From 9feef53bde208ae5b2a0a112e0df59e940c5fc9f Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Thu, 28 Nov 2019 23:00:37 +0100 Subject: [PATCH] (v0.8.0.9037) complete documentation rewrite --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/amr.R | 2 +- R/data.R | 2 +- R/first_isolate.R | 2 +- R/g.test.R | 4 ++-- R/join_microorganisms.R | 2 +- R/kurtosis.R | 2 +- R/mdro.R | 2 +- R/mic.R | 2 +- R/rsi.R | 2 +- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 10 +++++----- docs/reference/AMR.html | 4 ++-- docs/reference/as.mic.html | 2 +- docs/reference/as.rsi.html | 4 ++-- docs/reference/first_isolate.html | 4 ++-- docs/reference/g.test.html | 12 ++++++++---- docs/reference/index.html | 2 +- docs/reference/join.html | 4 ++-- docs/reference/kurtosis.html | 4 ++-- docs/reference/mdro.html | 4 ++-- docs/reference/microorganisms.html | 4 ++-- man/AMR.Rd | 2 +- man/as.mic.Rd | 2 +- man/as.rsi.Rd | 2 +- man/first_isolate.Rd | 2 +- man/g.test.Rd | 6 ++++-- man/join.Rd | 2 +- man/kurtosis.Rd | 2 +- man/mdro.Rd | 2 +- man/microorganisms.Rd | 2 +- tests/testthat/test-mo_property.R | 2 +- 37 files changed, 59 insertions(+), 53 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0ac09bcc..6f1722f0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.8.0.9036 +Version: 0.8.0.9037 Date: 2019-11-28 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 1ee4f377..9b3b0669 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.8.0.9036 +# AMR 0.8.0.9037 ## Last updated: 28-Nov-2019 ### Breaking diff --git a/R/amr.R b/R/amr.R index e061ae50..b4ee82e0 100644 --- a/R/amr.R +++ b/R/amr.R @@ -46,7 +46,7 @@ #' For suggestions, comments or questions, please contact us at: #' #' Matthijs S. Berends \cr -#' m.s.berends [at] umcg [dot] nl \cr +#' m.s.berends at umcg dot nl \cr #' Department of Medical Microbiology, University of Groningen \cr #' University Medical Center Groningen \cr #' Post Office Box 30001 \cr diff --git a/R/data.R b/R/data.R index fd69b7cb..f86386bf 100755 --- a/R/data.R +++ b/R/data.R @@ -80,7 +80,7 @@ #' - `prevalence`\cr Prevalence of the microorganism, see [as.mo()] #' @details Manually added were: #' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri) -#' - 2 entries of *Staphylococcus* (coagulase-negative [CoNS] and coagulase-positive [CoPS]) +#' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS)) #' - 3 entries of *Trichomonas* (*Trichomonas vaginalis*, and its family and genus) #' - 1 entry of *Blastocystis* (*Blastocystis hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993) #' - 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus) diff --git a/R/first_isolate.R b/R/first_isolate.R index fa463160..5814d4b1 100755 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -41,7 +41,7 @@ #' @param include_unknown logical to determine 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 ... parameters passed on to the [first_isolate()] function #' @details **WHY THIS IS SO IMPORTANT** \cr -#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [[1]](https://www.ncbi.nlm.nih.gov/pubmed/17304462). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all *S. aureus* isolates would be overestimated, because you included this MRSA more than once. It would be [selection bias](https://en.wikipedia.org/wiki/Selection_bias). +#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [(ref)](https://www.ncbi.nlm.nih.gov/pubmed/17304462). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all *S. aureus* isolates would be overestimated, because you included this MRSA more than once. It would be [selection bias](https://en.wikipedia.org/wiki/Selection_bias). #' #' All isolates with a microbial ID of `NA` will be excluded as first isolate. #' diff --git a/R/g.test.R b/R/g.test.R index 7d644c25..5a5002c9 100755 --- a/R/g.test.R +++ b/R/g.test.R @@ -21,7 +21,7 @@ #' *G*-test for Count Data #' -#' [g.test()] performs chi-squared contingency table tests and goodness-of-fit tests, just like [chisq.test()] but is more reliable [1]. A *G*-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a ***G*-test of goodness-of-fit**), or to see whether the proportions of one variable are different for different values of the other variable (called a ***G*-test of independence**). +#' [g.test()] performs chi-squared contingency table tests and goodness-of-fit tests, just like [chisq.test()] but is more reliable (1). A *G*-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a ***G*-test of goodness-of-fit**), or to see whether the proportions of one variable are different for different values of the other variable (called a ***G*-test of independence**). #' @inherit stats::chisq.test params return #' @details If `x` is a matrix with one row or column, or if `x` is a vector and `y` is not given, then a *goodness-of-fit test* is performed (`x` is treated as a one-dimensional contingency table). The entries of `x` must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in `p`, or are all equal if `p` is not given. #' @@ -64,7 +64,7 @@ #' #' If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use *G*-tests for each category, of course. #' @seealso [chisq.test()] -#' @references [1] McDonald, J.H. 2014. **Handbook of Biological Statistics (3rd ed.)