Added documentation back for code coverage

man/ANOVA.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convenience_functions.R
+\name{ANOVA}
+\alias{ANOVA}
+\title{Wrapper for oneway.test(var.equal = T)}
+\usage{
+ANOVA(formula)
+}
+\arguments{
+\item{formula}{An anova formula (\code{variable ~ grouping variable})}
+}
+\description{
+Wrapper for oneway.test(var.equal = T)
+}
+\seealso{
+\code{\link{oneway.test}}
+}

man/IQR.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convenience_functions.R
+\name{IQR}
+\alias{IQR}
+\title{Return the inter-quartile range}
+\usage{
+IQR(x)
+}
+\arguments{
+\item{x}{A vector}
+}
+\value{
+The IQR
+}
+\description{
+Safe version of IQR for statify
+}

man/as.data.frame.desctable.Rd

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

man/chisq.test.Rd

@@ -0,0 +1,171 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convenience_functions.R
+\name{chisq.test}
+\alias{chisq.test}
+\alias{chisq.test.default}
+\alias{chisq.test.formula}
+\title{Pearson's Chi-squared Test for Count Data}
+\source{
+The code for Monte Carlo simulation is a C translation of the Fortran algorithm of Patefield (1981).
+}
+\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}{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.}
+
+\item{y}{a numeric vector; ignored if \code{x} is a matrix or a formula. 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.}
+}
+\value{
+A list with class \code{"htest"} containing the following components:
+statistic: the value the chi-squared test statistic.
+
+parameter: the degrees of freedom of the approximate chi-squared
+          distribution of the test statistic, \code{NA} if the p-value is
+          computed by Monte Carlo simulation.
+
+ p.value: the p-value for the test.
+
+  method: a character string indicating the type of test performed, and
+          whether Monte Carlo simulation or continuity correction was
+          used.
+
+data.name: a character string giving the name(s) of the data.
+
+observed: the observed counts.
+
+expected: the expected counts under the null hypothesis.
+
+residuals: the Pearson residuals, ‘(observed - expected) /
+          sqrt(expected)’.
+
+  stdres: standardized residuals, \code{(observed - expected) / sqrt(V)},
+          where \code{V} is the residual cell variance (Agresti, 2007,
+          section 2.4.5 for the case where \code{x} is a matrix, ‘n * p * (1
+          - p)’ otherwise).
+}
+\description{
+\code{chisq.test} performs chi-squared contingency table tests and goodness-of-fit tests, with an added method for formulas.
+}
+\details{
+If \code{x} is a matrix with one row or column, or if \code{x} is a vector
+and \code{y} is not given, then a _goodness-of-fit test_ is performed
+(\code{x} is treated as a one-dimensional contingency table).  The
+entries of \code{x} must be non-negative integers.  In this case, the
+hypothesis tested is whether the population probabilities equal
+those in \code{p}, or are all equal if \code{p} is not given.
+
+If \code{x} is a matrix with at least two rows and columns, it is taken
+as a two-dimensional contingency table: the entries of \code{x} must be
+non-negative integers.  Otherwise, \code{x} and \code{y} must be vectors or
