Merge remote-tracking branch 'origin/fix' into dev

DESCRIPTION

@@ -1,7 +1,8 @@
 Package: desctable
 Title: Produce Descriptive and Comparative Tables Easily
 Version: 0.1.7
-Authors@R: person("Maxime", "Wack", email = "maximewack@free.fr", role = c("aut", "cre"))
+Authors@R: c(person("Maxime", "Wack", email = "maximewack@free.fr", role = c("aut", "cre")),
+             person("Adrien", "Boukobza", email = "hadrien_b@hotmail.fr", role = c("aut")))
 Description: Easily create descriptive and 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,
@@ -23,5 +24,5 @@ Suggests:
     rmarkdown,
     purrr,
     survival
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 VignetteBuilder: knitr

R/build.R

@@ -137,7 +137,7 @@ varColumn <- function(data, labels = NULL) {
 #' @export
 #' @examples
 #' iris %>%
-#'   desctable
+#'   desctable()
 #'
 #' # Does the same as stats_auto here
 #' iris %>%

man/chisq.test.Rd

@@ -11,13 +11,25 @@ The code for Monte Carlo simulation is a C translation of the Fortran algorithm
 \usage{
 chisq.test(x, y, correct, p, rescale.p, simulate.p.value, B)
 
-\method{chisq.test}{default}(x, y = NULL, correct = TRUE,
-  p = rep(1/length(x), length(x)), rescale.p = FALSE,
-  simulate.p.value = FALSE, B = 2000)
+\method{chisq.test}{default}(
+  x,
+  y = NULL,
+  correct = TRUE,
+  p = rep(1/length(x), length(x)),
+  rescale.p = FALSE,
+  simulate.p.value = FALSE,
+  B = 2000
+)
 
-\method{chisq.test}{formula}(x, y = NULL, correct = T,
-  p = rep(1/length(x), length(x)), rescale.p = F,
-  simulate.p.value = F, B = 2000)
+\method{chisq.test}{formula}(
+  x,
+  y = NULL,
+  correct = T,
+  p = rep(1/length(x), length(x)),
+  rescale.p = F,
+  simulate.p.value = F,
+  B = 2000
+)
 }
 \arguments{
 \item{x}{a numeric vector, or matrix, or formula of the form \code{lhs ~ rhs} where \code{lhs} and \code{rhs} are factors. \code{x} and \code{y} can also both be factors.}

man/datatable.Rd

@@ -8,26 +8,48 @@
 \usage{
 datatable(data, ...)
 
-\method{datatable}{default}(data, options = list(), class = "display",
-  callback = DT::JS("return table;"), caption = NULL,
-  filter = c("none", "bottom", "top"), escape = TRUE,
-  style = "default", width = NULL, height = NULL, elementId = NULL,
+\method{datatable}{default}(
+  data,
+  options = list(),
+  class = "display",
+  callback = DT::JS("return table;"),
+  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, ...)
-
-\method{datatable}{desctable}(data, options = list(paging = F, info = F,
-  search = F, dom = "Brtip", fixedColumns = T, fixedHeader = T, buttons =
-  c("copy", "excel")), class = "display",
-  callback = DT::JS("return table;"), caption = NULL,
-  filter = c("none", "bottom", "top"), escape = FALSE,
-  style = "default", width = NULL, height = NULL, elementId = NULL,
+  selection = c("multiple", "single", "none"),
+  extensions = list(),
+  plugins = NULL,
+  ...
+)
+
+\method{datatable}{desctable}(
+  data,
+  options = list(paging = F, info = F, search = F, dom = "Brtip", fixedColumns = T,
+    fixedHeader = T, buttons = c("copy", "excel")),
+  class = "display",
+  callback = DT::JS("return table;"),
+  caption = NULL,
+  filter = c("none", "bottom", "top"),
+  escape = FALSE,
+  style = "default",
+  width = NULL,
+  height = NULL,
+  elementId = NULL,
   fillContainer = getOption("DT.fillContainer", NULL),
   autoHideNavigation = getOption("DT.autoHideNavigation", NULL),
   selection = c("multiple", "single", "none"),
   extensions = c("FixedHeader", "FixedColumns", "Buttons"),
-  plugins = NULL, rownames = F, digits = 2, ...)
+  plugins = NULL,
+  rownames = F,
+  digits = 2,
+  ...
+)
 }
 \arguments{
 \item{data}{a data object (either a matrix or a data frame)}
@@ -65,10 +87,15 @@ 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')}}
+third), or \code{c('Species', 'Sepal.Length')}; since the row names take
+the first column to display, you should add the numeric column indices
+by one when using \code{rownames}}
 