**. Sparky House Publishing, Baltimore, Maryland. . +#' @references 1. McDonald, J.H. 2014. **Handbook of Biological Statistics (3rd ed.)**. Sparky House Publishing, Baltimore, Maryland. . #' @source The code for this function is identical to that of [chisq.test()], except that: #' - The calculation of the statistic was changed to \eqn{2 * sum(x * log(x / E))} #' - Yates' continuity correction was removed as it does not apply to a *G*-test diff --git a/R/join_microorganisms.R b/R/join_microorganisms.R index fc1946e0..8fff6342 100755 --- a/R/join_microorganisms.R +++ b/R/join_microorganisms.R @@ -29,7 +29,7 @@ #' @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` (like `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("my_genus_species" = "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 ... other parameters to pass on to [dplyr::join()] -#' @details **Note:** As opposed to the [dplyr::join()] functions of `dplyr`, [`characters`] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix. See [dplyr::join()] for more information. +#' @details **Note:** As opposed to the [dplyr::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. See [dplyr::join()] for more information. #' @inheritSection AMR Read more on our website! #' @export #' @examples diff --git a/R/kurtosis.R b/R/kurtosis.R index b44f2e6d..ca7f9060 100755 --- a/R/kurtosis.R +++ b/R/kurtosis.R @@ -22,7 +22,7 @@ #' Kurtosis of the sample #' #' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. -#' @param x a vector of values, a [`matrix`] or a [`data frame`] +#' @param x a vector of values, a [`matrix`] or a [`data.frame`] #' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds. #' @exportMethod kurtosis #' @seealso [skewness()] diff --git a/R/mdro.R b/R/mdro.R index 867eadc5..b960986e 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -43,7 +43,7 @@ #' - `guideline = "MRGN"`\cr #' The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6 #' - `guideline = "BRMO"`\cr -#' The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" ([link](https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH)) +#' The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" ([link](https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH)) #' #' Please suggest your own (country-specific) guidelines by letting us know: . #' diff --git a/R/mic.R b/R/mic.R index 8c0a0c2a..b43be081 100755 --- a/R/mic.R +++ b/R/mic.R @@ -27,7 +27,7 @@ #' @param na.rm a logical indicating whether missing values should be removed #' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST and CLSI. #' @return Ordered [`factor`] with new class [`mic`] -#' @aliases MIC +#' @aliases mic #' @export #' @importFrom dplyr %>% #' @seealso [as.rsi()] diff --git a/R/rsi.R b/R/rsi.R index 156fd574..0a56789c 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -46,7 +46,7 @@ #' #' This AMR package honours this new insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates. #' @return Ordered factor with new class [`rsi`] -#' @aliases RSI +#' @aliases rsi #' @export #' @importFrom dplyr %>% desc arrange filter #' @seealso [as.mic()] diff --git a/docs/404.html b/docs/404.html index 2646ad93..49190f5a 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9036 + 0.8.0.9037 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index bd1e94d4..225ad7ed 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9036 + 0.8.0.9037 diff --git a/docs/articles/index.html b/docs/articles/index.html index 81de98eb..1d94262f 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9036 + 0.8.0.9037 diff --git a/docs/authors.html b/docs/authors.html index b3988d08..7315946e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9036 + 0.8.0.9037 diff --git a/docs/index.html b/docs/index.html index 6829cb28..3cee3e91 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ AMR (for R) - 0.8.0.9036 + 0.8.0.9037 diff --git a/docs/news/index.html b/docs/news/index.html index b02bf027..621c021b 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9036 + 0.8.0.9037 @@ -231,9 +231,9 @@ -
+