+factors of the same length; cases with missing values are removed,
+the objects are coerced to factors, and the contingency table is
+computed from these.  Then Pearson's chi-squared test is performed
+of the null hypothesis that the joint distribution of the cell
+counts in a 2-dimensional contingency table is the product of the
+row and column marginals.
+
+If \code{simulate.p.value} is \code{FALSE}, the p-value is computed from the
+asymptotic chi-squared distribution of the test statistic;
+continuity correction is only used in the 2-by-2 case (if
+\code{correct} is \code{TRUE}, the default).  Otherwise the p-value is
+computed for a Monte Carlo test (Hope, 1968) with \code{B} replicates.
+
+In the contingency table case simulation is done by random
+sampling from the set of all contingency tables with given
+marginals, and works only if the marginals are strictly positive.
+Continuity correction is never used, and the statistic is quoted
+without it.  Note that this is not the usual sampling situation
+assumed for the chi-squared test but rather that for Fisher's
+exact test.
+
+In the goodness-of-fit case simulation is done by random sampling
+from the discrete distribution specified by \code{p}, each sample being
+of size \code{n = sum(x)}.  This simulation is done in R and may be
+slow.
+}
+\examples{
+\dontrun{
+## From Agresti(2007) p.39
+M <- as.table(rbind(c(762, 327, 468), c(484, 239, 477)))
+dimnames(M) <- list(gender = c("F", "M"),
+                    party = c("Democrat","Independent", "Republican"))
+(Xsq <- chisq.test(M))  # Prints test summary
+Xsq$observed   # observed counts (same as M)
+Xsq$expected   # expected counts under the null
+Xsq$residuals  # Pearson residuals
+Xsq$stdres     # standardized residuals
+
+
+## Effect of simulating p-values
+x <- matrix(c(12, 5, 7, 7), ncol = 2)
+chisq.test(x)$p.value           # 0.4233
+chisq.test(x, simulate.p.value = TRUE, B = 10000)$p.value
+                                # around 0.29!
+
+## Testing for population probabilities
+## Case A. Tabulated data
+x <- c(A = 20, B = 15, C = 25)
+chisq.test(x)
+chisq.test(as.table(x))             # the same
+x <- c(89,37,30,28,2)
+p <- c(40,20,20,15,5)
+try(
+chisq.test(x, p = p)                # gives an error
+)
+chisq.test(x, p = p, rescale.p = TRUE)
+                                # works
+p <- c(0.40,0.20,0.20,0.19,0.01)
+                                # Expected count in category 5
+                                # is 1.86 < 5 ==> chi square approx.
+chisq.test(x, p = p)            #               maybe doubtful, but is ok!
+chisq.test(x, p = p, simulate.p.value = TRUE)
+
+## Case B. Raw data
+x <- trunc(5 * runif(100))
+chisq.test(table(x))            # NOT 'chisq.test(x)'!
+
+###
+}
+}
+\references{
+Hope, A. C. A. (1968) A simplified Monte Carlo significance test
+procedure.  _J. Roy, Statist. Soc. B_ *30*, 582-598.
+
+Patefield, W. M. (1981) Algorithm AS159.  An efficient method of
+generating r x c tables with given row and column totals.
+_Applied Statistics_ *30*, 91-97.
+
+Agresti, A. (2007) _An Introduction to Categorical Data Analysis,
+2nd ed._, New York: John Wiley & Sons.  Page 38.
+}
+\seealso{
+For goodness-of-fit testing, notably of continuous distributions, \code{\link{ks.test}}.
+}