 \item{style}{the style name (\url{http://datatables.net/manual/styling/});
-currently only \code{'default'} and \code{'bootstrap'} are supported}
+currently only \code{'default'}, \code{'bootstrap'}, and
+\code{'bootstrap4'} are supported. Note that DT doesn't contain the theme
+files so in order to display the style correctly, you have to link
+the necessary files in the header.}
 
 \item{width}{Width/Height in pixels (optional, defaults to automatic
 sizing)}
@@ -99,7 +126,8 @@ extensions (\url{https://datatables.net/extensions/index})}
 
 \item{plugins}{a character vector of the names of DataTables plug-ins
 (\url{https://rstudio.github.io/DT/plugins.html}).  Note that only those
-plugins supported by the \code{DT} package can be used here.}
+plugins supported by the \code{DT} package can be used here. You can see
+the available plugins by calling \code{DT:::available_plugins()}}
 
 \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

man/desctable.Rd

@@ -8,11 +8,9 @@
 \usage{
 desctable(data, stats, tests, labels)
 
-\method{desctable}{default}(data, stats = stats_auto, tests,
-  labels = NULL)
+\method{desctable}{default}(data, stats = stats_auto, tests, labels = NULL)
 
-\method{desctable}{grouped_df}(data, stats = stats_auto,
-  tests = tests_auto, labels = NULL)
+\method{desctable}{grouped_df}(data, stats = stats_auto, tests = tests_auto, labels = NULL)
 }
 \arguments{
 \item{data}{The dataframe to analyze}

man/fisher.test.Rd

@@ -6,14 +6,35 @@
 \alias{fisher.test.formula}
 \title{Fisher's Exact Test for Count Data}
 \usage{
-fisher.test(x, y, workspace, hybrid, control, or, alternative, conf.int,
-  conf.level, simulate.p.value, B)
+fisher.test(
+  x,
+  y,
+  workspace,
+  hybrid,
+  control,
+  or,
+  alternative,
+  conf.int,
+  conf.level,
+  simulate.p.value,
+  B
+)
 
 \method{fisher.test}{default}(x, ...)
 
-\method{fisher.test}{formula}(x, y = NULL, workspace = 200000,
-  hybrid = F, control = list(), or = 1, alternative = "two.sided",
-  conf.int = T, conf.level = 0.95, simulate.p.value = F, B = 2000)
+\method{fisher.test}{formula}(
+  x,
+  y = NULL,
+  workspace = 200000,
+  hybrid = F,
+  control = list(),
+  or = 1,
+  alternative = "two.sided",
+  conf.int = T,
+  conf.level = 0.95,
+  simulate.p.value = F,
+  B = 2000
+)
 }
 \arguments{
 \item{x}{either a two-dimensional contingency table in matrix form, a factor object, or a formula of the form \code{lhs ~ rhs} where \code{lhs} and \code{rhs} are factors.}

man/pander.desctable.Rd

@@ -4,9 +4,16 @@
 \alias{pander.desctable}
 \title{Pander method for desctable}
 \usage{
-pander.desctable(x = NULL, digits = 2, justify = "left",
-  missing = "", keep.line.breaks = T, split.tables = Inf,
-  emphasize.rownames = F, ...)
+pander.desctable(
+  x = NULL,
+  digits = 2,
+  justify = "left",
+  missing = "",
+  keep.line.breaks = T,
+  split.tables = Inf,
+  emphasize.rownames = F,
+  ...
+)
 }
 \arguments{
 \item{x}{A desctable}