-AMR 0.8.0.9036 Unreleased +AMR 0.8.0.9037 Unreleased

@@ -616,7 +616,7 @@ Please as.mo() function
  • This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as ‘increased exposure’ and not ‘intermediate’ anymore. For functions like portion_df() and count_df() this means that their new parameter combine_SI is TRUE at default. Our plotting function ggplot_rsi() also reflects this change since it uses count_df() internally.
  • The age() function gained a new parameter exact to determine ages with decimals
    • -
  • Removed deprecated functions guess_mo(), guess_atc(), EUCAST_rules(), interpretive_reading(), rsi() +
  • Removed deprecated functions guess_mo(), guess_atc(), EUCAST_rules(), interpretive_reading(), rsi()
  • Frequency tables (freq()):

    • @@ -268,7 +268,7 @@

    For suggestions, comments or questions, please contact us at:

    Matthijs S. Berends
    -m.s.berends at umcg dot nl
    +m.s.berends at umcg dot nl
    Department of Medical Microbiology, University of Groningen
    University Medical Center Groningen
    Post Office Box 30001
    diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index fc94688b..be281cc5 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -85,7 +85,7 @@ AMR (for R) - 0.8.0.9036 + 0.8.0.9037

    diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index 01ebdf8b..d12ad1f1 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -85,7 +85,7 @@ AMR (for R) - 0.8.0.9036 + 0.8.0.9037
    @@ -257,7 +257,7 @@ x -

    vector of values (for class mic: an MIC value in mg/L, for class disk: a disk diffusion radius in millimeters)

    +

    vector of values (for class mic: an MIC value in mg/L, for class disk: a disk diffusion radius in millimeters)

    ... diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index 405b293a..e0f4a60f 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -85,7 +85,7 @@ AMR (for R) - 0.8.0.9036 + 0.8.0.9037 @@ -362,7 +362,7 @@

    Details

    WHY THIS IS SO IMPORTANT
    -To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [1](https://www.ncbi.nlm.nih.gov/pubmed/17304462). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all S. aureus isolates would be overestimated, because you included this MRSA more than once. It would be selection bias.

    +To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode (ref). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all S. aureus isolates would be overestimated, because you included this MRSA more than once. It would be selection bias.

    All isolates with a microbial ID of NA will be excluded as first isolate.

    The functions filter_first_isolate() and filter_first_weighted_isolate() are helper functions to quickly filter on first isolates. The function filter_first_isolate() is essentially equal to:

     x %>%
    mutate(only_firsts = first_isolate(x, ...)) %>%
diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html
index 05903459..662a0ebb 100644
--- a/docs/reference/g.test.html
+++ b/docs/reference/g.test.html
@@ -51,7 +51,7 @@
   
 
 
-
+
 
 
 
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.8.0.9036
+        0.8.0.9037
       
     
 
@@ -234,7 +234,7 @@
     
 
     
    
-    
    g.test() performs chi-squared contingency table tests and goodness-of-fit tests, just like chisq.test() but is more reliable 1. A G-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a G-test of goodness-of-fit), or to see whether the proportions of one variable are different for different values of the other variable (called a G-test of independence).
    