man/datatable.Rd

@@ -0,0 +1,155 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/output.R
+\name{datatable}
+\alias{datatable}
+\alias{datatable.default}
+\alias{datatable.desctable}
+\title{Create an HTML table widget using the DataTables library}
+\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,
+  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,
+  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,
+  ...)
+}
+\arguments{
+\item{data}{a data object (either a matrix or a data frame)}
+
+\item{...}{arguments passed to \code{format}.}
+
+\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{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{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})}
+
+\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{digits}{the desired number of digits after the decimal
+    point (\code{format = "f"}) or \emph{significant} digits
+    (\code{format = "g"}, \code{= "e"} or \code{= "fg"}).
+
+    Default: 2 for integer, 4 for real numbers.  If less than 0,
+    the C default of 6 digits is used.  If specified as more than 50, 50
+    will be used with a warning unless \code{format = "f"} where it is
+    limited to typically 324. (Not more than 15--21 digits need be
+    accurate, depending on the OS and compiler used.  This limit is
+    just a precaution against segfaults in the underlying C runtime.)
+  }
+}
+\description{
+This function creates an HTML widget to display rectangular data (a matrix or data frame) using the JavaScript library DataTables, with a method for \code{desctable} objects.
+}
+\note{
+You are recommended to escape the table content for security reasons (e.g. XSS attacks) when using this function in Shiny or any other dynamic web applications.
+}
+\examples{
+library(DT)
+
+# see the package vignette for examples and the link to website
+vignette('DT', package = 'DT')
+
+# some boring edge cases for testing purposes
+m = matrix(nrow = 0, ncol = 5, dimnames = list(NULL, letters[1:5]))
+datatable(m)  # zero rows
+datatable(as.data.frame(m))
+
+m = matrix(1, dimnames = list(NULL, 'a'))
+datatable(m)  # one row and one column
+datatable(as.data.frame(m))
+
+m = data.frame(a = 1, b = 2, c = 3)
+datatable(m)
+datatable(as.matrix(m))
+
+# dates
+datatable(data.frame(
+  date = seq(as.Date("2015-01-01"), by = "day", length.out = 5), x = 1:5
+))
+datatable(data.frame(x = Sys.Date()))
+datatable(data.frame(x = Sys.time()))
+
+###
+}
+\references{
+See \url{http://rstudio.github.io/DT} for the full documentation.
+}

