Documentation

DESCRIPTION

@@ -3,8 +3,8 @@ Title: Produce Descriptive and Comparative Tables Easily
 Version: 0.0.0.9000
 Authors@R: person("Maxime", "Wack", email = "maximewack@free.fr", role = c("aut", "cre"))
 Description: This package provides functions to easily create descriptive and
-    comparative tables. It makes use and integrates directly with the dplyr family
-    of packages and pipes. Tables are produced as data frames/lists of data frames
+    comparative tables. It makes use and integrates directly with the tidyverse family
+    of packages, and pipes. Tables are produced as data frames/lists of data frames
     for easy manipulation after creation, and ready to be saved as csv, piped to
     datatable or pander to integrate into reports.
 Depends:
@@ -16,8 +16,8 @@ Imports:
     dplyr,
     purrr,
     stringr,
-    tibble
-Suggests:
+    tibble,
     DT,
     pander
+Suggests:
 RoxygenNote: 6.0.1

NAMESPACE

@@ -2,15 +2,20 @@
 
 S3method(print,desctable)
 export("%>%")
+export(ANOVA)
 export(IQR)
 export(Q1)
 export(Q3)
 export(Range)
+export(chisq.test)
+export(datatable)
 export(desctable)
 export(desctable.default)
 export(desctable.grouped_df)
+export(fisher.test)
 export(group_by)
 export(list_normal)
+export(pander.desctable)
 export(parse_formula)
 export(percent)
 export(petrify)

R/arg_functions.R

@@ -1,5 +1,15 @@
 #' Functions to create a list of statistics to use in desctable
 #'
+#' These functions take a dataframe as argument and return a list of statistcs in the form accepted by desctable.
+#'
+#' Already defined are
+#' - stats_default with length, mean/%, sd, med and IQR
+#' - stats_normal with length, mean/% and sd
+#' - stats_nonnormal with length, median/% and IQR
+#' - 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.
+#'
 #' @param data The dataframe to apply the statistic to
 #' @return A list of statistics to use, potentially assessed from the dataframe
 #' @export
@@ -70,8 +80,13 @@ stats_auto <- function(data)
 
 #' Functions to choose a statistical test
 #'
+#' These functions take a variable and a grouping variable as arguments, and return a statistcal test to use.
+#'
+#' Currently, only 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.
+#'
 #' @param var The variable to test
 #' @param grp The variable for the groups
+#' @return A statistical test function
 #' @export
 tests_auto <- function(var, grp)
 {

