diff --git a/R/data.R b/R/data.R index a098d626..a14bdcb1 100755 --- a/R/data.R +++ b/R/data.R @@ -150,7 +150,7 @@ #' #' A data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by \code{\link{as.mo}}. #' @inheritSection as.mo ITIS -#' @format A \code{\link{data.frame}} with 2,384 observations and 5 variables: +#' @format A \code{\link{data.frame}} with 2,383 observations and 5 variables: #' \describe{ #' \item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS} #' \item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source} diff --git a/README.md b/README.md index 27e12dec..61fca18c 100755 --- a/README.md +++ b/README.md @@ -30,6 +30,7 @@ Erwin E.A. Hassing2, * [Install from CRAN](#install-from-cran) * [Install from GitHub](#install-from-github) * [How to use it?](#how-to-use-it) + * [ITIS](#itis) * [New classes](#new-classes) * [Overwrite/force resistance based on EUCAST rules](#overwriteforce-resistance-based-on-eucast-rules) * [Other (microbial) epidemiological functions](#other-microbial-epidemiological-functions) @@ -40,11 +41,7 @@ Erwin E.A. Hassing2, ## Why this package? This R package was intended **to make microbial epidemiology easier**. Most functions contain extensive help pages to get started. - - -This `AMR` package contains the **complete microbial taxonomic data** (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. This allows users to use authoritative taxonomic information for their data analyses on any microorganisms, not only human pathogens. - -Combined with several new functions, this `AMR` package basically does four important things: +The `AMR` package basically does four important things: 1. It **cleanses existing data**, by transforming it to reproducible and profound *classes*, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect: @@ -122,6 +119,11 @@ library(AMR) help(package = "AMR") ``` +## ITIS + + +This `AMR` package contains the **complete microbial taxonomic data** (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. This allows users to use authoritative taxonomic information for their data analyses on any microorganisms, not only human pathogens. + ### New classes This package contains two new S3 classes: `mic` for MIC values (e.g. from Vitek or Phoenix) and `rsi` for antimicrobial drug interpretations (i.e. S, I and R). Both are actually ordered factors under the hood (an MIC of `2` being higher than `<=1` but lower than `>=32`, and for class `rsi` factors are ordered as `S < I < R`). Both classes have extensions for existing generic functions like `print`, `summary` and `plot`. @@ -148,6 +150,8 @@ plot(septic_patients$cipr) ![example_1_rsi](man/figures/rsi_example1.png) + + Or use the `ggplot2` and `dplyr` packages to create more appealing plots: ```r library(dplyr) diff --git a/data/microorganisms.old.rda b/data/microorganisms.old.rda index 26f2a436..ca40a9d4 100644 Binary files a/data/microorganisms.old.rda and b/data/microorganisms.old.rda differ diff --git a/man/figures/plus.png b/man/figures/plus.png new file mode 100644 index 00000000..357f17a4 Binary files /dev/null and b/man/figures/plus.png differ diff --git a/man/microorganisms.old.Rd b/man/microorganisms.old.Rd index 71ccd54d..78237f2d 100644 --- a/man/microorganisms.old.Rd +++ b/man/microorganisms.old.Rd @@ -4,7 +4,7 @@ \name{microorganisms.old} \alias{microorganisms.old} \title{Data set with old taxonomic data from ITIS} -\format{A \code{\link{data.frame}} with 2,384 observations and 5 variables: +\format{A \code{\link{data.frame}} with 2,383 observations and 5 variables: \describe{ \item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS} \item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}