diff --git a/.travis.yml b/.travis.yml
index 03445b63..27136ca9 100755
--- a/.travis.yml
+++ b/.travis.yml
@@ -33,7 +33,6 @@ jobs:
matrix:
allow_failures:
- r: 3.1
- - r: 3.2
- r: devel
r_packages: covr
cache: packages
diff --git a/NEWS.md b/NEWS.md
index faabe1af..804d8d91 100755
--- a/NEWS.md
+++ b/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 Χ2 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
diff --git a/R/bactid.R b/R/bactid.R
index ba677b59..75ed14eb 100644
--- a/R/bactid.R
+++ b/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) %>%
-#' as.bactid())
+#' mutate(bactid = guess_bactid(paste(genus, species)))
#' }
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'
- | toupper(x.backup[i]) == 'PRSP') {
- # peni resistant S. pneumoniae
- x[i] <- 'Streptococcus pneumoniae'
- }
- if (toupper(x.backup[i]) == 'VISP'
- | toupper(x.backup[i]) == 'VRSP') {
- # vanco resistant S. pneumoniae
- x[i] <- 'Streptococcus pneumoniae'
+ if (toupper(x.backup[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
+ # peni R, peni I, vanco I, vanco R: S. pneumoniae
+ x[i] <- 'STCPNE'
}
}
diff --git a/README.md b/README.md
index 1f147965..805465f6 100755
--- a/README.md
+++ b/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)
-[](http://cran.r-project.org/package=AMR) [](http://cran.r-project.org/package=AMR)
+[](http://cran.r-project.org/package=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))
- 
Install using [RStudio](http://www.rstudio.com) (recommended):
- Click on `Tools` and then `Install Packages...`
diff --git a/man/as.bactid.Rd b/man/as.bactid.Rd
index 3a17bc6a..ebd58f68 100644
--- a/man/as.bactid.Rd
+++ b/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) \%>\%
- as.bactid())
+ mutate(bactid = guess_bactid(paste(genus, species)))
}
}
\seealso{