###
###
### From spida-test
### Modified by GM 2016-03-07
### - added ability to drop 'All' easily for
### barcharts
### Modified by GM 2013-08-20
### 1. Added ability to use pr and pct in Tab
### dropping total margins but keeping by default "All"
### margins
### 2. Added utility function 'dropLast'
### Modified by GM 2009-09-26
### tab( ..., pct = 1) standardizes rows so thay add to 100
### tab( ..., pr = 1) standardizes rows so thay add to 1
### tab( ..., pr = 0) standardizes entire table so it sums to 1
###
### Incorporate testing from package rdc
####
# Changes:
# 2014:
# October 16: added tab.table, tab.matrix, tab.array
#
# TODO: update tab.Rd to explain new features in Tab
# and keep = "All"
#' Drop last facets of array
#'
#' Primarily used to strips totals from a table bordered by totals
#' by dropping the last facet.
#'
#' @param arr array
#' @param drop drop parameter in subsetting, default FALSE
#' @param keep names of facets to be kept, default NULL
#'
#' @examples
#' (arr <- array(1:24,2:4))
#' arr %>% dropLast
#' arr %>% dropLast(drop = TRUE)
#' tab(iris, ~ Species)
#' tab(iris, ~ Species) %>% dropLast
#' tab(iris, ~ Species + I(Sepal.Length > 5)) %>% dropLast
#' # row percentages:
#' tab(iris, ~ Species + I(Sepal.Length > 5), pct= 1)
#' tab(iris, ~ Species + I(Sepal.Length > 5), pct= 1) %>% dropLast
#' tab(iris, ~ Species + I(Sepal.Length > 5), pct= 1) %>% dropLast(keep = "All")
#' @export
dropLast <- function(arr, drop = FALSE, keep = NULL) {
# NEW: 2013-08-20, G. Monette
# utility function to drop totals from tab
ind.last <- dim(arr)
ind.keep <- as.list(- ind.last) # drop last index of each dim unless name in keep
last <- function(x) x[length(x)]
names.last <- sapply( dimnames(arr), last)
disp(names.last)
if (!is.null(keep)) {
no.drop <- names.last %in% keep
ind.keep[no.drop] <- lapply( ind.last[no.drop], seq_len)
}
call <- c(list(arr), ind.keep, drop = drop)
disp(call)
do.call( `[`,call)
}
#' Drop last elements of an array if it is a "Total"
#'
#' Used to drop "Total" rows and columns after using \code{\link{tab}}. Synonyms for
#' legacy: \code{Tab} and \code{pab}.
#'
#' @param mat a matrix, array or table
#' @param names_to_drop (default "Total")
#' @param drop (default FALSE) should one-element dimension be dropped as dimensions
#' @seealso tab, Tab, dropLast
#' @export
dropLastTotal <- function (mat, names_to_drop = "Total", drop = FALSE) {
cl <- class(mat)
last <- function(x) x[length(x)]
cutlast <- function(x) if(length(x)>0) x[-length(x)] else x
ind.last <- dim(mat)
ns <- dimnames(mat)
# disp(ns)
keep <- lapply(ind.last, seq_len)
# disp(keep)
for(i in seq_along(keep)) {
# disp(i)
# disp(keep[[i]])
if( last(ns[[i]]) %in% names_to_drop) keep[[i]] <- cutlast(keep[[i]])
}
# disp(keep)
call <- c(list(mat), keep, drop = drop)
ret <- do.call(`[`, call)
class(ret) <- cl
ret
}
#' Table of frequencies or relative frequencies bordered with totals and
#' including NAs
#'
#' Generates a table of frequencies or relative frequencies or relative
#' percentages
#'
#' @param \dots as with \code{table}, one or more objects which can be interpreted as factors (including character strings), or a list (or data frame) whose components can be so interpreted.
#' @param data a data frame in which formula are interpreted
#' @param fmla a formula whose right-hand side names the variables to be used for tabulation. The optional left-hand side specifies a variable to be used for weights.
#' @param useNA whether to include NA levels. The default is "ifany". Can also
#' be set to "no" or "always".
#' @param pct margins to be scaled to sum to 100. This is the vector of margin indices on which percentages are conditioned. For example, with the call \code{tab(~ A + B + C, data, pct = 2:3)}, the table will contain conditional percentages for variable
#' \code{A} conditional of combinations of \code{B} and \code{C}.
#' @param pr margins to be scaled to sum to 1. This is the vector of margin indices on which percentages are conditioned.