R/build.R

@@ -29,8 +29,7 @@ statTable <- function(data, stats)
 #' Generate the variable column to display as row names
 #'
 #' Generates the variable column.
-#' Replaces the variable names by their label if given in the named character vector labels
-#' Inserts levels for factors
+#' Replaces the variable names by their label if given in the named character vector labels, and inserts levels for factors.
 #'
 #' 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.
@@ -69,20 +68,45 @@ varColumn <- function(data, labels = NULL)
 #' 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.
+#' labels must be given in the form c(unquoted_variable_name = "label")
 #'
-#' If data is a grouped dataframe (using group_by), subtables are created and statistic tests are perfored over each sub-group.
+#' The stats can be a function which takes a dataframe and returns a list of statistical functions to use.
+#' stats can also be a named list of statistical functions, or formulas. 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. If an element of the list is a formula, it can be used to conditionally use stats depending on the variable. The general form is `condition ~ T | F`, and can be nested, such as `is.factor ~ percent | (is.normal ~ mean | median)`, for example.
 #'
-#' For a simple descriptive table (without groups), the resulting dataframe is directly pipe-able to pander or DT, or can be exported like any dataframe to csv, etc.
-#' For a grouped table, the output is list of dataframes that can be manipulated, prior to passing to the petrify() function which will make it pipe-able to pander or DT.
-#' labels must be given in the form c(unquoted_variable_name = "label")
+#' The tests can be a function which takes a variable and a grouping variable, and returns an appropriate statistical test to use in that case.
+#' tests can also be a named list of statistical test functions, associating the name of a variable in the data, and a test to use specifically for that variable. You don't have to specify tests for all the variables: a default test for all other variables can be defined with the name .default, and an automatic test can be defined with the name .auto.
+#'
+#' If data is a grouped dataframe (using group_by), subtables are created and statistic tests are performed over each sub-group.
+#'
+#' The output is a desctable object, which is a list of named dataframes that can be further manipulated. Methods for printing, using in pander and DT::datatable are present. Printing reduces the object to a dataframe.
 #'
-#' @param data The dataframe to analyse
+#' @param data The dataframe to analyze
 #' @param stats A list of named statistics to apply to each element of the dataframe, or a function returning a list of named statistics
-#' @param tests A list of statistcal tests to use when calling desctable with a grouped_df
+#' @param tests A list of statistical tests to use when calling desctable with a grouped_df
 #' @param labels A named character vector of labels to use instead of variable names
-#' @return A table of statistics for all variables
-#' @seealso \code{\link{petrify}}
+#' @return A desctable object, which prints to a table of statistics for all variables
+#' @seealso \code{\link{stats_auto}}
+#' @seealso \code{\link{tests_auto}}
+#' @seealso \code{\link{print.desctable}}
+#' @seealso \code{\link{pander.desctable}}
+#' @seealso \code{\link{datatable.desctable}}
 #' @export
+#' @examples
+#' iris %>% desctable
+#'
+#' mtcars %>% desctable(labels = c(hp = "Horse Power"))
+#'
+#' iris %>%
+#'   group_by(Species) %>%
+#'   desctable
+#'
+#' mtcars %>%
+#'   group_by(vs, cyl) %>%
+#'   desctable
+#'
+#' iris %>%
+#'   group_by(Petal.Length > 5) %>%
+#'   desctable(tests = list(.auto = tests_auto, Species = chisq.test))
 desctable <- function(data, stats = stats_auto, tests = tests_auto, labels = NULL)
 {
   # Replace every logical vector with a factor and nice labels
@@ -116,6 +140,14 @@ desctable.grouped_df <- function(data, stats, tests, labels)
   `class<-`("desctable")
 }
 
+#' Create the subtables names
+#'
+#' Create the subtables names, as
+#' factor: level (n=sub-group length)
+#'
+#' @param grp Grouping factor
+#' @param df Dataframe containing the grouping factor
+#' @return A character vector with the names for the subtables
 subNames <- function(grp, df)
 {
   paste0(as.character(grp),
@@ -126,6 +158,12 @@ subNames <- function(grp, df)
          ")")
 }
 
+#' Create the pvalues column
+#'
+#' @param df Dataframe to use for the tests
+#' @param tests Test function or list of functions
+#' @param grp Grouping factor
+#' @return A numeric vector of pvalues
 testColumn <- function(df, tests, grp)
 {
   group <- eval(grp, df)
@@ -160,6 +198,13 @@ testColumn <- function(df, tests, grp)
     purrr::map2(ftests, testify, group) %>% purrr::flatten_dbl()
 }
 
+#' Create a subtable in a grouped desctable
+#'
+#' @param df Dataframe to use
+#' @param stats Stats list/function to use
+#' @param tests Tests list/function to use
+#' @param grps List of symbols for grouping factors
+#' @return A nested list of statTables and testColumns
 subTable <- function(df, stats, tests, grps)
 {
   # Final group, make tests
@@ -183,7 +228,7 @@ subTable <- function(df, stats, tests, grps)
   {
     group <- eval(grps[[1]], df)
 
-    # Recursively go through the grouping levels and build the subtables
+    # Go through the next grouping levels and build the subtables
     df %>%
       dplyr::select(- eval(grps[[1]])) %>%
       by(group, subTable, stats, tests, grps[-1]) %>%
@@ -215,6 +260,11 @@ petrify <- function(data, digits = 2, ...)
   data %>% lapply(prettyNum, digits = digits, ...) %>% lapply(base::gsub, pattern = "^NA$", replacement = "") %>% data.frame(check.names = F)
 }
 