man/desctable.Rd

@@ -0,0 +1,111 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{desctable}
+\alias{desctable}
+\alias{desctable.default}
+\alias{desctable.grouped_df}
+\title{Generate a statistics table}
+\usage{
+desctable(data, stats, tests, labels)
+
+\method{desctable}{default}(data, stats = stats_auto, tests, labels = NULL)
+
+\method{desctable}{grouped_df}(data, stats = stats_auto, tests = tests_auto,
+  labels = NULL)
+}
+\arguments{
+\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 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 desctable object, which prints to a table of statistics for all variables
+}
+\description{
+Generate a statistics table with the chosen statistical functions, and tests if given a \code{"grouped"} dataframe.
+}
+\section{Labels}{
+
+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")
+}
+
+\section{Stats}{
+
+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 \code{condition ~ T | F}, and can be nested, such as \code{is.factor ~ percent | (is.normal ~ mean | median)}, for example.
+}
+
+\section{Tests}{
+
+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.
+
+That test name must be expressed as a single-term formula (e.g. \code{~t.test}). You don't have to specify tests for all the variables: a default test for all other variables can be defined with the name \code{.default}, and an automatic test can be defined with the name \code{.auto}.
+
+If data is a grouped dataframe (using \code{group_by}), subtables are created and statistic tests are performed over each sub-group.
+}
+
+\section{Output}{
+
+The output is a desctable object, which is a list of named dataframes that can be further manipulated. Methods for printing, using in \pkg{pander} and \pkg{DT} are present. Printing reduces the object to a dataframe.
+}
+
+\examples{
+iris \%>\%
+  desctable
+
+# Does the same as stats_auto here
+iris \%>\% 
+  desctable(stats = list("N"      = length,
+                         "\%/Mean" = is.factor ~ percent | (is.normal ~ mean),
+                         "sd"     = is.normal ~ sd,
+                         "Med"    = is.normal ~ NA | median,
+                         "IQR"    = is.normal ~ NA | IQR))
+
+# With labels
+mtcars \%>\% desctable(labels = c(hp  = "Horse Power",
+                                cyl = "Cylinders",
+                                mpg = "Miles per gallon"))
+
+# With grouping on a factor
+iris \%>\%
+  group_by(Species) \%>\%
+  desctable(stats = stats_default)
+
+# With nested grouping, on arbitrary variables
+mtcars \%>\%
+  group_by(vs, cyl) \%>\%
+  desctable
+
+# With grouping on a condition, and choice of tests
+iris \%>\%
+  group_by(Petal.Length > 5) \%>\%
+  desctable(tests = list(.auto = tests_auto, Species = ~chisq.test))
+}
+\seealso{
+\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 +1,212 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convenience_functions.R
+\name{fisher.test}
+\alias{fisher.test}
+\alias{fisher.test.default}
+\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)
+
+\method{fisher.test}{default}(x, ...)
+
+\method{fisher.test}{formula}(x, y = NULL, workspace = 2e+05, 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.}
+
+\item{y}{a factor object; ignored if \code{x} is a matrix or a formula.}
+
+\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.
+    Since \R version 3.5.0, this also increases the internal stack size
+    which allows larger problems to be solved, however sometimes needing
+    hours.  In such cases, \code{simulate.p.values=TRUE} may be more
+    reasonable.}
+
+\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.}
+
+\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.}
+
+\item{...}{additional params to feed to original fisher.test}
+}
+\value{
+A list with class \code{"htest"} containing the following components:
+
+p.value: the p-value of the test.
+
+conf.int: a confidence interval for the odds ratio.  Only present in
+          the 2 by 2 case and if argument \code{conf.int = TRUE}.
+
+estimate: an estimate of the odds ratio.  Note that the _conditional_
+          Maximum Likelihood Estimate (MLE) rather than the
+          unconditional MLE (the sample odds ratio) is used.  Only
+          present in the 2 by 2 case.
+
+null.value: the odds ratio under the null, \code{or}.  Only present in the 2
+          by 2 case.
+
+alternative: a character string describing the alternative hypothesis.
+
+method: the character string \code{"Fisher's Exact Test for Count Data"}.
+
+data.name: a character string giving the names of the data.
+}
+\description{
+Performs Fisher's exact test for testing the null of independence
+of rows and columns in a contingency table with fixed marginals, or with a formula expression.
+}
+\details{
+If \code{x} is a matrix, it is taken as a two-dimensional contingency
+table, and hence its entries should be nonnegative integers.
