support groups for portion_df, update README

man/first_isolate.Rd

@@ -76,7 +76,7 @@ Determine first (weighted) isolates of all microorganisms of every patient per e
 }
 
 \examples{
-# septic_patients is a dataset available in the AMR package. It is true data.
+# septic_patients is a dataset available in the AMR package. It is true, genuine data.
 ?septic_patients
 
 library(dplyr)

man/ggplot_rsi.Rd

@@ -9,9 +9,11 @@
 \alias{theme_rsi}
 \title{AMR bar plots with \code{ggplot}}
 \usage{
-ggplot_rsi(data, x = "Antibiotic", facet = NULL)
+ggplot_rsi(data, position = "stack", x = "Antibiotic",
+  fill = "Interpretation", facet = NULL)
 
-geom_rsi(position = "stack", x = c("Antibiotic", "Interpretation"))
+geom_rsi(position = "stack", x = c("Antibiotic", "Interpretation"),
+  fill = "Interpretation")
 
 facet_rsi(facet = c("Interpretation", "Antibiotic"))
 
@@ -24,11 +26,13 @@ theme_rsi()
 \arguments{
 \item{data}{a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})}
 
-\item{x}{parameter to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"}}
-
-\item{facet}{parameter to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"}}
-
 \item{position}{position adjustment of bars, either \code{"stack"} (default) or \code{"dodge"}}
+
+\item{x}{variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"}}
+
+\item{fill}{variable to categorise using the plots legend}
+
+\item{facet}{variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"}}
 }
 \description{
 Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} functions.
@@ -74,4 +78,12 @@ septic_patients \%>\%
 septic_patients \%>\%
   select(amox, nitr, fosf, trim, cipr) \%>\%
   ggplot_rsi(x = "Interpretation", facet = "Antibiotic")
+
+# it also supports groups (don't forget to use facet on the group):
+septic_patients \%>\%
+  select(hospital_id, amox, cipr) \%>\%
+  group_by(hospital_id) \%>\%
+  ggplot_rsi() +
+  facet_grid("hospital_id") +
+  labs(title = "AMR of Amoxicillin And Ciprofloxacine Per Hospital")
 }

man/portion.Rd

@@ -11,6 +11,8 @@
 \title{Calculate resistance of isolates}
 \source{
 \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
+
+Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html}
 }
 \usage{
 portion_R(ab1, ab2 = NULL, minimum = 30, as_percent = FALSE)
@@ -49,7 +51,7 @@ These functions can be used to calculate the (co-)resistance of microbial isolat
 \details{
 \strong{Remember that you should filter your table to let it contain only first isolates!} Use \code{\link{first_isolate}} to determine them in your data set.
 
-\code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \code{data.frame} will have three rows (for R/I/S) and a column for each variable with class \code{"rsi"}.
+\code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
 
 The old \code{\link{rsi}} function is still available for backwards compatibility but is deprecated.
 \if{html}{
@@ -66,6 +68,9 @@ The old \code{\link{rsi}} function is still available for backwards compatibilit
 }
 }
 \examples{
+# septic_patients is a data set available in the AMR package. It is true, genuine data.
+?septic_patients
+
 # Calculate resistance
 portion_R(septic_patients$amox)
 portion_IR(septic_patients$amox)
@@ -114,6 +119,18 @@ septic_patients \%>\%
             combination_p = portion_S(cipr, gent, as_percent = TRUE),
             combination_n = n_rsi(cipr, gent))
 
+# Get portions S/I/R immediately of all rsi columns
+septic_patients \%>\%
+  select(amox, cipr) \%>\%
+  portion_df(translate = FALSE)
+
+# It also supports grouping variables
+septic_patients \%>\%
+  select(hospital_id, amox, cipr) \%>\%
+  group_by(hospital_id) \%>\%
+  portion_df(translate = FALSE)
+
+
 \dontrun{
 
 # calculate current empiric combination therapy of Helicobacter gastritis:

man/septic_patients.Rd

@@ -7,7 +7,7 @@
 \format{A data.frame with 2000 observations and 49 variables:
 \describe{
   \item{\code{date}}{date of receipt at the laboratory}
-  \item{\code{hospital_id}}{ID of the hospital}
+  \item{\code{hospital_id}}{ID of the hospital, from A to D}
   \item{\code{ward_icu}}{logical to determine if ward is an intensive care unit}
   \item{\code{ward_clinical}}{logical to determine if ward is a regular clinical ward}
   \item{\code{ward_outpatient}}{logical to determine if ward is an outpatient clinic}
@@ -21,7 +21,7 @@
 septic_patients
 }
 \description{
-An anonymised dataset containing 2000 microbial blood culture isolates with their antibiogram of septic patients found in 5 different hospitals in the Netherlands, between 2001 and 2017. This data.frame can be used to practice AMR analysis. For examples, press F1.
+An anonymised dataset containing 2000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This \code{data.frame} can be used to practice AMR analysis. For examples, press F1.
 }
 \examples{
 # ----------- #