+#' Print method for desctable
+#'
+#' @param x A desctable
+#' @param ... Additional print parameters
+#' @return A flat dataframe
 #' @export
 print.desctable <- function(x, ...)
 {

R/tests.R

@@ -1,3 +1,12 @@
+#' Transform any test function into a valid test function for the table
+#'
+#' 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
+#' @param x A vector
+#' @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
 testify <- function(x, f, group)
 {
   p <- tryCatch(f(x ~ group)$p.value[1],
@@ -8,30 +17,43 @@ testify <- function(x, f, group)
     p
 }
 
-fisher.test.default <- stats::fisher.test
-
-fisher.test <- function(...)
+#' Fisher test
+#'
+#' @inheritParams stats::fisher.test
+#' @seealso stats::fisher.test
+#' @export
+fisher.test <- function(x, y = NULL, workspace = 200000, hybrid = FALSE, control = list(), or = 1, alternative = "two.sided", conf.int = TRUE, conf.level = 0.95, simulate.p.value = FALSE, B = 2000)
 {
   UseMethod("fisher.test")
 }
 
-fisher.test.formula <- function(formula, ...)
+fisher.test.default <- stats::fisher.test
+
+fisher.test.formula <- function(x, ...)
 {
-  fisher.test.default(x = eval(formula[[2]], envir = parent.frame()), y = eval(formula[[3]], envir = parent.frame()), ...)
+  fisher.test.default(x = eval(x[[2]], envir = parent.frame()), y = eval(x[[3]], envir = parent.frame()), ...)
 }
 
-chisq.test.default <- stats::chisq.test
-
-chisq.test <- function(...)
+#' Chi-square test
+#'
+#' @inheritParams stats::chisq.test
+#' @export
+chisq.test <- function(x, y = NULL, correct = TRUE, p = rep(1/length(x), length(x)), rescale.p = FALSE, simulate.p.value = FALSE, B = 2000)
 {
   UseMethod("chisq.test")
 }
 
-chisq.test.formula <- function(formula, ...)
+chisq.test.default <- stats::chisq.test
+
+chisq.test.formula <- function(x, y = NULL, correct = TRUE, p = rep(1/length(x), length(x)), rescale.p = FALSE, simulate.p.value = FALSE, B = 2000, ...)
 {
-  chisq.test.default(x = eval(formula[[2]], envir = parent.frame()), y = eval(formula[[3]], envir = parent.frame()), ...)
+  chisq.test.default(x = eval(x[[2]], envir = parent.frame()), y = eval(x[[3]], envir = parent.frame()), ...)
 }
 
+#' Wrapper for summary(aov)
+#'
+#' @param formula An anova formula (variable ~ grouping variable)
+#' @export
 ANOVA <- function(formula)
 {
   summary(stats::aov(formula))[[1]] %>%

man/ANOVA.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tests.R
+\name{ANOVA}
+\alias{ANOVA}
+\title{Wrapper for summary(aov)}
+\usage{
+ANOVA(formula)
+}
+\arguments{
+\item{formula}{An anova formula (variable ~ grouping variable)}
+}
+\description{
+Wrapper for summary(aov)
+}

