Update documentation

- update documentation for new API
- add keywords, seealso and family desc_table
- update roxygen

NAMESPACE

@@ -15,6 +15,7 @@ export(ANOVA)
 export(IQR)
 export(chisq.test)
 export(datatable)
+export(desc_output)
 export(desc_table)
 export(desc_tests)
 export(desctable)

R/build.R

@@ -8,6 +8,7 @@
 #'
 #' @param stat The statistic to use
 #' @param data The dataframe to apply the statistic to
+#' @keywords internal
 #' @return A vector for one statistic column
 statColumn <- function(stat, data) {
   # Apply one statified stat function to every variable in the data
@@ -33,6 +34,7 @@ For example, `is.normal ~ mean | median` becomes `~ if (is.normal(.)) mean(.) el
 #'
 #' @param data The dataframe to apply the statistic to
 #' @param stats A list of named statistics to use
+#' @keywords internal
 #' @return A dataframe of all statistics for all variables
 statTable <- function(data, stats) {
   # If stats is a function, apply it to the data to obtain a list of stat functions
@@ -60,6 +62,7 @@ statTable <- function(data, stats) {
 #'
 #' @param data The dataframe to get the names from
 #' @param labels The optional named character vector containing the keypairs var = "Label"
+#' @keywords internal
 #' @return A dataframe with one variable named "Variables", a character vector of variable names/labels and levels
 varColumn <- function(data, labels = NULL) {
   # Every variable name that exists in the labels is to be replaced with its corresponding label
@@ -101,6 +104,7 @@ varColumn <- function(data, labels = NULL) {
 #' @param df Dataframe to use for the tests
 #' @param tests Test function or list of functions
 #' @param grp Grouping factor
+#' @keywords internal
 #' @return A numeric vector of pvalues
 testColumn <- function(df, tests, grp) {
   group <- eval(grp, df)
@@ -135,36 +139,45 @@ testColumn <- function(df, tests, grp) {
 
 #' Generate a statistics table
 #'
-#' Generate a statistics table with the chosen statistical functions, and tests if given a \code{"grouped"} dataframe.
+#' Generate a statistics table with the chosen statistical functions, nested if called with a grouped dataframe.
 #'
 #' @section Stats:
-#' The stats can be a function which takes a dataframe and returns a list of statistical functions to use.
+#' The statistical functions to use in the table are passed as additional arguments.
+#' If the argument is named (eg. \code{N = length}) the name will be used as the column title instead of the function
+#' name (here, \strong{N} instead of \strong{length}).
 #'
-#' stats can also be a named list of statistical functions, or purrr::map like formulas.
+#' Any R function can be a statistical function, as long as it returns only one value when applied to a vector, or as
+#' many values as there are levels in a factor, plus one.
+#'
+#' Users can also use \code{purrr::map}-like formulas as quick anonymous functions (eg. \code{Q1 = ~ quantile(., .25)} to get the first quantile in a
+#' column named \strong{Q1})
+#'
+#' If no statistical function is given to \code{desc_table}, the \code{.auto} argument is used to provide a function
+#' that automatically determines the most appropriate statistical functions to use based on the contents of the table.
 #'
-#' The names will be used as column names in the resulting table. If an element of the list is a function, it will be used as-is for the stats.
 #' @section Labels:
-#' labels is an option named character vector used to make the table prettier.
+#' \code{.labels} is a named character vector to provide "pretty" labels to variables.
 #'
 #' If given, the variable names for which there is a label will be replaced by their corresponding label.
 #'
 #' Not all variables need to have a label, and labels for non-existing variables are ignored.
 #'
-#' labels must be given in the form c(unquoted_variable_name = "label")
+#' labels must be given in the form \code{c(unquoted_variable_name = "label")}
 #'
 #' @section Output:
 #' The output is either a dataframe in the case of a simple descriptive table,
 #' or nested dataframes in the case of a comparative table.
 #'
 #' @param data The dataframe to analyze
+#' @param ...  A list of named statistics to apply to each element of the dataframe, or a function returning a list of named statistics
 #' @param .auto A function to automatically determine appropriate statistics
 #' @param .labels A named character vector of variable labels
-#' @param ...  list of named statistics to apply to each element of the dataframe, or a function returning a list of named statistics
-#' @return A desctable object, which prints to a table of statistics for all variables
+#' @return A simple or grouped descriptive table
 #' @seealso \code{\link{stats_auto}}
-#' @seealso \code{\link{desc_tests}}
-#' @seealso \code{\link{desc_output}}
+#' @seealso \code{\link{IQR}}
+#' @seealso \code{\link{percent}}
 #' @export
+#' @family desc_table core functions
 #' @examples
 #' iris %>%
 #'   desc_table()
@@ -172,15 +185,19 @@ testColumn <- function(df, tests, grp) {
 #' # Does the same as stats_auto here
 #' iris %>%
 #'   desc_table("N"      = length,
-#'              "Mean"   = ~ if (is.normal(.)) mean(.),
-#'              "sd"     = ~ if (is.normal(.)) sd(.),
-#'              "Med"    = stats::median,
-#'              "IQR"    = ~ if(!is.factor(.)) IQR(.))
+#'              "Min"    = min,
+#'              "Q1"     = ~quantile(., .25),
+#'              "Med"    = median,
+#'              "Mean"   = mean,
+#'              "Q3"     = ~quantile(., .75),
+#'              "Max"    = max,
+#'              "sd"     = sd,
+#'              "IQR"    = IQR)
 #'
 #' # With grouping on a factor
 #' iris %>%
 #'   group_by(Species) %>%
-#'   desc_table(.auto = stats_default)
+#'   desc_table(.auto = stats_auto)
 desc_table <- function(data, ..., .auto, .labels) {
   UseMethod("desc_table", data)
 }
@@ -246,12 +263,37 @@ desc_table.grouped_df <- function(data, ..., .auto = stats_auto, .labels = NULL)
 