#' @param total.margins if FALSE, generate table without margins
#' @param weights (not working temporarily) instead of generating a frequency table, generate a table
#' with the sum of the weights
#' @param keep names of margins to keep with 'Tab', default = "All". To drop
#' all margins, use default = "".
#' @param test (default FALSE) use \code{\link{chisq.test}}
#' @param simulate (default FALSE) simulate p-value with \code{\link{chisq.test}}
#' @param B (default 2000) number of replications for simulation
#' @return An object of class 'table' of dimension equal to the number of
#' variables, with optional margins showing totals. Elements of the matrix can
#' be frequencies, relative frequencies, percentages or sums of weights.
#' @aliases tab tab.formula tab.data.frame tab.default Tab
#' @seealso \code{\link{tab_}} to drop "Total" margins and
#' \code{\link{tab__}} to drop "Total" and "All" margins.
#' @author Georges Monette
#' @examples
#' titanic <- as.data.frame(Titanic)
#' head(titanic)
#' tab(titanic, Freq ~ Sex + Survived + Age , test = T)
#' tab(titanic, Freq ~ Sex + Age)
#' tab(titanic, Freq ~ Sex + Survived + Age)
#' round(tab(titanic, Freq ~ Sex + Survived + Age,
#' pct = c(1,3)),2)
#' round(Tab(titanic, Freq ~ Sex + Survived + Age,
#' pct = c(1,3)),2)
#' round(Tab(titanic, Freq ~ Sex + Survived + Age,
#' pct = c(1,3), keep = ""),2)
#' @export
tab <- function(x,...) UseMethod("tab")
#' @describeIn tab method class table
#' @export
tab.table <- function(x,...) {
data <- as.data.frame(x)
wt <- data$Freq
data$Freq <- NULL
tab.data.frame(data, ..., weights = wt)
}
#' @describeIn tab method for matrices
#' @export
tab.matrix <- function(x,...) tab(as.table(x),...)
#' @describeIn tab method for arrays
#' @export
tab.array <- function(x,...) tab(as.table(x),...)
#' @describeIn tab method for formulas
#' @export
tab.formula <- function( fmla, data = sys.frame(sys.parent()), ... ) tab.data.frame(data,fmla,...)
#' @describeIn tab method for data frames
#' @export
tab.data.frame <-
function (x, fmla,
total.margins = TRUE,
useNA = "ifany",
pct = NULL, pr = NULL,
test = FALSE,
weights = NULL,
na.rm = NULL,
all.label = "All",
simulate = FALSE,
B = 2000, ...)
{
# GM: 2014 08 22: modified handling of lhs to fix bug when variable in lhs
# also appears in rhs
if (missing(fmla)) {
fmla <- parse(text = paste(c("~",paste(names(x),collapse="+"))))
fmla <- eval(fmla)
environment(fmla) <- parent.frame()
}
if (is.null(weights) && (length(fmla) >2 )) {
weights <- model.frame(fmla[-3], x, na.action = NULL)[[1]]
xx <- model.frame(fmla[-2], x, na.action = NULL)
} else {
xx = model.frame(fmla, x, na.action = NULL)
#weights <- eval(substitute(weights), dd, environment(fmla)) # so weights is evaluated in parent.frame
}
if(!is.null(weights) && any(is.na(weights))) {
warning("NAs in weights set to -Inf")
weights[ is.na(weights) ] <- -Inf
}
# disp(weights)
if(simulate ==TRUE) test <- TRUE
xx = c(xx, list( total.margins = total.margins, useNA = useNA,
pct=pct, pr = pr, test=test, na.rm = na.rm,
weights = weights,all.label=all.label,
simulate=simulate) )
do.call("tab", xx)
}
#' @describeIn tab default method
#' @export
tab.default <- function (..., total.margins = TRUE,
pct = NULL, pr = NULL,
useNA = "ifany",
test = simulate,
weights = NULL,
na.rm = NULL,
all.label = "All",
simulate = FALSE,
B = 2000)
{
if(!is.null(na.rm)) useNA <- if(na.rm) "no" else "ifany"
aa <- list(...)
