emph guess_bactid

.travis.yml

@@ -33,7 +33,6 @@ jobs:
 matrix:
   allow_failures:
     - r: 3.1
-    - r: 3.2
     - r: devel
 r_packages: covr
 cache: packages

NEWS.md

@@ -7,7 +7,7 @@
   * Universal: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin,  trimethoprim/sulfamethoxazole
   * Gram-positive: vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampicin
   * Gram-negative: gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem
-* Functions `as.bactid` and `is.bactid` to transform/look up microbial ID's; this replaces the function `guess_bactid` but it will remain available for backwards compatibility
+* Functions `as.bactid` and `is.bactid` to transform/look up microbial ID's
 * For convience, new descriptive statistical functions `kurtosis` and `skewness` that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices
 * Function `g.test` to perform the Χ<sup>2</sup> distributed [*G*-test](https://en.wikipedia.org/wiki/G-test), which use is the same as `chisq.test`
 * Function `ratio` to transform a vector of values to a preset ratio

R/bactid.R

@@ -21,7 +21,9 @@
 #' Use this function to determine a valid ID based on a genus (and species). This input can be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
 #' @param x a character vector or a dataframe with one or two columns
 #' @rdname as.bactid
-#' @details Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. For example:
+#' @details \code{guess_bactid} does exactly the same as \code{as.bactid}.
+#'
+#' Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. For example:
 #' \itemize{
 #'   \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
 #'   \item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae}}
@@ -53,17 +55,16 @@
 #' library(dplyr)
 #' df$bactid <- df %>%
 #'   select(microorganism_name) %>%
-#'   as.bactid()
+#'   guess_bactid()
 #'
 #' # and can even contain 2 columns, which is convenient for genus/species combinations:
 #' df$bactid <- df %>%
 #'   select(genus, species) %>%
-#'   as.bactid()
+#'   guess_bactid()
 #'
 #' # same result:
 #' df <- df %>%
-#'   mutate(bactid = paste(genus, species) %>%
+#'   mutate(bactid = guess_bactid(paste(genus, species)))
-#'                     as.bactid())
 #' }
 as.bactid <- function(x) {
 
@@ -158,7 +159,8 @@ as.bactid <- function(x) {
         next
       }
       if (toupper(x.backup[i]) == 'MRSE') {
-        x[i] <- 'Staphylococcus epidermidis'
+        x[i] <- 'STAEPI'
+        next
       }
       if (toupper(x.backup[i]) == 'VRE') {
         x[i] <- 'ENC'
@@ -169,15 +171,9 @@ as.bactid <- function(x) {
         x[i] <- 'PSEAER'
         next
       }
-      if (toupper(x.backup[i]) == 'PISP'
+      if (toupper(x.backup[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
-          | toupper(x.backup[i]) == 'PRSP') {
+        # peni R, peni I, vanco I, vanco R: S. pneumoniae
-        # peni resistant S. pneumoniae
+        x[i] <- 'STCPNE'
-        x[i] <- 'Streptococcus pneumoniae'
-      }
-      if (toupper(x.backup[i]) == 'VISP'
-          | toupper(x.backup[i]) == 'VRSP') {
-        # vanco resistant S. pneumoniae
-        x[i] <- 'Streptococcus pneumoniae'
       }
     }
 

README.md

@@ -53,9 +53,9 @@ The functions to calculate microbial resistance use expressions that are not eva
 This package [is published on CRAN](http://cran.r-project.org/package=AMR), the official R network.
 
 ### Install from CRAN (recommended)
-[![CRAN_Badge](https://img.shields.io/cran/v/AMR.svg?label=CRAN)](http://cran.r-project.org/package=AMR) [![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](http://cran.r-project.org/package=AMR)
+[![CRAN_Badge](https://img.shields.io/cran/v/AMR.svg?label=CRAN&colorB=3679BC)](http://cran.r-project.org/package=AMR) [![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](http://cran.r-project.org/package=AMR)
 
-(Note: downloads measured only by [cran.rstudio.com](https://cran.rstudio.com/package=AMR), i.e. this excludes the official [cran.r-project.org](https://cran.r-project.org/package=AMR))
+(Note: Downloads measured only by [cran.rstudio.com](https://cran.rstudio.com/package=AMR), this excludes e.g. the official [cran.r-project.org](https://cran.r-project.org/package=AMR))
 
 - <img src="http://www.rstudio.com/favicon.ico" alt="RStudio favicon" height="20px"> Install using [RStudio](http://www.rstudio.com) (recommended):
   - Click on `Tools` and then `Install Packages...`

man/as.bactid.Rd

@@ -22,6 +22,8 @@ Character (vector) with class \code{"bactid"}. Unknown values will return \code{
 Use this function to determine a valid ID based on a genus (and species). This input can be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
 }
 \details{
+\code{guess_bactid} does exactly the same as \code{as.bactid}.
+
 Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. For example:
 \itemize{
   \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
@@ -51,17 +53,16 @@ df$bactid <- as.bactid(df$microorganism_name)
 library(dplyr)
 df$bactid <- df \%>\%
   select(microorganism_name) \%>\%
-  as.bactid()
+  guess_bactid()
 
 # and can even contain 2 columns, which is convenient for genus/species combinations:
 df$bactid <- df \%>\%
   select(genus, species) \%>\%
-  as.bactid()
+  guess_bactid()
 
 # same result:
 df <- df \%>\%
-  mutate(bactid = paste(genus, species) \%>\%
+  mutate(bactid = guess_bactid(paste(genus, species)))
-                    as.bactid())
 }
 }
 \seealso{