 #' Add tests to a desc_table
 #'
-#' @param desctable a desc_table
-#' @param ... A list of statistical tests to use when calling desc_table with a grouped_df
+#' Add test statistics to a grouped desc_table, with the tests specified as \code{variable = test}.
+#'
+#' @section Tests:
+#' The statistical test functions to use in the table are passed as additional named arguments. Tests must be preceded
+#' by a formula tilde (\code{~}).
+#' \code{name = ~test} will apply test \code{test} to variable \code{name}.
+#'
+#' Any R test function can be used, as long as it returns an object containing a \code{p.value} element, which is the
+#' case for most tests returning an object of class  \code{htest}.
+#'
+#' Users can also use \code{purrr::map}-like formulas as quick anonymous functions (eg. \code{~ t.test(., var.equal = T)} to
+#' compute a t test without the Welch correction.
+#'
+#' @param desctable A desc_table
+#' @param ... A list of statistical tests associated to variable names
 #' @param .auto A function to automatically determine the appropriate tests
 #' @param .default A default fallback test
+#' @seealso \code{\link{tests_auto}}
+#' @seealso \code{\link{no.test}}
+#' @seealso \code{\link{ANOVA}}
 #' @return A desc_table with tests
 #' @export
+#' @family desc_table core functions
+#' @examples
+#' iris %>%
+#'   group_by(Species) %>%
+#'   desc_table() %>%
+#'   desc_tests(Sepal.Length = ~kruskal.test,
+#'              Sepal.Width  = ~oneway.test,
+#'              Petal.Length = ~oneway.test(., var.equal = T),
+#'              Petal.Length = ~oneway.test(., var.equal = F))
 desc_tests <- function(desctable, .auto = tests_auto, .default = NULL, ...) {
   if (which.desctable(desctable) != "grouped")
     stop("Unexpected input. `desc_tests` must be used on the output of `desc_table` on a grouped dataframe.\n

