diff --git a/NEWS.md b/NEWS.md index ddc4b17a..aca760a5 100755 --- a/NEWS.md +++ b/NEWS.md @@ -23,7 +23,7 @@ * Introduction to AMR as a vignette #### Changed -* Added 226 microorganisms to the `microorganisms` data set and removed the few viruses it contained, now *n* = 2,664 (2,225 bacteria, 285 fungi/yeasts, 153 parasites, 1 other) +* Added 231 microorganisms to the `microorganisms` data set and removed the few viruses it contained, now *n* = 2,669 (2,230 bacteria, 285 fungi/yeasts, 153 parasites, 1 other) * Added three antimicrobial agents to the `antibiotics` data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05) * Added 163 trade names to the `antibiotics` data set, it now contains 298 different trade names in total, e.g.: ```r diff --git a/R/data.R b/R/data.R index d6505cb2..38a9807b 100755 --- a/R/data.R +++ b/R/data.R @@ -122,8 +122,8 @@ #' Data set with human pathogenic microorganisms #' -#' A data set containing 2,664 (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}. -#' @format A \code{\link{tibble}} with 2,664 observations and 16 variables: +#' A data set containing 2,669 (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}. +#' @format A \code{\link{tibble}} with 2,669 observations and 16 variables: #' \describe{ #' \item{\code{mo}}{ID of microorganism} #' \item{\code{bactsys}}{Bactsyscode of microorganism} @@ -158,7 +158,7 @@ #' Translation table for UMCG with ~1,100 microorganisms #' #' A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}. -#' @format A \code{\link{tibble}} with 1,090 observations and 2 variables: +#' @format A \code{\link{tibble}} with 1,095 observations and 2 variables: #' \describe{ #' \item{\code{umcg}}{Code of microorganism according to UMCG MMB} #' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}} diff --git a/README.md b/README.md index ba748292..b1b7be25 100755 --- a/README.md +++ b/README.md @@ -44,7 +44,7 @@ This `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: - * Use `as.mo` to get an ID of a microorganism. The IDs are quite obvious - the ID of *E. coli* is "ESCCOL" and the ID of *S. aureus* is "STAAUR". The function takes almost any text as input that looks like the name or code of a microorganism like "E. coli", "esco" and "esccol". Even `as.mo("MRSA")` will return the ID of *S. aureus*. Moreover, it can group all coagulase negative and positive *Staphylococci*, and can transform *Streptococci* into Lancefield groups. To find bacteria based on your input, this package contains a freely available database of ~2,650 different (potential) human pathogenic microorganisms. + * Use `as.mo` to get an ID of a microorganism. The IDs are quite obvious - the ID of *E. coli* is "ESCCOL" and the ID of *S. aureus* is "STAAUR". The function takes almost any text as input that looks like the name or code of a microorganism like "E. coli", "esco" and "esccol". Even `as.mo("MRSA")` will return the ID of *S. aureus*. Moreover, it can group all coagulase negative and positive *Staphylococci*, and can transform *Streptococci* into Lancefield groups. To find bacteria based on your input, this package contains a freely available database of almost 3,000 different (potential) human pathogenic microorganisms. * Use `as.rsi` to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like "<=0.002; S" (combined MIC/RSI) will result in "S". * Use `as.mic` to cleanse your MIC values. It produces a so-called factor (called *ordinal* in SPSS) with valid MIC values as levels. A value like "<=0.002; S" (combined MIC/RSI) will result in "<=0.002". * Use `as.atc` to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values "Furabid", "Furadantin", "nitro" all return the ATC code of Nitrofurantoine. diff --git a/data/microorganisms.rda b/data/microorganisms.rda index 1ab46d3b..cd8e5b99 100755 Binary files a/data/microorganisms.rda and b/data/microorganisms.rda differ diff --git a/data/microorganisms.umcg.rda b/data/microorganisms.umcg.rda index 5f43db47..c3258c19 100755 Binary files a/data/microorganisms.umcg.rda and b/data/microorganisms.umcg.rda differ diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index c6a2796c..b02f309d 100755 --- a/man/microorganisms.Rd +++ b/man/microorganisms.Rd @@ -4,7 +4,7 @@ \name{microorganisms} \alias{microorganisms} \title{Data set with human pathogenic microorganisms} -\format{A \code{\link{tibble}} with 2,664 observations and 16 variables: +\format{A \code{\link{tibble}} with 2,669 observations and 16 variables: \describe{ \item{\code{mo}}{ID of microorganism} \item{\code{bactsys}}{Bactsyscode of microorganism} @@ -27,7 +27,7 @@ microorganisms } \description{ -A data set containing 2,664 (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}. +A data set containing 2,669 (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}. } \seealso{ \code{\link{guess_mo}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}} diff --git a/man/microorganisms.umcg.Rd b/man/microorganisms.umcg.Rd index edf38ee0..7b99880a 100755 --- a/man/microorganisms.umcg.Rd +++ b/man/microorganisms.umcg.Rd @@ -4,7 +4,7 @@ \name{microorganisms.umcg} \alias{microorganisms.umcg} \title{Translation table for UMCG with ~1,100 microorganisms} -\format{A \code{\link{tibble}} with 1,090 observations and 2 variables: +\format{A \code{\link{tibble}} with 1,095 observations and 2 variables: \describe{ \item{\code{umcg}}{Code of microorganism according to UMCG MMB} \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}} diff --git a/vignettes/AMR.Rmd b/vignettes/AMR.Rmd index c785a189..9eed8f21 100755 --- a/vignettes/AMR.Rmd +++ b/vignettes/AMR.Rmd @@ -23,7 +23,7 @@ This `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: - * Use `as.mo` to get an ID of a microorganism. The IDs are quite obvious - the ID of *E. coli* is "ESCCOL" and the ID of *S. aureus* is "STAAUR". The function takes almost any text as input that looks like the name or code of a microorganism like "E. coli", "esco" and "esccol". Even `as.mo("MRSA")` will return the ID of *S. aureus*. Moreover, it can group all coagulase negative and positive *Staphylococci*, and can transform *Streptococci* into Lancefield groups. To find bacteria based on your input, this package contains a freely available database of ~2,650 different (potential) human pathogenic microorganisms. + * Use `as.mo` to get an ID of a microorganism. The IDs are quite obvious - the ID of *E. coli* is "ESCCOL" and the ID of *S. aureus* is "STAAUR". The function takes almost any text as input that looks like the name or code of a microorganism like "E. coli", "esco" and "esccol". Even `as.mo("MRSA")` will return the ID of *S. aureus*. Moreover, it can group all coagulase negative and positive *Staphylococci*, and can transform *Streptococci* into Lancefield groups. To find bacteria based on your input, this package contains a freely available database of almost 3,000 different (potential) human pathogenic microorganisms. * Use `as.rsi` to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like "<=0.002; S" (combined MIC/RSI) will result in "S". * Use `as.mic` to cleanse your MIC values. It produces a so-called factor (called *ordinal* in SPSS) with valid MIC values as levels. A value like "<=0.002; S" (combined MIC/RSI) will result in "<=0.002". * Use `as.atc` to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values "Furabid", "Furadantin", "nitro" all return the ATC code of Nitrofurantoine.