+    
    g.test() performs chi-squared contingency table tests and goodness-of-fit tests, just like chisq.test() but is more reliable (1). A G-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a G-test of goodness-of-fit), or to see whether the proportions of one variable are different for different values of the other variable (called a G-test of independence).
    
     
    
 
     
    g.test(x, y = NULL, p = rep(1/length(x), length(x)), rescale.p = FALSE)
    
@@ -334,7 +334,11 @@
 
    On our website https://msberends.gitlab.io/AMR you can find a tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.
    
     
    References
    
 
-    
    1 McDonald, J.H. 2014. Handbook of Biological Statistics (3rd ed.). Sparky House Publishing, Baltimore, Maryland. http://www.biostathandbook.com/gtestgof.html.
    
+    
+
      
+
    1. McDonald, J.H. 2014. Handbook of Biological Statistics (3rd ed.). Sparky House Publishing, Baltimore, Maryland. http://www.biostathandbook.com/gtestgof.html.
      2. 
+
    
+
     
    See also
    
 
     
    chisq.test()
    
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 5de7a7bb..e1f0eda9 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -84,7 +84,7 @@
       
       
         AMR (for R)
-        0.8.0.9036
+        0.8.0.9037
       
     
 
diff --git a/docs/reference/join.html b/docs/reference/join.html
index ac2c22d1..83c9c22f 100644
--- a/docs/reference/join.html
+++ b/docs/reference/join.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.8.0.9036
+        0.8.0.9037
       
     
 
@@ -272,7 +272,7 @@
 
     
    Details
    
 
-    
    Note: As opposed to the dplyr::join() functions of dplyr, characters vectors are supported and at default existing columns will get a suffix "2" and the newly joined columns will not get a suffix. See dplyr::join() for more information.
    
+    
    Note: As opposed to the dplyr::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. See dplyr::join() for more information.
    
     
    Read more on our website!
    
 
     
diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html
index 68b766cc..fbfe601e 100644
--- a/docs/reference/kurtosis.html
+++ b/docs/reference/kurtosis.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.8.0.9036
+        0.8.0.9037
       
     
 
@@ -253,7 +253,7 @@
     
     
       x
-      
    a vector of values, a matrix or a data frame
    
+      
    a vector of values, a matrix or a data.frame
    
     
     
       na.rm
diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html
index a3696044..dbb427b3 100644
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.8.0.9036
+        0.8.0.9037
       
     
 
@@ -325,7 +325,7 @@ The international guideline for multi-drug resistant tuberculosis - World Health
 
  • guideline = "MRGN"
    
 The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6
    • 
 
  • guideline = "BRMO"
    
-The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) ZKH" (link)
    • 
+The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (link)
    
 
 
 
    Please suggest your own (country-specific) guidelines by letting us know: https://gitlab.com/msberends/AMR/issues/new.
    
diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html
index 64d5dc0f..cf38ddd2 100644
--- a/docs/reference/microorganisms.html
+++ b/docs/reference/microorganisms.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.8.0.9036
+        0.8.0.9037
       
     
 
@@ -261,7 +261,7 @@
 
     
    Manually added were:
      
 
    • 11 entries of Streptococcus (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
      • 
-
    • 2 entries of Staphylococcus (coagulase-negative CoNS and coagulase-positive CoPS)
      • 
+
    • 2 entries of Staphylococcus (coagulase-negative (CoNS) and coagulase-positive (CoPS))
      • 
 
    • 3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)
      • 
 
    • 1 entry of Blastocystis (Blastocystis hominis), although it officially does not exist (Noel et al. 2005, PMID 15634993)
      • 
 