R/deprecated.R

@@ -46,6 +46,7 @@ pander::pander
 #' @seealso \code{\link{pander.desctable}}
 #' @seealso \code{\link{datatable.desctable}}
 #' @export
+#' @keywords deprecated
 #' @examples
 #' iris %>%
 #'   desctable()
@@ -117,6 +118,7 @@ desctable.grouped_df <- function(data, stats = stats_auto, tests = tests_auto, l
 #' @param grp Grouping factor
 #' @param df Dataframe containing the grouping factor
 #' @return A character vector with the names for the subtables
+#' @keywords deprecated internal
 subNames <- function(grp, df) {
   paste0(as.character(grp),
          ": ",
@@ -134,6 +136,7 @@ subNames <- function(grp, df) {
 #' @param tests Tests list/function to use
 #' @param grps List of symbols for grouping factors
 #' @return A nested list of statTables and testColumns
+#' @keywords deprecated internal
 subTable <- function(df, stats, tests, grps) {
   # Final group, compute tests
   if (length(grps) == 1) {
@@ -167,6 +170,7 @@ subTable <- function(df, stats, tests, grps) {
 #' @param ... Additional print parameters
 #' @return A flat dataframe
 #' @export
+#' @keywords deprecated
 print.desctable <- function(x, ...) {
   print(as.data.frame(x))
 }
@@ -178,6 +182,7 @@ print.desctable <- function(x, ...) {
 #' @param ... Additional as.data.frame parameters
 #' @return A flat dataframe
 #' @export
+#' @keywords deprecated
 as.data.frame.desctable <- function(x, ...) {
   # Discard "markdown" formatting of variable names
   x$Variables$Variables <- gsub("\\*\\*(.*?)\\*\\*", "\\1", x$Variables$Variables)
@@ -204,6 +209,7 @@ as.data.frame.desctable <- function(x, ...) {
 #' @inheritParams pander::pandoc.table
 #' @seealso \code{\link{pandoc.table}}
 #' @export
+#' @keywords deprecated
 pander.desctable <- function(x = NULL,
                              digits = 2,
                              justify = "left",
@@ -272,6 +278,7 @@ pander.desctable <- function(x = NULL,
 #' ###
 #' @inheritParams DT::datatable
 #' @export
+#' @keywords deprecated
 datatable <- function(data, ...) {
   UseMethod("datatable", data)
 }
@@ -370,6 +377,7 @@ datatable.desctable <- function(data,
 #'
 #' @param x Object to set the "desctable" class to
 #' @return The object with the class "desctable"
+#' @keywords deprecated internal
 set_desctable_class <- function(x) {
   class(x) <- "desctable"
 
@@ -392,6 +400,7 @@ set_desctable_class <- function(x) {
 #' @param x The variable to test it on
 #' @param f A formula to parse
 #' @return A function to use as a stat/test
+#' @keywords deprecated internal
 parse_formula <- function(x, f) {
   parse_f <- function(x) {
     if (length(x) == 1) as.character(x)
@@ -420,6 +429,7 @@ parse_formula <- function(x, f) {
 #'
 #' @param head A headerList object
 #' @return A names vector
+#' @keywords deprecated internal
 head_pander <- function(head) {
   if (is.integer(head[[1]])) {
     head %>%
@@ -443,6 +453,7 @@ head_pander <- function(head) {
 #'
 #' @param head A headerList object
 #' @return An htmltools$tags object containing the header
+#' @keywords deprecated internal
 head_datatable <- function(head) {
   TRs <- list()
 
@@ -461,6 +472,7 @@ head_datatable <- function(head) {
 #'
 #' @param head A headerList object
 #' @return A names vector
+#' @keywords deprecated internal
 head_dataframe <- function(head) {
   if (is.integer(head[[1]])) {
     head %>%
@@ -488,6 +500,7 @@ head_dataframe <- function(head) {
 #' @param desctable A desctable object
 #' @param output An output format for the header
 #' @return A header object in the output format
+#' @keywords deprecated internal
 header <- function(desctable, output = c("pander", "datatable", "dataframe")) {
   desctable[-1] %>%
     flatten_desctable() %>%
@@ -529,6 +542,7 @@ header <- function(desctable, output = c("pander", "datatable", "dataframe")) {
 #'
 #' @param desctable a desctable
 #' @return a nested list of headers with colspans
+#' @keywords deprecated internal
 headerList <- function(desctable) {
   if (is.data.frame(desctable)) length(desctable)
   else {
@@ -546,6 +560,7 @@ headerList <- function(desctable) {
 #'
 #' @param desctable A desctable object
 #' @return A flat dataframe
+#' @keywords deprecated internal
 flatten_desctable <- function(desctable) {
   if (is.data.frame(desctable)) desctable
   else {

