diff --git a/DESCRIPTION b/DESCRIPTION
index 76a7bc83..a9dd97d9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: AMR
-Version: 1.1.0.9018
-Date: 2020-05-22
+Version: 1.1.0.9019
+Date: 2020-05-25
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index be5d3b54..c1eb90b1 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,5 @@
-# AMR 1.1.0.9018
-## Last updated: 22-May-2020
+# AMR 1.1.0.9019
+## Last updated: 25-May-2020
### 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.
@@ -20,7 +20,8 @@
* Improvements for algorithm in `as.ab()`, so that e.g. `as.ab("ampi sul")` and `ab_name("ampi sul")` work
* Functions `ab_atc()` and `ab_group()` now return `NA` if no antimicrobial agent could be found
* Small fix for some text input that could not be coerced as valid MIC values
-* Fixed interpretation of generic CLSI interpretation rules (thanks to Anthony Underwood)
+* Fix for interpretation of generic CLSI interpretation rules (thanks to Anthony Underwood)
+* Fix for `set_mo_source()` to make sure that column `mo` will always be the second column
### Other
* Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()`
diff --git a/R/ab_property.R b/R/ab_property.R
index a51fa8be..3a021818 100644
--- a/R/ab_property.R
+++ b/R/ab_property.R
@@ -22,7 +22,7 @@
#' Property of an antibiotic
#'
#' Use these functions to return a specific property of an antibiotic from the [antibiotics] data set. All input values will be evaluated internally with [as.ab()].
-#' @inheritSection lifecycle Maturing lifecycle
+#' @inheritSection lifecycle Stable lifecycle
#' @param x any (vector of) text that can be coerced to a valid microorganism code with [as.ab()]
#' @param tolower logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".
#' @param property one of the column names of one of the [antibiotics] data set
@@ -33,7 +33,7 @@
#' @param ... other parameters passed on to [as.ab()]
#' @details All output will be [translate]d where possible.
#'
-#' The function [ab_url()] will return the direct URL to the official WHO website. A warning will be returned if the reauired ATC code is not available.
+#' The function [ab_url()] will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.
#' @inheritSection as.ab Source
#' @rdname ab_property
#' @name ab_property
diff --git a/R/mo_property.R b/R/mo_property.R
index c6409fdf..40a08dca 100755
--- a/R/mo_property.R
+++ b/R/mo_property.R
@@ -22,6 +22,7 @@
#' Property of a microorganism
#'
#' Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. Please see *Examples*.
+#' @inheritSection lifecycle Stable lifecycle
#' @param x any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param property one of the column names of the [microorganisms] data set or `"shortname"`
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
diff --git a/R/mo_source.R b/R/mo_source.R
index b44b79d4..611b7524 100644
--- a/R/mo_source.R
+++ b/R/mo_source.R
@@ -19,13 +19,13 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
-#' Use predefined reference data set
+#' User-defined reference data set for microorganisms
#'
#' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()].
#'
#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package.
#' @inheritSection lifecycle Stable lifecycle
-#' @param path location of your reference file, see Details
+#' @param path location of your reference file, see Details. Can be `""`, `NULL` or `FALSE` to delete the reference file.
#' @rdname mo_source
#' @name mo_source
#' @aliases set_mo_source get_mo_source
@@ -35,11 +35,12 @@
#'
#' [get_mo_source()] will return the data set by reading `"~/.mo_source.rds"` with [readRDS()]. If the original file has changed (the file defined with `path`), it will call [set_mo_source()] to update the data file automatically.
#'
-#' Reading an Excel file (`.xlsx`) with only one row has a size of 8-9 kB. The compressed file used by this package will have a size of 0.1 kB and can be read by [get_mo_source()] in only a couple of microseconds (a millionth of a second).
+#' Reading an Excel file (`.xlsx`) with only one row has a size of 8-9 kB. The compressed file created with [set_mo_source()] will then have a size of 0.1 kB and can be read by [get_mo_source()] in only a couple of microseconds (millionths of a second).
#'
-#' ## How it works
+#' @section How to setup:
+#'
+#' Imagine this data on a sheet of an Excel file (mo codes were looked up in the [microorganisms] data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
#'
-#' Imagine this data on a sheet of an Excel file (mo codes were looked up in the `microorganisms` data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
#' ```
#' | A | B |
#' --|--------------------|--------------|
@@ -50,27 +51,31 @@
#' ```
#'
#' We save it as `"home/me/ourcodes.xlsx"`. Now we have to set it as a source:
+#'
#' ```
#' set_mo_source("home/me/ourcodes.xlsx")
-#' # Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
+#' #> NOTE: Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'
+#' #> (columns "Organisation XYZ" and "mo")
#' ```
#'
-#' It has now created a file `"~/.mo_source.rds"` with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.