+Otherwise, both \code{x} and \code{y} must be vectors of the same length.
+Incomplete cases are removed, the vectors are coerced into factor
+objects, and the contingency table is computed from these.
+
+For 2 by 2 cases, p-values are obtained directly using the
+(central or non-central) hypergeometric distribution. Otherwise,
+computations are based on a C version of the FORTRAN subroutine
+FEXACT which implements the network developed by Mehta and Patel
+(1986) and improved by Clarkson, Fan and Joe (1993).  The FORTRAN
+code can be obtained from \url{http://www.netlib.org/toms/643}.
+Note this fails (with an error message) when the entries of the
+table are too large.  (It transposes the table if necessary so it
+has no more rows than columns.  One constraint is that the product
+of the row marginals be less than 2^31 - 1.)
+
+For 2 by 2 tables, the null of conditional independence is
+equivalent to the hypothesis that the odds ratio equals one.
+\code{Exact} inference can be based on observing that in general, given
+all marginal totals fixed, the first element of the contingency
+table has a non-central hypergeometric distribution with
+non-centrality parameter given by the odds ratio (Fisher, 1935).
+The alternative for a one-sided test is based on the odds ratio,
+so \code{alternative = "greater"} is a test of the odds ratio being
+bigger than \code{or}.
+
+Two-sided tests are based on the probabilities of the tables, and
+take as \code{more extreme} all tables with probabilities less than or
+equal to that of the observed table, the p-value being the sum of
+such probabilities.
+
+For larger than 2 by 2 tables and \code{hybrid = TRUE}, asymptotic
+chi-squared probabilities are only used if the ‘Cochran
+conditions’ are satisfied, that is if no cell has count zero, and
+more than 80% of the cells have counts at least 5: otherwise the
+exact calculation is used.
+
+Simulation is done conditional on the row and column marginals,
+and works only if the marginals are strictly positive.  (A C
+translation of the algorithm of Patefield (1981) is used.)
+}
+\examples{
+\dontrun{
+## Agresti (1990, p. 61f; 2002, p. 91) Fisher's Tea Drinker
+## A British woman claimed to be able to distinguish whether milk or
+##  tea was added to the cup first.  To test, she was given 8 cups of
+##  tea, in four of which milk was added first.  The null hypothesis
+##  is that there is no association between the true order of pouring
+##  and the woman's guess, the alternative that there is a positive
+##  association (that the odds ratio is greater than 1).
+TeaTasting <-
+matrix(c(3, 1, 1, 3),
+       nrow = 2,
+       dimnames = list(Guess = c("Milk", "Tea"),
+                       Truth = c("Milk", "Tea")))
+fisher.test(TeaTasting, alternative = "greater")
+## => p = 0.2429, association could not be established
+
+## Fisher (1962, 1970), Criminal convictions of like-sex twins
+Convictions <-
+matrix(c(2, 10, 15, 3),
+       nrow = 2,
+       dimnames =
+       list(c("Dizygotic", "Monozygotic"),
+            c("Convicted", "Not convicted")))
+Convictions
+fisher.test(Convictions, alternative = "less")
+fisher.test(Convictions, conf.int = FALSE)
+fisher.test(Convictions, conf.level = 0.95)$conf.int
+fisher.test(Convictions, conf.level = 0.99)$conf.int
+
+## A r x c table  Agresti (2002, p. 57) Job Satisfaction
+Job <- matrix(c(1,2,1,0, 3,3,6,1, 10,10,14,9, 6,7,12,11), 4, 4,
+dimnames = list(income = c("< 15k", "15-25k", "25-40k", "> 40k"),
+                satisfaction = c("VeryD", "LittleD", "ModerateS", "VeryS")))
+fisher.test(Job)
+fisher.test(Job, simulate.p.value = TRUE, B = 1e5)
+
+###
+}
+}
+\references{
+Agresti, A. (1990) _Categorical data analysis_.  New York: Wiley.
+Pages 59-66.
+
+Agresti, A. (2002) _Categorical data analysis_. Second edition.
+New York: Wiley.  Pages 91-101.
+
+Fisher, R. A. (1935) The logic of inductive inference.  _Journal
+of the Royal Statistical Society Series A_ *98*, 39-54.
+
+Fisher, R. A. (1962) Confidence limits for a cross-product ratio.
+_Australian Journal of Statistics_ *4*, 41.
+
+Fisher, R. A. (1970) _Statistical Methods for Research Workers._
+Oliver & Boyd.
+
+Mehta, C. R. and Patel, N. R. (1986) Algorithm 643. FEXACT: A
+Fortran subroutine for Fisher's exact test on unordered r*c
+contingency tables.  _ACM Transactions on Mathematical Software_,
+*12*, 154-161.
+
+Clarkson, D. B., Fan, Y. and Joe, H. (1993) A Remark on Algorithm
+643: FEXACT: An Algorithm for Performing Fisher's Exact Test in r
+x c Contingency Tables.  _ACM Transactions on Mathematical
+Software_, *19*, 484-488.
+
+Patefield, W. M. (1981) Algorithm AS159.  An efficient method of
+generating r x c tables with given row and column totals.
+_Applied Statistics_ *30*, 91-97.
+}
+\seealso{
+\code{\link{chisq.test}}
+
+\code{fisher.exact} in package \pkg{kexact2x2} for alternative
+interpretations of two-sided tests and confidence intervals for 2
+by 2 tables.
+}