R/output.R

@@ -1,12 +1,26 @@
-##' Output a desctable to the desired target
+##' Output a desctable to the desired target format
+##'
+##' Output a simple or grouped desctable to a different formats.
+##' Currently available formats are\itemize{
+##'   \item data.frame ("df")
+##'   \item pander ("pander")
+##'   \item datatable ("DT")
+##' }
+##'
+##' All numerical values will be rounded to the digits argument.
+##' If statistical tests are presents, p values below 1E-digits will be replaced with "≤ 1E-digits"
+##' (eg. "≤ 0.01" for values below 0.01 when digits = 2)
 ##'
 ##' @title desc_output
 ##' @param desctable The desctable to output
-##' @param target The desired target. One of ~df~, ~pander~, or ~DT~.
-##' @param digits The number of digits to display. The p values will be simplified under 10^-digits
-##' @param ... Other arguments to pass to data.frame, pander::pander, or DT::datatable
+##' @param target The desired target. One of "df", "pander", or "DT".
+##' @param digits The number of digits to display. The p values will be simplified under 1E-digits
+##' @param ... Other arguments to pass to \code{data.frame}, \code{pander::pander}, or \code{DT::datatable}
 ##' @return The output object (or corresponding side effect)
 ##' @export
+##' @seealso \code{\link[DT]{datatable}}
+##' @seealso \code{\link[pander]{pander}}
+##' @family desc_table core functions
 desc_output <- function(desctable, target = c("df", "pander", "DT"), digits = 2, ...) {
   switch(which.desctable(desctable),
          simple = switch(target,

R/stats.R

@@ -13,6 +13,7 @@
 #' @param x A vector
 #' @export
 #' @return The results for the function applied on the vector, compatible with the format of the result table
+#' @keywords internal
 statify <- function(x, f) {
   # Discard NA values
   x <- stats::na.omit(x)

R/tests.R

@@ -7,6 +7,7 @@
 #' @param f The function to try to apply, or a formula combining two functions
 #' @param group Grouping factor
 #' @return The results for the function applied on the vector, compatible with the format of the result table
+#' @keywords internal
 testify <- function(x, f, group) {
   # Extract the name of the function
   f %>%

R/utils.R

@@ -7,6 +7,7 @@
 #' @param y A vector or list of vectors to insert into x
 #' @param position The position / vector of positions to insert vector(s) y in vector x
 #' @return The combined vector
+#' @keywords internal
 insert <- function(x, y, position) {
   # y is supposed to be a list of vectors. If it is a single vector, make it a simple list containing that vector
   if (!is.list(y)) y <- list(y)
@@ -40,6 +41,7 @@ insert <- function(x, y, position) {
 #'
 #' @param desctable A potential desctable to check
 #' @return The type of desctable or FALSE
+#' @keywords internal
 which.desctable <- function(desctable)
 {
   attributes <- list()

man/as.data.frame.desctable.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/output.R
+% Please edit documentation in R/deprecated.R
 \name{as.data.frame.desctable}
 \alias{as.data.frame.desctable}
 \title{As.data.frame method for desctable}
@@ -17,3 +17,4 @@ A flat dataframe
 \description{
 As.data.frame method for desctable
 }
+\keyword{deprecated}

man/datatable.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/output.R
+% Please edit documentation in R/deprecated.R
 \name{datatable}
 \alias{datatable}
 \alias{datatable.default}
@@ -191,3 +191,4 @@ datatable(data.frame(x = Sys.time()))
 \references{
 See \url{https://rstudio.github.io/DT/} for the full documentation.
 }
+\keyword{deprecated}

