Add support for taxonomic synonyms and update taxonomic names

.Rbuildignore

@@ -1,5 +1,7 @@
-^renv$
-^renv\.lock$
-^\.github$
-^.*\.Rproj$
-^\.Rproj\.user$
+^renv$
+^renv\.lock$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+^README\.Rmd$

DESCRIPTION

@@ -1,18 +1,18 @@
 Package: whatbacteria
 Title: whatbacteria
-Version: 0.0.1.0
+Version: 0.2.0.9000
 Author: Vincent Tu <tuv@email.chop.edu>
-Maintainer: Vincent Tu <tuv@email.chop.edu>
+Maintainer: Kyle Bittinger <kylebittinger@gmail.com>
 Description: Taxon phenotype and susceptibility databases for the mirix package.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3
 Suggests:
     knitr,
     rmarkdown,
     testthat (>= 3.0.0)
-Depends: 
-    R (>= 2.10)
+Depends:
+    R (>= 4.1.0)
 Config/testthat/edition: 3

R/data.R

@@ -1,27 +1,37 @@
-#' Gram stain and aerobic status of bacterial taxa
-#' @format A data frame with the following columns:
-#' \describe{
-#'   \item{taxon}{The name of the taxon}
-#'   \item{rank}{The rank of the taxon}
-#'   \item{aerobic_status}{
-#'     The aerobic status. One of "aerobe", "facultative anaerobe", or
-#'     "obligate anaerobe".}
-#'   \item{gram_stain}{
-#'     How the taxon appears when Gram-stained. One of "Gram-positive" or
-#'     "Gram-negative".}
-#'   \item{doi}{DOI of the publication from which the information was obtained.}
-#' }
-"taxon_phenotypes"
-
-#' Antibiotic susceptibility of bacterial taxa
-#' @format A data frame with the following columns:
-#' \describe{
-#'   \item{taxon}{The name of the taxon}
-#'   \item{rank}{The rank of the taxon}
-#'   \item{antibiotic}{The antibiotic or antibiotic class}
-#'   \item{value}{
-#'     The susceptibility of the taxon to the antibiotic, one of "susceptible"
-#'     or "resistant".}
-#'   \item{doi}{DOI of the publication from which the information was obtained.}
-#' }
-"taxon_susceptibility"
+#' Gram stain and aerobic status of bacterial taxa
+#' @format A data frame with the following columns:
+#' \describe{
+#'   \item{taxon}{The name of the taxon}
+#'   \item{rank}{The rank of the taxon}
+#'   \item{aerobic_status}{
+#'     The aerobic status. One of "aerobe", "facultative anaerobe", or
+#'     "obligate anaerobe".}
+#'   \item{gram_stain}{
+#'     How the taxon appears when Gram-stained. One of "Gram-positive" or
+#'     "Gram-negative".}
+#'   \item{doi}{DOI of the publication from which the information was obtained.}
+#' }
+"taxon_phenotypes"
+
+#' Antibiotic susceptibility of bacterial taxa
+#' @format A data frame with the following columns:
+#' \describe{
+#'   \item{taxon}{The name of the taxon}
+#'   \item{rank}{The rank of the taxon}
+#'   \item{antibiotic}{The antibiotic or antibiotic class}
+#'   \item{value}{
+#'     The susceptibility of the taxon to the antibiotic, one of "susceptible"
+#'     or "resistant".}
+#'   \item{doi}{DOI of the publication from which the information was obtained.}
+#' }
+"taxon_susceptibility"
+
+#' Synonyms for bacterial taxa
+#' @format A data frame with the following columns:
+#' \describe{
+#'   \item{name}{The synonym}
+#'   \item{rank}{The rank of the taxon}
+#'   \item{correct_name}{The "correct" name for the taxon, as it is used in
+#'     other package data.}
+#' }
+"taxon_synonyms"