man/flatten_desctable.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{flatten_desctable}
+\alias{flatten_desctable}
+\title{Flatten a desctable to a dataframe recursively}
+\usage{
+flatten_desctable(desctable)
+}
+\arguments{
+\item{desctable}{A desctable object}
+}
+\value{
+A flat dataframe
+}
+\description{
+Flatten a desctable to a dataframe recursively
+}

man/group_by.Rd

@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/imports.R
+\name{group_by}
+\alias{group_by}
+\title{Group a tbl by one or more variables.}
+\usage{
+group_by(.data, ..., add = FALSE)
+}
+\description{
+Group a tbl by one or more variables.
+}
+\keyword{internal}

man/head_dataframe.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{head_dataframe}
+\alias{head_dataframe}
+\title{Build the header for dataframe}
+\usage{
+head_dataframe(head)
+}
+\arguments{
+\item{head}{A headerList object}
+}
+\value{
+A names vector
+}
+\description{
+Build the header for dataframe
+}

man/head_datatable.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{head_datatable}
+\alias{head_datatable}
+\title{Build the header for datatable}
+\usage{
+head_datatable(head)
+}
+\arguments{
+\item{head}{A headerList object}
+}
+\value{
+An htmltools$tags object containing the header
+}
+\description{
+Build the header for datatable
+}

man/head_pander.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{head_pander}
+\alias{head_pander}
+\title{Build the header for pander}
+\usage{
+head_pander(head)
+}
+\arguments{
+\item{head}{A headerList object}
+}
+\value{
+A names vector
+}
+\description{
+Build the header for pander
+}

man/header.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{header}
+\alias{header}
+\title{Build header}
+\usage{
+header(desctable, output = c("pander", "datatable", "dataframe"))
+}
+\arguments{
+\item{desctable}{A desctable object}
+
+\item{output}{An output format for the header}
+}
+\value{
+A header object in the output format
+}
+\description{
+Take a desctable object and create a suitable header for the mentionned output.
+Output can be one of "pander", "datatable", or "dataframe".
+}

man/headerList.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{headerList}
+\alias{headerList}
+\title{Build a header list object}
+\usage{
+headerList(desctable)
+}
+\arguments{
+\item{desctable}{A desctable}
+}
+\value{
+A nested list of headers with colspans
+}
+\description{
+Build a header list object
+}

man/insert.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{insert}
+\alias{insert}
+\title{Insert a vector y inside another vector x at position}
+\usage{
+insert(x, y, position)
+}
+\arguments{
+\item{x}{A vector}
+
+\item{y}{A vector or list of vectors}
+
+\item{position}{The position / vector of positions to insert vector(s) y in vector x}
+}
+\value{
+The combined vector
+}
+\description{
+Insert a vector y inside another vector x at position
+}

man/is.normal.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convenience_functions.R
+\name{is.normal}
+\alias{is.normal}
+\title{Test if distribution is normal}
+\usage{
+is.normal(x)
+}
+\arguments{
+\item{x}{A numerical vector}
+}
+\value{
+A boolean
+}
+\description{
+Test if distribution is normal.
+The condition for normality is length > 30 and non-significant Shapiro-Wilks test with p > .1
+}

man/no.test.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convenience_functions.R
+\name{no.test}
+\alias{no.test}
+\title{No test}
+\usage{
+no.test(formula)
+}
+\arguments{
+\item{formula}{A formula}
+}
+\description{
+An empty test
+}

man/pander.desctable.Rd

@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/output.R
+\name{pander.desctable}
+\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, ...)
+}
+\arguments{
+\item{x}{A desctable}
+
+\item{digits}{passed to \code{format}. Can be a vector specifying values for each column (has to be the same length as number of columns).}
+
+\item{justify}{defines alignment in cells passed to \code{format}. Can be \code{left}, \code{right} or \code{centre}, which latter can be also spelled as \code{center}. Defaults to \code{centre}. Can be abbreviated to a string consisting of the letters \code{l}, \code{c} and \code{r} (e.g. 'lcr' instead of c('left', 'centre', 'right').}
+
+\item{missing}{string to replace missing values}
+
+\item{keep.line.breaks}{(default: \code{FALSE}) if to keep or remove line breaks from cells in a table}
+
+\item{split.tables}{where to split wide tables to separate tables. The default value (\code{80}) suggests the conventional number of characters used in a line, feel free to change (e.g. to \code{Inf} to disable this feature) if you are not using a VT100 terminal any more :)}
+
+\item{emphasize.rownames}{boolean (default: \code{TRUE}) if row names should be highlighted}
+
+\item{...}{unsupported extra arguments directly placed into \code{/dev/null}}
+}
+\description{
+Pander method to output a desctable
+}
+\details{
+Uses \code{pandoc.table}, with some default parameters (\code{digits = 2}, \code{justify = "left"}, \code{missing = ""}, \code{keep.line.breaks = T}, \code{split.tables = Inf}, and \code{emphasize.rownames = F}), that you can override if needed.
+}
+\seealso{
+\code{\link{pandoc.table}}
+}