man/desc_output.Rd

@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/output.R
+\name{desc_output}
+\alias{desc_output}
+\title{desc_output}
+\usage{
+desc_output(desctable, target = c("df", "pander", "DT"), digits = 2, ...)
+}
+\arguments{
+\item{desctable}{The desctable to output}
+
+\item{target}{The desired target. One of "df", "pander", or "DT".}
+
+\item{digits}{The number of digits to display. The p values will be simplified under 1E-digits}
+
+\item{...}{Other arguments to pass to \code{data.frame}, \code{pander::pander}, or \code{DT::datatable}}
+}
+\value{
+The output object (or corresponding side effect)
+}
+\description{
+Output a desctable to the desired target format
+}
+\details{
+Output a simple or grouped desctable to a different formats.
+Currently available formats are\itemize{
+  \item data.frame ("df")
+  \item pander ("pander")
+  \item datatable ("DT")
+}
+
+All numerical values will be rounded to the digits argument.
+If statistical tests are presents, p values below 1E-digits will be replaced with "≤ 1E-digits"
+(eg. "≤ 0.01" for values below 0.01 when digits = 2)
+}
+\seealso{
+\code{\link[DT]{datatable}}
+
+\code{\link[pander]{pander}}
+
+Other desc_table core functions: 
+\code{\link{desc_table}()},
+\code{\link{desc_tests}()}
+}
+\concept{desc_table core functions}

man/desc_table.Rd

@@ -0,0 +1,98 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{desc_table}
+\alias{desc_table}
+\alias{desc_table.default}
+\alias{desc_table.data.frame}
+\alias{desc_table.grouped_df}
+\title{Generate a statistics table}
+\usage{
+desc_table(data, ..., .auto, .labels)
+
+\method{desc_table}{default}(data, ..., .auto, .labels)
+
+\method{desc_table}{data.frame}(data, ..., .labels = NULL, .auto = stats_auto)
+
+\method{desc_table}{grouped_df}(data, ..., .auto = stats_auto, .labels = NULL)
+}
+\arguments{
+\item{data}{The dataframe to analyze}
+
+\item{...}{A list of named statistics to apply to each element of the dataframe, or a function returning a list of named statistics}
+
+\item{.auto}{A function to automatically determine appropriate statistics}
+
+\item{.labels}{A named character vector of variable labels}
+}
+\value{
+A simple or grouped descriptive table
+}
+\description{
+Generate a statistics table with the chosen statistical functions, nested if called with a grouped dataframe.
+}
+\section{Stats}{
+
+The statistical functions to use in the table are passed as additional arguments.
+If the argument is named (eg. \code{N = length}) the name will be used as the column title instead of the function
+name (here, \strong{N} instead of \strong{length}).
+
+Any R function can be a statistical function, as long as it returns only one value when applied to a vector, or as
+many values as there are levels in a factor, plus one.
+
+Users can also use \code{purrr::map}-like formulas as quick anonymous functions (eg. \code{Q1 = ~ quantile(., .25)} to get the first quantile in a
+column named \strong{Q1})
+
+If no statistical function is given to \code{desc_table}, the \code{.auto} argument is used to provide a function
+that automatically determines the most appropriate statistical functions to use based on the contents of the table.
+}
+
+\section{Labels}{
+
+\code{.labels} is a named character vector to provide "pretty" labels to variables.
+
+If given, the variable names for which there is a label will be replaced by their corresponding label.
+
+Not all variables need to have a label, and labels for non-existing variables are ignored.
+
+labels must be given in the form \code{c(unquoted_variable_name = "label")}
+}
+
+\section{Output}{
+
+The output is either a dataframe in the case of a simple descriptive table,
+or nested dataframes in the case of a comparative table.
+}
+
+\examples{
+iris \%>\%
+  desc_table()
+
+# Does the same as stats_auto here
+iris \%>\%
+  desc_table("N"      = length,
+             "Min"    = min,
+             "Q1"     = ~quantile(., .25),
+             "Med"    = median,
+             "Mean"   = mean,
+             "Q3"     = ~quantile(., .75),
+             "Max"    = max,
+             "sd"     = sd,
+             "IQR"    = IQR)
+
+# With grouping on a factor
+iris \%>\%
+  group_by(Species) \%>\%
+  desc_table(.auto = stats_auto)
+}
+\seealso{
+\code{\link{stats_auto}}
+
+\code{\link{IQR}}
+
+\code{\link{percent}}
+
+Other desc_table core functions: 
+\code{\link{desc_output}()},
+\code{\link{desc_tests}()}
+}
+\concept{desc_table core functions}