man/chisq.test.Rd

@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tests.R
+\name{chisq.test}
+\alias{chisq.test}
+\title{Chi-square test}
+\usage{
+chisq.test(x, y = NULL, correct = TRUE, p = rep(1/length(x), length(x)),
+  rescale.p = FALSE, simulate.p.value = FALSE, B = 2000)
+}
+\arguments{
+\item{x}{a numeric vector or matrix. \code{x} and \code{y} can also
+    both be factors.}
+
+\item{y}{a numeric vector; ignored if \code{x} is a matrix.  If
+    \code{x} is a factor, \code{y} should be a factor of the same length.}
+
+\item{correct}{a logical indicating whether to apply continuity
+    correction when computing the test statistic for 2 by 2 tables: one
+    half is subtracted from all \eqn{|O - E|} differences; however, the
+    correction will not be bigger than the differences themselves.  No correction
+    is done if \code{simulate.p.value = TRUE}.}
+
+\item{p}{a vector of probabilities of the same length of \code{x}.
+    An error is given if any entry of \code{p} is negative.}
+
+\item{rescale.p}{a logical scalar; if TRUE then \code{p} is rescaled
+    (if necessary) to sum to 1.  If \code{rescale.p} is FALSE, and
+    \code{p} does not sum to 1, an error is given.}
+
+\item{simulate.p.value}{a logical indicating whether to compute
+    p-values by Monte Carlo simulation.}
+
+\item{B}{an integer specifying the number of replicates used in the
+    Monte Carlo test.}
+}
+\description{
+Chi-square test
+}

man/datatable.Rd

@@ -0,0 +1,104 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{datatable}
+\alias{datatable}
+\title{Datatable}
+\usage{
+datatable(data, options = list(), class = "display",
+  callback = JS("return table;"), rownames, colnames, container,
+  caption = NULL, filter = c("none", "bottom", "top"), escape = TRUE,
+  style = "default", width = NULL, height = NULL, elementId = NULL,
+  fillContainer = getOption("DT.fillContainer", NULL),
+  autoHideNavigation = getOption("DT.autoHideNavigation", NULL),
+  selection = c("multiple", "single", "none"), extensions = list(),
+  plugins = NULL)
+}
+\arguments{
+\item{data}{a data object (either a matrix or a data frame)}
+
+\item{options}{a list of initialization options (see
+\url{http://datatables.net/reference/option/}); the character options
+wrapped in \code{\link[htmlwidgets]{JS}()} will be treated as literal
+JavaScript code instead of normal character strings; you can also set
+options globally via \code{\link{options}(DT.options = list(...))}, and
+global options will be merged into this \code{options} argument if set}
+
+\item{class}{the CSS class(es) of the table; see
+\url{http://datatables.net/manual/styling/classes}}
+
+\item{callback}{the body of a JavaScript callback function with the argument
+\code{table} to be applied to the DataTables instance (i.e. \code{table})}
+
+\item{rownames}{\code{TRUE} (show row names) or \code{FALSE} (hide row names)
+or a character vector of row names; by default, the row names are displayed
+in the first column of the table if exist (not \code{NULL})}
+
+\item{colnames}{if missing, the column names of the data; otherwise it can be
+an unnamed character vector of names you want to show in the table header
+instead of the default data column names; alternatively, you can provide a
+\emph{named} numeric or character vector of the form \code{'newName1' = i1,
+'newName2' = i2} or \code{c('newName1' = 'oldName1', 'newName2' =
+'oldName2', ...)}, where \code{newName} is the new name you want to show in
+the table, and \code{i} or \code{oldName} is the index of the current
+column name}
+
+\item{container}{a sketch of the HTML table to be filled with data cells; by
+default, it is generated from \code{htmltools::tags$table()} with a table
+header consisting of the column names of the data}
+
+\item{caption}{the table caption; a character vector or a tag object
+generated from \code{htmltools::tags$caption()}}
+
+\item{filter}{whether/where to use column filters; \code{none}: no filters;
+\code{bottom/top}: put column filters at the bottom/top of the table; range
+sliders are used to filter numeric/date/time columns, select lists are used
+for factor columns, and text input boxes are used for character columns; if
+you want more control over the styles of filters, you can provide a list to
+this argument of the form \code{list(position = 'top', clear = TRUE, plain
+= FALSE)}, where \code{clear} indicates whether you want the clear buttons
+in the input boxes, and \code{plain} means if you want to use Bootstrap
+form styles or plain text input styles for the text input boxes}
+
+\item{escape}{whether to escape HTML entities in the table: \code{TRUE} means
+to escape the whole table, and \code{FALSE} means not to escape it;
+alternatively, you can specify numeric column indices or column names to
+indicate which columns to escape, e.g. \code{1:5} (the first 5 columns),
+\code{c(1, 3, 4)}, or \code{c(-1, -3)} (all columns except the first and
+third), or \code{c('Species', 'Sepal.Length')}}
+
+\item{style}{the style name (\url{http://datatables.net/manual/styling/});
+currently only \code{'default'} and \code{'bootstrap'} are supported}
+
+\item{width}{Width/Height in pixels (optional, defaults to automatic
+sizing)}
+
+\item{height}{Width/Height in pixels (optional, defaults to automatic
+sizing)}
+
+\item{elementId}{An id for the widget (a random string by default).}
+
+\item{fillContainer}{\code{TRUE} to configure the table to automatically fill
+it's containing element. If the table can't fit fully into it's container
+then vertical and/or horizontal scrolling of the table cells will occur.}
+
+\item{autoHideNavigation}{\code{TRUE} to automatically hide navigational UI
+when the number of total records is less than the page size.}
+
+\item{selection}{the row/column selection mode (single or multiple selection
+or disable selection) when a table widget is rendered in a Shiny app;
+alternatively, you can use a list of the form \code{list(mode = 'multiple',
+selected = c(1, 3, 8), target = 'row')} to pre-select rows; the element
+\code{target} in the list can be \code{'column'} to enable column
+selection, or \code{'row+column'} to make it possible to select both rows
+and columns (click on the footer to select columns), or \code{'cell'} to
+select cells}
+
+\item{extensions}{a character vector of the names of the DataTables
+extensions (\url{http://datatables.net/extensions/index})}
+
+\item{plugins}{a character vector of the names of DataTables plug-ins
+(\url{http://rstudio.github.io/DT/plugins.html})}
+}
+\description{
+Datatable
+}