+#' It has now created a file `"~/.mo_source.rds"` with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.
#'
#' And now we can use it in our functions:
+#'
#' ```
#' as.mo("lab_mo_ecoli")
-#' [1] B_ESCHR_COLI
+#' #> [1] B_ESCHR_COLI
#'
#' mo_genus("lab_mo_kpneumoniae")
-#' [1] "Klebsiella"
+#' #> [1] "Klebsiella"
#'
#' # other input values still work too
#' as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
-#' [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
+#' #> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
#' ```
#'
-#' If we edit the Excel file to, let's say, by adding row 4 like this:
+#' If we edit the Excel file by, let's say, adding row 4 like this:
+#'
#' ```
#' | A | B |
#' --|--------------------|--------------|
@@ -82,36 +87,41 @@
#' ```
#'
#' ...any new usage of an MO function in this package will update your data file:
+#'
#' ```
#' as.mo("lab_mo_ecoli")
-#' # Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
-#' [1] B_ESCHR_COLI
+#' #> NOTE: Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'
+#' #> (columns "Organisation XYZ" and "mo")
+#' #> [1] B_ESCHR_COLI
#'
#' mo_genus("lab_Staph_aureus")
-#' [1] "Staphylococcus"
+#' #> [1] "Staphylococcus"
#' ```
#'
-#' To remove the reference data file completely, just use `""` or `NULL` as input for `[set_mo_source()]`:
+#' To delete the reference data file, just use `""`, `NULL` or `FALSE` as input for [set_mo_source()]:
+#'
#' ```
#' set_mo_source(NULL)
#' # Removed mo_source file '~/.mo_source.rds'.
#' ```
+#'
+#' If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of [as.mo()]. If the mo_source file is manually deleted (i.e. without using [set_mo_source()]), the references to the mo_source file will be removed upon the next use of [as.mo()].
#' @export
#' @inheritSection AMR Read more on our website!
set_mo_source <- function(path) {
file_location <- path.expand("~/mo_source.rds")
- if (!is.character(path) | length(path) > 1) {
- stop("`path` must be a character of length 1.")
+ if (length(path) > 1) {
+ stop("`path` must be of length 1.")
}
- if (path %in% c(NULL, "")) {
+ if (is.null(path) || path %in% c(FALSE, "")) {
options(mo_source = NULL)
options(mo_source_timestamp = NULL)
if (file.exists(file_location)) {
unlink(file_location)
- message("Removed mo_source file '", file_location, "'.")
+ message(font_red(paste0("Removed mo_source file '", font_bold(file_location), "'")))
}
return(invisible())
}
@@ -154,13 +164,13 @@ set_mo_source <- function(path) {
# check integrity
mo_source_isvalid(df)
- df <- df %>% filter(!is.na(mo))
+ df <- subset(df, !is.na(mo))
# keep only first two columns, second must be mo
if (colnames(df)[1] == "mo") {
- df <- df[, c(2, 1)]
+ df <- df[, c(colnames(df)[2], "mo")]
} else {
- df <- df[, c(1, 2)]
+ df <- df[, c(colnames(df)[1], "mo")]
}
df <- as.data.frame(df, stringAsFactors = FALSE)
@@ -174,30 +184,40 @@ set_mo_source <- function(path) {
saveRDS(df, file_location)
options(mo_source = path)
options(mo_source_timestamp = as.character(file.info(path)$mtime))
- message(action, " mo_source file '", file_location, "' from '", path, "'.")