    • 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
      • 
diff --git a/man/AMR.Rd b/man/AMR.Rd
index 18b6ef1a..1b89d985 100644
--- a/man/AMR.Rd
+++ b/man/AMR.Rd
@@ -36,7 +36,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 For suggestions, comments or questions, please contact us at:
 
 Matthijs S. Berends \cr
-m.s.berends \link{at} umcg \link{dot} nl \cr
+m.s.berends at umcg dot nl \cr
 Department of Medical Microbiology, University of Groningen \cr
 University Medical Center Groningen \cr
 Post Office Box 30001 \cr
diff --git a/man/as.mic.Rd b/man/as.mic.Rd
index 330574c0..4cee1a6e 100755
--- a/man/as.mic.Rd
+++ b/man/as.mic.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/mic.R
 \name{as.mic}
 \alias{as.mic}
-\alias{MIC}
+\alias{mic}
 \alias{is.mic}
 \title{Class 'mic'}
 \usage{
diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd
index 85f30563..9450be42 100755
--- a/man/as.rsi.Rd
+++ b/man/as.rsi.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/rsi.R
 \name{as.rsi}
 \alias{as.rsi}
-\alias{RSI}
+\alias{rsi}
 \alias{as.rsi.mic}
 \alias{as.rsi.disk}
 \alias{as.rsi.data.frame}
diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd
index 013e1cc5..cc2a7ebe 100755
--- a/man/first_isolate.Rd
+++ b/man/first_isolate.Rd
@@ -94,7 +94,7 @@ Determine first (weighted) isolates of all microorganisms of every patient per e
 }
 \details{
 \strong{WHY THIS IS SO IMPORTANT} \cr
-To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [\link{1}](https://www.ncbi.nlm.nih.gov/pubmed/17304462). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all \emph{S. aureus} isolates would be overestimated, because you included this MRSA more than once. It would be \href{https://en.wikipedia.org/wiki/Selection_bias}{selection bias}.
+To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode \href{https://www.ncbi.nlm.nih.gov/pubmed/17304462}{(ref)}. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all \emph{S. aureus} isolates would be overestimated, because you included this MRSA more than once. It would be \href{https://en.wikipedia.org/wiki/Selection_bias}{selection bias}.
 
 All isolates with a microbial ID of \code{NA} will be excluded as first isolate.
 
diff --git a/man/g.test.Rd b/man/g.test.Rd
index fee57e8d..fbcda011 100644
--- a/man/g.test.Rd
+++ b/man/g.test.Rd
@@ -49,7 +49,7 @@ A list with class \code{"htest"} containing the following
     section 2.4.5 for the case where \code{x} is a matrix, \code{n * p * (1 - p)} otherwise).}
 }
 \description{
-\code{\link[=g.test]{g.test()}} performs chi-squared contingency table tests and goodness-of-fit tests, just like \code{\link[=chisq.test]{chisq.test()}} but is more reliable \link{1}. A \emph{G}-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a \strong{\emph{G}-test of goodness-of-fit}), or to see whether the proportions of one variable are different for different values of the other variable (called a \strong{\emph{G}-test of independence}).
+\code{\link[=g.test]{g.test()}} performs chi-squared contingency table tests and goodness-of-fit tests, just like \code{\link[=chisq.test]{chisq.test()}} but is more reliable (1). A \emph{G}-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a \strong{\emph{G}-test of goodness-of-fit}), or to see whether the proportions of one variable are different for different values of the other variable (called a \strong{\emph{G}-test of independence}).
 }
 \details{
 If \code{x} is a matrix with one row or column, or if \code{x} is a vector and \code{y} is not given, then a \emph{goodness-of-fit test} is performed (\code{x} is treated as a one-dimensional contingency table). The entries of \code{x} must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in \code{p}, or are all equal if \code{p} is not given.
@@ -137,7 +137,9 @@ g.test(x)
 