man/datatable.desctable.Rd

@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{datatable.desctable}
+\alias{datatable.desctable}
+\title{datatable method for desctable}
+\usage{
+\method{datatable}{desctable}(data = NULL, ...)
+}
+\arguments{
+\item{data}{A desctable}
+
+\item{...}{Additional datatable parameters}
+}
+\description{
+datatable method for desctable
+}

man/desctable.Rd

@@ -13,16 +13,16 @@ desctable.default(data, stats, tests, labels)
 desctable.grouped_df(data, stats, tests, labels)
 }
 \arguments{
-\item{data}{The dataframe to analyse}
+\item{data}{The dataframe to analyze}
 
 \item{stats}{A list of named statistics to apply to each element of the dataframe, or a function returning a list of named statistics}
 
-\item{tests}{A list of statistcal tests to use when calling desctable with a grouped_df}
+\item{tests}{A list of statistical tests to use when calling desctable with a grouped_df}
 
 \item{labels}{A named character vector of labels to use instead of variable names}
 }
 \value{
-A table of statistics for all variables
+A desctable object, which prints to a table of statistics for all variables
 }
 \description{
 Generate a statistics table with variable names/labels and levels
@@ -31,13 +31,43 @@ Generate a statistics table with variable names/labels and levels
 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.
+labels must be given in the form c(unquoted_variable_name = "label")
 
-If data is a grouped dataframe (using group_by), subtables are created and statistic tests are perfored over each sub-group.
+The stats can be a function which takes a dataframe and returns a list of statistical functions to use.
+stats can also be a named list of statistical functions, or formulas. 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. If an element of the list is a formula, it can be used to conditionally use stats depending on the variable. The general form is `condition ~ T | F`, and can be nested, such as `is.factor ~ percent | (is.normal ~ mean | median)`, for example.
 