man/parse_formula.Rd

@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.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
+}

man/percent.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convenience_functions.R
+\name{percent}
+\alias{percent}
+\title{Return the percentages for the levels of a factor}
+\usage{
+percent(x)
+}
+\arguments{
+\item{x}{A factor}
+}
+\value{
+A nlevels(x) + 1 length vector of percentages
+}
+\description{
+Return a compatible vector of length nlevels(x) + 1
+to print the percentages of each level of a factor
+}

man/pipe.Rd

@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/imports.R
+\name{\%>\%}
+\alias{\%>\%}
+\title{Pipe operator}
+\usage{
+lhs \%>\% rhs
+}
+\description{
+Pipe operator
+}
+\keyword{internal}

man/print.desctable.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/output.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/statColumn.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{statColumn}
+\alias{statColumn}
+\title{Generate one statistic for all variables}
+\usage{
+statColumn(stat, data)
+}
+\arguments{
+\item{stat}{The statistic to use}
+
+\item{data}{The dataframe to apply the statistic to}
+}
+\value{
+A vector for one statistic column
+}
+\description{
+Generate one statistic for all variables
+}

man/statTable.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{statTable}
+\alias{statTable}
+\title{Generate the table of all statistics for all variables}
+\usage{
+statTable(data, stats)
+}
+\arguments{
+\item{data}{The dataframe to apply the statistic to}
+
+\item{stats}{A list of named statistics to use}
+}
+\value{
+A dataframe of all statistics for all variables
+}
+\description{
+Generate the table of all statistics for all variables
+}

man/statify.Rd

@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stats.R
+\name{statify}
+\alias{statify}
+\alias{statify.default}
+\alias{statify.formula}
+\title{Transform any function into a valid stat function for the table}
+\usage{
+statify(x, f)
+
+\method{statify}{default}(x, f)
+
+\method{statify}{formula}(x, f)
+}
+\arguments{
+\item{x}{A vector}
+
+\item{f}{The function to try to apply, or a formula combining two functions}
+}
+\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 stat function for the table
+}
+\details{
+NA values are removed from the data
+
+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
+
+See \code{parse_formula} for the usage for formulaes.
+}

man/stats_default.Rd

@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stats.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}
+\usage{
+stats_default(data)
+
+stats_normal(data)
+
+stats_nonnormal(data)
+
+stats_auto(data)
+}
+\arguments{
+\item{data}{The dataframe to apply the statistic to}
+}
+\value{
+A list of statistics to use, potentially assessed from the dataframe
+}
+\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.
+}

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

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tests.R
+\name{tests_auto}
+\alias{tests_auto}
+\title{Functions to choose a statistical test}
+\usage{
+tests_auto(var, grp)
+}
+\arguments{
+\item{var}{The variable to test}
+
+\item{grp}{The variable for the groups}
+}
+\value{
+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.
+}
+\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.
+}

man/varColumn.Rd

@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build.R
+\name{varColumn}
+\alias{varColumn}
+\title{Generate the variable column to display as row names}
+\usage{
+varColumn(data, labels = NULL)
+}
+\arguments{
+\item{data}{The dataframe to get the names from}
+
+\item{labels}{The optional named character vector containing the keypairs var = "Label"}
+}
+\value{
+A dataframe with one variable named "Variables", a character vector of variable names/labels and levels
+}
+\description{
+Generates the variable column.
+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.
+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.
+}