+ message(font_blue(paste0("NOTE: ",
+ action, " mo_source file '", font_bold(file_location), "'",
+ " from '", font_bold(path), "'",
+ '\n (columns "', colnames(df)[1], '" and "', colnames(df)[2], '")')))
}
#' @rdname mo_source
#' @export
get_mo_source <- function() {
if (is.null(getOption("mo_source", NULL))) {
- NULL
- } else {
- old_time <- as.POSIXct(getOption("mo_source_timestamp"))
- new_time <- as.POSIXct(as.character(file.info(getOption("mo_source", ""))$mtime))
-
- if (is.na(new_time)) {
- # source file was deleted, remove reference too
- set_mo_source("")
- return(NULL)
- }
- if (new_time != old_time) {
- # set updated source
- set_mo_source(getOption("mo_source"))
- }
- file_location <- path.expand("~/mo_source.rds")
- readRDS(file_location)
+ return(NULL)
}
+
+ if (!file.exists(path.expand("~/mo_source.rds"))) {
+ options(mo_source = NULL)
+ options(mo_source_timestamp = NULL)
+ message(font_blue("NOTE: Removed references to deleted mo_source file (see ?mo_source)"))
+ return(NULL)
+ }
+
+ old_time <- as.POSIXct(getOption("mo_source_timestamp"))
+ new_time <- as.POSIXct(as.character(file.info(getOption("mo_source", ""))$mtime))
+
+ if (is.na(new_time)) {
+ # source file was deleted, remove reference too
+ set_mo_source("")
+ return(NULL)
+ }
+ if (new_time != old_time) {
+ # set updated source
+ set_mo_source(getOption("mo_source"))
+ }
+ file_location <- path.expand("~/mo_source.rds")
+ readRDS(file_location)
}
mo_source_isvalid <- function(x, refer_to_name = "`reference_df`", stop_on_error = TRUE) {
diff --git a/docs/404.html b/docs/404.html
index 9a2803fa..322b2c22 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.1.0.9018
+ 1.1.0.9019
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 2c558f42..4ceeb702 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.1.0.9018
+ 1.1.0.9019
diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html
index fd2e26e5..1d459a7a 100644
--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
@@ -39,7 +39,7 @@
AMR (for R)
- 1.1.0.9015
+ 1.1.0.9019
@@ -186,7 +186,7 @@
How to conduct AMR analysis
Matthijs S. Berends
- 20 May 2020
+ 25 May 2020
Source: vignettes/AMR.Rmd
AMR.Rmd
@@ -195,7 +195,7 @@
-Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 20 May 2020.
+Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 25 May 2020.
Introduction
@@ -226,21 +226,21 @@
-| 2020-05-20 |
+2020-05-25 |
abcd |
Escherichia coli |
S |
S |
-| 2020-05-20 |
+2020-05-25 |
abcd |
Escherichia coli |
S |
R |
-| 2020-05-20 |
+2020-05-25 |
efgh |
Escherichia coli |
R |
@@ -336,41 +336,63 @@
-| 2013-03-27 |
-L8 |
+2015-03-17 |
+U1 |
+Hospital D |
+Escherichia coli |
+S |
+S |
+S |
+S |
+F |
+
+
+| 2017-08-02 |
+P6 |
Hospital B |
Streptococcus pneumoniae |
R |
S |
S |
S |
+F |
+
+
+| 2017-06-24 |
+E4 |
+Hospital C |
+Escherichia coli |
+S |
+S |
+S |
+S |
M |
-| 2015-12-30 |
-K1 |
-Hospital B |
-Staphylococcus aureus |
+2011-02-12 |
+I10 |
+Hospital D |
+Streptococcus pneumoniae |
+R |
S |
S |
R |
-S |
M |
-| 2016-06-06 |
-D3 |
-Hospital B |
+2010-03-17 |
+Q3 |
+Hospital C |
Staphylococcus aureus |
-S |
-S |
R |
S |
-M |
+S |
+S |
+F |
-| 2011-07-04 |
-H10 |
+2010-08-19 |
+A7 |
Hospital D |
Escherichia coli |
S |
@@ -379,28 +401,6 @@
S |
M |
-
-| 2012-04-12 |
-M3 |
-Hospital B |
-Staphylococcus aureus |
-R |
-S |
-S |
-S |
-M |
-
-
-| 2017-03-06 |
-S4 |
-Hospital C |
-Escherichia coli |
-S |
-S |
-S |
-S |
-F |
-
Now, let’s start the cleaning and the analysis!
@@ -432,16 +432,16 @@ Longest: 1
| 1 |
M |
-10,319 |
-51.60% |
-10,319 |
-51.60% |
+10,403 |
+52.02% |
+10,403 |
+52.02% |
| 2 |
F |
-9,681 |
-48.41% |
+9,597 |
+47.99% |
20,000 |
100.00% |
@@ -456,11 +456,7 @@ Longest: 1
mutate_at(
vars(
AMX:
GEN),
as.rsi)