-For a simple descriptive table (without groups), the resulting dataframe is directly pipe-able to pander or DT, or can be exported like any dataframe to csv, etc.
-For a grouped table, the output is list of dataframes that can be manipulated, prior to passing to the petrify() function which will make it pipe-able to pander or DT.
-labels must be given in the form c(unquoted_variable_name = "label")
+The tests can be a function which takes a variable and a grouping variable, and returns an appropriate statistical test to use in that case.
+tests can also be a named list of statistical test functions, associating the name of a variable in the data, and a test to use specifically for that variable. You don't have to specify tests for all the variables: a default test for all other variables can be defined with the name .default, and an automatic test can be defined with the name .auto.
+
+If data is a grouped dataframe (using group_by), subtables are created and statistic tests are performed over each sub-group.
+
+The output is a desctable object, which is a list of named dataframes that can be further manipulated. Methods for printing, using in pander and DT::datatable are present. Printing reduces the object to a dataframe.
+}
+\examples{
+iris \%>\% desctable
+
+mtcars \%>\% desctable(labels = c(hp = "Horse Power"))
+
+iris \%>\%
+  group_by(Species) \%>\%
+  desctable
+
+mtcars \%>\%
+  group_by(vs, cyl) \%>\%
+  desctable
+
+iris \%>\%
+  group_by(Petal.Length > 5) \%>\%
+  desctable(tests = list(.auto = tests_auto, Species = chisq.test))
 }
 \seealso{
-\code{\link{petrify}}
+\code{\link{stats_auto}}
+
+\code{\link{tests_auto}}
+
+\code{\link{print.desctable}}
+
+\code{\link{pander.desctable}}
+
+\code{\link{datatable.desctable}}
 }

man/fisher.test.Rd

@@ -0,0 +1,61 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tests.R
+\name{fisher.test}
+\alias{fisher.test}
+\title{Fisher test}
+\usage{
+fisher.test(x, y = NULL, workspace = 2e+05, hybrid = FALSE,
+  control = list(), or = 1, alternative = "two.sided", conf.int = TRUE,
+  conf.level = 0.95, simulate.p.value = FALSE, B = 2000)
+}
+\arguments{
+\item{x}{either a two-dimensional contingency table in matrix form,
+    or a factor object.}
+
+\item{y}{a factor object; ignored if \code{x} is a matrix.}
+
+\item{workspace}{an integer specifying the size of the workspace
+    used in the network algorithm.  In units of 4 bytes.  Only used for
+    non-simulated p-values larger than \eqn{2 \times 2}{2 by 2} tables.}
+
+\item{hybrid}{a logical. Only used for larger than \eqn{2 \times 2}{2 by 2}
+    tables, in which cases it indicates whether the exact probabilities
+    (default) or a hybrid approximation thereof should be computed.
+    See \sQuote{Details}.}
+
+\item{control}{a list with named components for low level algorithm
+    control.  At present the only one used is \code{"mult"}, a positive
+    integer \eqn{\ge 2} with default 30 used only for larger than
+    \eqn{2 \times 2}{2 by 2} tables.  This says how many times as much
+    space should be allocated to paths as to keys: see file
+    \file{fexact.c} in the sources of this package.}
+
+\item{or}{the hypothesized odds ratio.  Only used in the
+    \eqn{2 \times 2}{2 by 2} case.}
+
+\item{alternative}{indicates the alternative hypothesis and must be
+    one of \code{"two.sided"}, \code{"greater"} or \code{"less"}.
+    You can specify just the initial letter.  Only used in the
+    \eqn{2 \times 2}{2 by 2} case.}
+
+\item{conf.int}{logical indicating if a confidence interval for the
+    odds ratio in a \eqn{2 \times 2}{2 by 2} table should be
+    computed (and returned).}
+
+\item{conf.level}{confidence level for the returned confidence
+    interval.  Only used in the \eqn{2 \times 2}{2 by 2} case and if
+    \code{conf.int = TRUE}.}
+
+\item{simulate.p.value}{a logical indicating whether to compute
+    p-values by Monte Carlo simulation, in larger than \eqn{2 \times
+      2}{2 by 2} tables.}
+
+\item{B}{an integer specifying the number of replicates used in the
+    Monte Carlo test.}
+}
+\description{
+Fisher test
+}
+\seealso{
+stats::fisher.test
+}