man/desc_tests.Rd

@@ -0,0 +1,57 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{desc_tests}
+\alias{desc_tests}
+\title{Add tests to a desc_table}
+\usage{
+desc_tests(desctable, .auto = tests_auto, .default = NULL, ...)
+}
+\arguments{
+\item{desctable}{A desc_table}
+
+\item{.auto}{A function to automatically determine the appropriate tests}
+
+\item{.default}{A default fallback test}
+
+\item{...}{A list of statistical tests associated to variable names}
+}
+\value{
+A desc_table with tests
+}
+\description{
+Add test statistics to a grouped desc_table, with the tests specified as \code{variable = test}.
+}
+\section{Tests}{
+
+The statistical test functions to use in the table are passed as additional named arguments. Tests must be preceded
+by a formula tilde (\code{~}).
+\code{name = ~test} will apply test \code{test} to variable \code{name}.
+
+Any R test function can be used, as long as it returns an object containing a \code{p.value} element, which is the
+case for most tests returning an object of class  \code{htest}.
+
+Users can also use \code{purrr::map}-like formulas as quick anonymous functions (eg. \code{~ t.test(., var.equal = T)} to
+compute a t test without the Welch correction.
+}
+
+\examples{
+iris \%>\%
+  group_by(Species) \%>\%
+  desc_table() \%>\%
+  desc_tests(Sepal.Length = ~kruskal.test,
+             Sepal.Width  = ~oneway.test,
+             Petal.Length = ~oneway.test(., var.equal = T),
+             Petal.Length = ~oneway.test(., var.equal = F))
+}
+\seealso{
+\code{\link{tests_auto}}
+
+\code{\link{no.test}}
+
+\code{\link{ANOVA}}
+
+Other desc_table core functions: 
+\code{\link{desc_output}()},
+\code{\link{desc_table}()}
+}
+\concept{desc_table core functions}

man/desctable.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/build.R
+% Please edit documentation in R/deprecated.R
 \name{desctable}
 \alias{desctable}
 \alias{desctable.default}
@@ -108,3 +108,4 @@ iris \%>\%
 
 \code{\link{datatable.desctable}}
 }
+\keyword{deprecated}

man/flatten_desctable.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
+% Please edit documentation in R/deprecated.R
 \name{flatten_desctable}
 \alias{flatten_desctable}
 \title{Flatten a desctable to a dataframe recursively}
@@ -15,3 +15,5 @@ A flat dataframe
 \description{
 Flatten a desctable to a dataframe recursively
 }
+\keyword{deprecated}
+\keyword{internal}

man/head_dataframe.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
+% Please edit documentation in R/deprecated.R
 \name{head_dataframe}
 \alias{head_dataframe}
 \title{Build the header for dataframe}
@@ -15,3 +15,5 @@ A names vector
 \description{
 Build the header for dataframe
 }
+\keyword{deprecated}
+\keyword{internal}

man/head_datatable.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
+% Please edit documentation in R/deprecated.R
 \name{head_datatable}
 \alias{head_datatable}
 \title{Build the header for datatable}
@@ -15,3 +15,5 @@ An htmltools$tags object containing the header
 \description{
 Build the header for datatable
 }
+\keyword{deprecated}
+\keyword{internal}

man/head_pander.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
+% Please edit documentation in R/deprecated.R
 \name{head_pander}
 \alias{head_pander}
 \title{Build the header for pander}
@@ -15,3 +15,5 @@ A names vector
 \description{
 Build the header for pander
 }
+\keyword{deprecated}
+\keyword{internal}

man/header.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
+% Please edit documentation in R/deprecated.R
 \name{header}
 \alias{header}
 \title{Build header}
@@ -18,3 +18,5 @@ A header object in the output format
 Take a desctable object and create a suitable header for the mentionned output.
 Output can be one of "pander", "datatable", or "dataframe".
 }
+\keyword{deprecated}
+\keyword{internal}

