MDRO, freq tables, new print format for tibbles

man/EUCAST.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/EUCAST.R
+% Please edit documentation in R/eucast.R
 \name{EUCAST_rules}
 \alias{EUCAST_rules}
 \alias{interpretive_reading}

man/MDRO.Rd

@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mdro.R
+\name{MDRO}
+\alias{MDRO}
+\alias{BRMO}
+\alias{MRGN}
+\title{Determine multidrug-resistant organisms (MDRO)}
+\usage{
+MDRO(tbl, country, col_bactid = "bactid", info = TRUE,
+  aminoglycosides = c("gent", "tobr", "kana"), quinolones = c("cipr",
+  "norf"), carbapenems = c("imip", "mero", "erta"), ceftazidime = "cfta",
+  piperacillin = "pita", trimethoprim_sulfa = "trsu", penicillin = "peni",
+  vancomycin = "vanc")
+
+BRMO(tbl, country = "nl", ...)
+
+MRGN(tbl, country = "de", ...)
+}
+\arguments{
+\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
+
+\item{country}{country to determine guidelines. Should be a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).}
+
+\item{col_bactid}{column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$bactid}, see \code{\link{microorganisms}}}
+
+\item{info}{print progress}
+
+\item{aminoglycosides, quinolones, carbapenems}{character vector with column names of antibiotics}
+
+\item{ceftazidime, piperacillin, trimethoprim_sulfa, penicillin, vancomycin}{column names of antibiotics}
+
+\item{...}{parameters that are passed on to \code{MDR}}
+}
+\value{
+Ordered factor with values \code{Positive}, \code{Unconfirmed}, \code{Negative}.
+}
+\description{
+Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
+}

man/freq.Rd

@@ -0,0 +1,71 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/freq.R
+\name{freq}
+\alias{freq}
+\alias{frequency_tbl}
+\title{Frequency table}
+\usage{
+freq(x, sort.count = TRUE, nmax = 15, na.rm = TRUE, markdown = FALSE,
+  toConsole = TRUE, digits = 2, sep = " ")
+
+frequency_tbl(x, sort.count = TRUE, nmax = 15, na.rm = TRUE,
+  markdown = FALSE, toConsole = TRUE, digits = 2, sep = " ")
+}
+\arguments{
+\item{x}{data}
+
+\item{sort.count}{Sort on count. Use \code{FALSE} to sort alphabetically on item.}
+
+\item{nmax}{number of row to print. Use \code{nmax = 0} or \code{nmax = NA} to print all rows.}
+
+\item{na.rm}{a logical value indicating whether NA values should be removed from the frequency table. The header will always print the amount of\code{NA}s.}
+
+\item{markdown}{print table in markdown format (this forces \code{nmax = NA})}
+
+\item{toConsole}{Print table to the console. Use \code{FALSE} to assign the table to an object.}
+
+\item{digits}{how many significant digits are to be used for numeric values (not for the items themselves, that depends on \code{\link{getOption}("digits")})}
+
+\item{sep}{a character string to separate the terms when selecting multiple columns}
+}
+\description{
+Create a frequency table of a vector of data, a single column or a maximum of 9 columns of a data frame. Supports markdown for reports.
+}
+\details{
+For numeric values, the next values will be calculated and shown into the header:
+\itemize{
+  \item{Mean, using \code{\link[base]{mean}}}
+  \item{Standard deviation, using \code{\link[stats]{sd}}}
+  \item{Five numbers of Tukey (min, Q1, median, Q3, max), using \code{\link[stats]{fivenum}}}
+  \item{Outliers (count and list), using \code{\link{boxplot.stats}}}
+  \item{Coefficient of variation (CV), the standard deviation divided by the mean}
+  \item{Coefficient of quartile variation (CQV, sometimes called coefficient of dispersion), calculated as \code{(Q3 - Q1) / (Q3 + Q1)} using \code{\link{quantile}} with \code{type = 6} as quantile algorithm to comply with SPSS standards}
+}
+}
+\examples{
+library(dplyr)
+
+freq(septic_patients$hospital_id)
+
+septic_patients \%>\%
+  filter(hospital_id == "A") \%>\%
+  select(bactid) \%>\%
+  freq()
+
+# select multiple columns; they will be pasted together
+septic_patients \%>\%
+  left_join_microorganisms \%>\%
+  filter(hospital_id == "A") \%>\%
+  select(genus, species) \%>\%
+  freq()
+
+# save frequency table to an object
+years <- septic_patients \%>\%
+  mutate(year = format(date, "\%Y")) \%>\%
+  select(year) \%>\%
+  freq(toConsole = FALSE)
+}
+\keyword{freq}
+\keyword{frequency}
+\keyword{summarise}
+\keyword{summary}