 }
 \references{
-\link{1} McDonald, J.H. 2014. \strong{Handbook of Biological Statistics (3rd ed.)}. Sparky House Publishing, Baltimore, Maryland. \url{http://www.biostathandbook.com/gtestgof.html}.
+\enumerate{
+\item McDonald, J.H. 2014. \strong{Handbook of Biological Statistics (3rd ed.)}. Sparky House Publishing, Baltimore, Maryland. \url{http://www.biostathandbook.com/gtestgof.html}.
+}
 }
 \seealso{
 \code{\link[=chisq.test]{chisq.test()}}
diff --git a/man/join.Rd b/man/join.Rd
index 53aaac64..50f517b8 100755
--- a/man/join.Rd
+++ b/man/join.Rd
@@ -36,7 +36,7 @@ anti_join_microorganisms(x, by = NULL, ...)
 Join the data set \link{microorganisms} easily to an existing table or character vector.
 }
 \details{
-\strong{Note:} As opposed to the \code{\link[dplyr:join]{dplyr::join()}} functions of \code{dplyr}, \code{\link{characters}} vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. See \code{\link[dplyr:join]{dplyr::join()}} for more information.
+\strong{Note:} As opposed to the \code{\link[dplyr:join]{dplyr::join()}} functions of \code{dplyr}, \code{\link{character}} vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. See \code{\link[dplyr:join]{dplyr::join()}} for more information.
 }
 \section{Read more on our website!}{
 
diff --git a/man/kurtosis.Rd b/man/kurtosis.Rd
index 59b08786..b3d0d9d0 100644
--- a/man/kurtosis.Rd
+++ b/man/kurtosis.Rd
@@ -16,7 +16,7 @@ kurtosis(x, na.rm = FALSE)
 \method{kurtosis}{data.frame}(x, na.rm = FALSE)
 }
 \arguments{
-\item{x}{a vector of values, a \code{\link{matrix}} or a \code{\link{data frame}}}
+\item{x}{a vector of values, a \code{\link{matrix}} or a \code{\link{data.frame}}}
 
 \item{na.rm}{a logical value indicating whether \code{NA} values should be stripped before the computation proceeds.}
 }
diff --git a/man/mdro.Rd b/man/mdro.Rd
index 0a824c01..29a6499c 100644
--- a/man/mdro.Rd
+++ b/man/mdro.Rd
@@ -85,7 +85,7 @@ The international guideline for multi-drug resistant tuberculosis - World Health
 \item \code{guideline = "MRGN"}\cr
 The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6
 \item \code{guideline = "BRMO"}\cr
-The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) \link{ZKH}" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})
+The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})
 }
 
 Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd
index 34c0dc79..946696d6 100755
--- a/man/microorganisms.Rd
+++ b/man/microorganisms.Rd
@@ -31,7 +31,7 @@ A data set containing the microbial taxonomy of six kingdoms from the Catalogue
 Manually added were:
 \itemize{
 \item 11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
-\item 2 entries of \emph{Staphylococcus} (coagulase-negative \link{CoNS} and coagulase-positive \link{CoPS})
+\item 2 entries of \emph{Staphylococcus} (coagulase-negative (CoNS) and coagulase-positive (CoPS))
 \item 3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)
 \item 1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
 \item 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
diff --git a/tests/testthat/test-mo_property.R b/tests/testthat/test-mo_property.R
index 93b4f3e2..7477d741 100644
--- a/tests/testthat/test-mo_property.R
+++ b/tests/testthat/test-mo_property.R
@@ -45,7 +45,7 @@ test_that("mo_property works", {
   expect_equal(class(mo_synonyms(c("Candida albicans", "Escherichia coli"))), "list")
   expect_equal(names(mo_info("Escherichia coli")), c("kingdom", "phylum", "class", "order",
                                             "family", "genus", "species", "subspecies",
-                                            "synonyms", "url", "ref"))
+                                            "synonyms", "gramstain", "url", "ref"))
   expect_equal(class(mo_info(c("Escherichia coli", "Staphylococcus aureus"))), "list")
 
   expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")