man/pander.desctable.Rd

@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{pander.desctable}
+\alias{pander.desctable}
+\title{Pander method for desctable}
+\usage{
+pander.desctable(x = NULL, ...)
+}
+\arguments{
+\item{x}{A desctable}
+
+\item{...}{Additional pander parameters}
+}
+\description{
+Pander method for desctable
+}

man/print.desctable.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{print.desctable}
+\alias{print.desctable}
+\title{Print method for desctable}
+\usage{
+\method{print}{desctable}(x, ...)
+}
+\arguments{
+\item{x}{A desctable}
+
+\item{...}{Additional print parameters}
+}
+\value{
+A flat dataframe
+}
+\description{
+Print method for desctable
+}

man/stats_default.Rd

@@ -22,5 +22,14 @@ stats_auto(data)
 A list of statistics to use, potentially assessed from the dataframe
 }
 \description{
-Functions to create a list of statistics to use in desctable
+These functions take a dataframe as argument and return a list of statistcs in the form accepted by desctable.
+}
+\details{
+Already defined are
+- stats_default with length, mean/%, sd, med and IQR
+- stats_normal with length, mean/% and sd
+- stats_nonnormal with length, median/% and IQR
+- 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.
 }

man/subNames.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{subNames}
+\alias{subNames}
+\title{Create the subtables names}
+\usage{
+subNames(grp, df)
+}
+\arguments{
+\item{grp}{Grouping factor}
+
+\item{df}{Dataframe containing the grouping factor}
+}
+\value{
+A character vector with the names for the subtables
+}
+\description{
+Create the subtables names, as
+factor: level (n=sub-group length)
+}

man/subTable.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{subTable}
+\alias{subTable}
+\title{Create a subtable in a grouped desctable}
+\usage{
+subTable(df, stats, tests, grps)
+}
+\arguments{
+\item{df}{Dataframe to use}
+
+\item{stats}{Stats list/function to use}
+
+\item{tests}{Tests list/function to use}
+
+\item{grps}{List of symbols for grouping factors}
+}
+\value{
+A nested list of statTables and testColumns
+}
+\description{
+Create a subtable in a grouped desctable
+}

man/testColumn.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{testColumn}
+\alias{testColumn}
+\title{Create the pvalues column}
+\usage{
+testColumn(df, tests, grp)
+}
+\arguments{
+\item{df}{Dataframe to use for the tests}
+
+\item{tests}{Test function or list of functions}
+
+\item{grp}{Grouping factor}
+}
+\value{
+A numeric vector of pvalues
+}
+\description{
+Create the pvalues column
+}

man/testify.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tests.R
+\name{testify}
+\alias{testify}
+\title{Transform any test function into a valid test function for the table}
+\usage{
+testify(x, f, group)
+}
+\arguments{
+\item{x}{A vector}
+
+\item{f}{The function to try to apply, or a formula combining two functions}
+
+\item{group}{Grouping factor}
+}
+\value{
+The results for the function applied on the vector, compatible with the format of the result table
+}
+\description{
+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
+}

man/tests_auto.Rd

@@ -11,6 +11,12 @@ tests_auto(var, grp)
 
 \item{grp}{The variable for the groups}
 }
+\value{
+A statistical test function
+}
 \description{
-Functions to choose a statistical test
+These functions take a variable and a grouping variable as arguments, and return a statistcal test to use.
+}
+\details{
+Currently, only 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.
 }

man/varColumn.Rd

@@ -16,8 +16,7 @@ A dataframe with one variable named "Variables", a character vector of variable
 }
 \description{
 Generates the variable column.
-Replaces the variable names by their label if given in the named character vector labels
-Inserts levels for factors
+Replaces the variable names by their label if given in the named character vector labels, and inserts levels for factors.
 }
 \details{
 labels is an option named character vector used to make the table prettier.