man/like.Rd

@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/misc.R
+\name{like}
+\alias{like}
+\alias{\%like\%}
+\title{Pattern Matching}
+\source{
+Inherited from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, but made it case insensitive at default.
+}
+\usage{
+x \%like\% pattern
+}
+\arguments{
+\item{x}{a character vector where matches are sought, or an
+    object which can be coerced by \code{as.character} to a character
+    vector.  \link{Long vectors} are supported.}
+
+\item{pattern}{character string containing a \link{regular expression}
+    (or character string for \code{fixed = TRUE}) to be matched
+    in the given character vector.  Coerced by
+    \code{\link{as.character}} to a character string if possible.  If a
+    character vector of length 2 or more is supplied, the first element
+    is used with a warning.  Missing values are allowed except for
+    \code{regexpr} and \code{gregexpr}.}
+}
+\value{
+A \code{logical} vector
+}
+\description{
+Convenience function to compare a vector with a pattern, like \code{\link[base]{grep}}. It always returns a \code{logical} vector and is always case-insensitive.
+}
+\examples{
+library(dplyr)
+# get unique occurences of bacteria whose name start with 'Ent'
+septic_patients \%>\%
+  left_join_microorganisms() \%>\%
+  filter(fullname \%like\% '^Ent') \%>\%
+  pull(fullname) \%>\%
+  unique()
+}

man/mo_property.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/EUCAST.R
+% Please edit documentation in R/eucast.R
 \name{mo_property}
 \alias{mo_property}
 \title{Poperties of a microorganism}

man/print.Rd

@@ -0,0 +1,55 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/print.R
+\name{print}
+\alias{print}
+\alias{print.tbl_df}
+\alias{print.tbl}
+\alias{print.data.table}
+\title{Printing Data Tables and Tibbles}
+\usage{
+\method{print}{tbl_df}(x, nmax = 10, header = TRUE, row.names = TRUE,
+  right = FALSE, width = 1, na = "<NA>", ...)
+
+\method{print}{tbl}(x, ...)
+
+\method{print}{data.table}(x, nmax = 10, header = TRUE, row.names = TRUE,
+  print.keys = FALSE, right = FALSE, width = 1, na = "<NA>", ...)
+}
+\arguments{
+\item{x}{object of class \code{data.frame}.}
+
+\item{nmax}{amount of rows to print in total. When the total amount of rows exceeds this limit, the first and last \code{nmax / 2} rows will be printed. Use \code{nmax = NA} to print all rows.}
+
+\item{header}{print header with information about data size and tibble grouping}
+
+\item{row.names}{logical (or character vector), indicating whether (or
+    what) row names should be printed.}
+
+\item{right}{logical, indicating whether or not strings should be
+    right-aligned.  The default is right-alignment.}
+
+\item{width}{amount of white spaces to keep between columns, must be at least 1}
+
+\item{na}{value to print instead of NA}
+
+\item{...}{optional arguments to \code{print} or \code{plot} methods.}
+
+\item{print.keys}{print keys for \code{data.table}}
+}
+\description{
+Print a data table or tibble. It prints: \cr- The \strong{first and last rows} like \code{data.table}s are printed by the \code{data.table} package,\cr- A \strong{header} and \strong{left aligned text} like \code{tibble}s are printed by the \code{tibble} package with info about grouped variables,\cr- \strong{Unchanged values} and \strong{support for row names} like \code{data.frame}s are printed by the \code{base} package.
+}
+\examples{
+# still showing all values unchanged:
+library(dplyr)
+starwars
+print(starwars, width = 3)
+
+# compare the significance notation of this
+starwars \%>\% select(birth_year)
+# with this
+tibble:::print.tbl_df(starwars \%>\% select(birth_year))
+
+# supports info about groups (look at header)
+starwars \%>\% group_by(homeworld, gender)
+}