man/headerList.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
+% Please edit documentation in R/deprecated.R
 \name{headerList}
 \alias{headerList}
 \title{build a header list object}
@@ -15,3 +15,5 @@ a nested list of headers with colspans
 \description{
 build a header list object
 }
+\keyword{deprecated}
+\keyword{internal}

man/insert.Rd

@@ -20,3 +20,4 @@ The combined vector
 The vectors in the y list will be inserted
 at positions respectively *after* the x[position] element of x
 }
+\keyword{internal}

man/pander.desctable.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/output.R
+% Please edit documentation in R/deprecated.R
 \name{pander.desctable}
 \alias{pander.desctable}
 \title{Pander method for desctable}
@@ -41,3 +41,4 @@ Uses \code{pandoc.table}, with some default parameters (\code{digits = 2}, \code
 \seealso{
 \code{\link{pandoc.table}}
 }
+\keyword{deprecated}

man/parse_formula.Rd

@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/deprecated.R
+\name{parse_formula}
+\alias{parse_formula}
+\title{Parse a formula}
+\usage{
+parse_formula(x, f)
+}
+\arguments{
+\item{x}{The variable to test it on}
+
+\item{f}{A formula to parse}
+}
+\value{
+A function to use as a stat/test
+}
+\description{
+Parse a formula defining the conditions to pick a stat/test
+}
+\details{
+Parse a formula defining the conditions to pick a stat/test
+and return the function to use.
+The formula is to be given in the form of
+conditional ~ T | F
+and conditions can be nested such as
+conditional1 ~ (conditional2 ~ T | F) | F
+The FALSE option can be omitted, and the TRUE can be replaced with NA
+}
+\keyword{deprecated}
+\keyword{internal}

man/print.desctable.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/output.R
+% Please edit documentation in R/deprecated.R
 \name{print.desctable}
 \alias{print.desctable}
 \title{Print method for desctable}
@@ -17,3 +17,4 @@ A flat dataframe
 \description{
 Print method for desctable
 }
+\keyword{deprecated}

man/reexports.Rd

@@ -1,11 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/imports.R
+% Please edit documentation in R/deprecated.R, R/imports.R
 \docType{import}
 \name{reexports}
 \alias{reexports}
+\alias{pander}
 \alias{\%>\%}
 \alias{group_by}
-\alias{pander}
 \title{Objects exported from other packages}
 \keyword{internal}
 \description{

man/set_desctable_class.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
+% Please edit documentation in R/deprecated.R
 \name{set_desctable_class}
 \alias{set_desctable_class}
 \title{Set the "desctable" class to the passed object}
@@ -15,3 +15,5 @@ The object with the class "desctable"
 \description{
 Set the "desctable" class to the passed object
 }
+\keyword{deprecated}
+\keyword{internal}

man/statColumn.Rd

@@ -22,3 +22,4 @@ to produce a single statistics column.
 The result is either a numeric vector, or a character vector if
 the content of the column is not made entirely of numbers.
 }
+\keyword{internal}

man/statTable.Rd

@@ -19,3 +19,4 @@ If stats is a list of functions or purrr::map like formulas, use them.
 If it is a single function, use it with the entire data as
 its argument to produce a list of statistical functions to use.
 }
+\keyword{internal}

man/statify.Rd

@@ -26,3 +26,4 @@ Applying the function on a factor should return nlevels + 1 value, or one value
 
 See \code{parse_formula} for the usage for formulaes.
 }
+\keyword{internal}

man/stats_auto.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stats.R
+\name{stats_auto}
+\alias{stats_auto}
+\title{Function to create a list of statistics to use in desctable}
+\usage{
+stats_auto(data)
+}
+\arguments{
+\item{data}{The dataframe to apply the statistic to}
+}
+\value{
+A list of statistics to use, assessed from the content of the dataframe
+}
+\description{
+This function takes a dataframe as argument and returns a list of statistcs in the form accepted by desctable.
+}
+\details{
+You can define your own automatic function, as long as it takes a dataframe as argument and returns a list of functions, or formulas defining conditions to use a stat function.
+}

