first_isolate(example_isolates, method = "episode-based")))
-  expect_identical(filter_first_weighted_isolate(example_isolates),
-                   subset(example_isolates, first_isolate(example_isolates, method = "phenotype-based")))
+                   subset(example_isolates, first_isolate(example_isolates)))
+
  
  # notice that all mo's are distinct, so all are TRUE
  expect_true(all(example_isolates %pm>%
Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	e405de079c	(v1.6.0.9014) as.rsi() for numeric values	2021-04-30 13:18:48 +02:00
dr. M.S. (Matthijs) Berends	a9fd4aa49f	(v1.6.0.9013) website update	2021-04-29 17:16:30 +02:00