man/stats_default.Rd

@@ -1,37 +1,24 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/stats.R
+% Please edit documentation in R/deprecated.R
 \name{stats_default}
 \alias{stats_default}
 \alias{stats_normal}
 \alias{stats_nonnormal}
-\alias{stats_auto}
-\title{Functions to create a list of statistics to use in desctable}
+\title{Define a list of default statistics}
 \usage{
 stats_default(data)
 
 stats_normal(data)
 
 stats_nonnormal(data)
-
-stats_auto(data)
 }
 \arguments{
-\item{data}{The dataframe to apply the statistic to}
+\item{data}{A dataframe}
 }
 \value{
-A list of statistics to use, potentially assessed from the dataframe
+A list of statistical functions
 }
 \description{
-These functions take a dataframe as argument and return a list of statistcs in the form accepted by desctable.
-}
-\details{
-Already defined are
-\enumerate{
-\item stats_default with length, \%, mean, sd, med and IQR
-\item stats_normal with length, \%, mean and sd
-\item stats_nonnormal with length, %, median and IQR
-\item stats_auto, which picks stats depending of the data
-}
-
-You can define your own automatic functions, as long as they take a dataframe as argument and return a list of functions or formulas defining conditions to use a stat function.
+Define a list of default statistics
 }
+\keyword{deprecated}

man/subNames.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/build.R
+% Please edit documentation in R/deprecated.R
 \name{subNames}
 \alias{subNames}
 \title{Create the subtables names}
@@ -18,3 +18,5 @@ A character vector with the names for the subtables
 Create the subtables names, as
 factor: level (n=sub-group length)
 }
+\keyword{deprecated}
+\keyword{internal}

man/subTable.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/build.R
+% Please edit documentation in R/deprecated.R
 \name{subTable}
 \alias{subTable}
 \title{Create a subtable in a grouped desctable}
@@ -21,3 +21,5 @@ A nested list of statTables and testColumns
 \description{
 Create a subtable in a grouped desctable
 }
+\keyword{deprecated}
+\keyword{internal}

man/testColumn.Rd

@@ -19,3 +19,4 @@ A numeric vector of pvalues
 \description{
 Create the pvalues column
 }
+\keyword{internal}

man/testify.Rd

@@ -21,3 +21,4 @@ Transform a function into a valid test function for the table
 Applying the function on a numerical vector should return one value
 Applying the function on a factor should return nlevels + 1 value, or one value per factor level
 }
+\keyword{internal}

man/tests_auto.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/tests.R
 \name{tests_auto}
 \alias{tests_auto}
-\title{Functions to choose a statistical test}
+\title{Function to choose a statistical test}
 \usage{
 tests_auto(var, grp)
 }
@@ -15,8 +15,9 @@ tests_auto(var, grp)
 A statistical test function
 }
 \description{
-These functions take a variable and a grouping variable as arguments, and return a statistcal test to use, expressed as a single-term formula.
+This function takes a variable and a grouping variable as arguments, and returns a statistcal test to use, expressed as a single-term formula.
 }
 \details{
-Currently, only \code{tests_auto} is defined, and picks between t test, wilcoxon, anova, kruskal-wallis and fisher depending on the number of groups, the type of the variable, the normality and homoskedasticity of the distributions.
+This function uses appropriate non-parametric tests depending on the number of levels (wilcoxon.test for two levels
+and kruskal.test for more), and fisher.test with fallback on chisq.test on error for factors.
 }

man/varColumn.Rd

@@ -23,3 +23,4 @@ labels is an option named character vector used to make the table prettier.
 If given, the variable names for which there is a label will be replaced by their corresponding label.
 Not all variables need to have a label, and labels for non-existing variables are ignored.
 }
+\keyword{internal}

man/which.desctable.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{which.desctable}
+\alias{which.desctable}
+\title{Is the object possibly a desctable?}
+\usage{
+which.desctable(desctable)
+}
+\arguments{
+\item{desctable}{A potential desctable to check}
+}
+\value{
+The type of desctable or FALSE
+}
+\description{
+Check if the object is produced by desc_table.
+Return a string:
+- simple
+- grouped
+or FALSE if not a desctable
+}
+\keyword{internal}