if (length(aa) == 1 && is.list(aa[[1]])) {
aa <- c(aa[[1]],list( total.margins = total.margins,
useNA = useNA, pr = pr, pct = pct, test=test,
na.rm = na.rm, weights = weights))
# disp(aa[[1]])
return(do.call("tab", aa[[1]]))
}
if (is.null(names(aa))) {
nns = names(match.call())
names(aa) = nns[2:(1 + length(aa))]
}
if(FALSE) {
if(useNA == "ifany") {
for (ii in 1:length(aa)) {
if(sum(is.na(aa[[ii]]))>0) levels(aa[[ii]]) <- unique(c(levels(aa[[ii]]) ,NA))
# aa[[ii]] <- factor(aa[[ii]], exclude = NULL) # table uses 'ifany' correctly when a number but not for factors
}
}
if(useNA == 'no'){
for (ii in 1:length(aa)) {
levels(aa[[ii]]) <- na.omit(levels(aa[[ii]]))
}
}
if(useNA=='yes'){
for (ii in 1:length(aa)) {
levels(aa[[ii]]) <- na.omit(levels(aa[[ii]]))
}
}
}
if( is.null(weights)){
aa[["useNA"]] <- useNA
aa[["na.rm"]] <- NULL
ret <- do.call("table", aa)
} else {
ret <- as.table(tapply(weights, aa, sum ) )
ret[is.na(ret)] <- 0
}
if (test) {
if( length(dim(ret)) < 3) {
test.out <- chisq.test(ret)
} else if ( length(dim(ret)) == 3) {
test.out <- apply( ret, 3:length(dim(ret)), chisq.test,
simulate.p.value = simulate,
B= B)
} else if ( length(dim(ret)) > 3) {
test.out <- .mat2arr(apply( ret, 3:length(dim(ret)), chisq.test,
simulate.p.value = simulate,
B= B))
}
}
if ( !is.null(pr)) ret <- acond( ret, MARGIN = pr, all.label = all.label)
else if ( !is.null(pct)) ret <- 100* acond( ret, MARGIN = pct, all.label = all.label)
else if (total.margins) ret = atotal(ret)
if( test ) attr(ret,'test') <- test.out
ret <- as.table(ret)
if( test ) class(ret) <- c('tab', class(ret))
ret
}
#' Print method for 'tab' object
#'
#' @export
print.tab <- function(x,...) {
NextMethod()
print(attr(x,'test'))
invisible(x)
}
#' Transform a frequency table into relative frequencies relative to a margin.
#'
#' @param x a table
#' @param MARGIN on which to condition
#' @param total.margin logical whether to include a total margin (default TRUE)
#' @param all.label label for marginal distribution
#' @export
acond <- function (x, MARGIN = NULL, total.margins = TRUE, all.label = "All")
{
debug <- F
x <- if( total.margins ) atotal(x)
if (is.null(MARGIN)|| max(MARGIN) < 1)
return(x/x[length(x)])
d <- dim(x)
if (debug) {
cat("dim(x)\n")
print(d)
}
dn <- dimnames(x)
if (debug) {
cat("dimnames(x)\n")
print(dn)
}
n <- length(d)
m <- length(MARGIN)
if ( length(setdiff( MARGIN, 1:n)) > 0) stop("MARGIN must select dimensions of x, or be equal to 0")
perm <- c(MARGIN, setdiff(1:n, MARGIN))
perm.inverse <- order(perm)
if (debug)
disp(perm)
if (debug)
disp(perm.inverse)
x <- aperm(x, perm)
d <- dim(x)
zl <- list(x)
for (ii in 1:length(d)) zl[[ii + 1]] <- seq(if (ii <= m)
1
else d[ii], d[ii])
tots <- do.call("[", zl)
ret <- array(c(x)/c(tots), dim = d)
ret <- aperm(ret, perm.inverse)
if (debug)
disp(dim(ret))
if (debug)
disp(dn)
for ( ii in MARGIN) dn[[ii]][length(dn[[ii]])] <- all.label
dimnames(ret) <- dn
ret
}
#' @rdname acond
#' @export
aprop <- acond # older name
#' Add all marginal sums to an array
#'
#' atotal adds by default a border of sums to an array. The function FUN may be used instead of 'sum'. Additional
#' arguments to FUN can also be given.
#'
#' @param arr array for which margins need to be added
#' @param FUN function to compute margins, default: sum
#' @param label for margin, default: 'Total'
#' @param \dots additional arguments to 'FUN'
#' @author Georges Monette
#' @return an array with dimension dim(arr) + 1
#' @export
atotal <- function(arr, FUN = sum, label = 'Total', ...) {
d <- dim(arr)
cls <- class(arr)
dim1 <- FALSE # to handle 1-dimensional tables
if (length(d) == 1) {
dim1 <- TRUE
dn <- dimnames(arr)
arr <- c(arr)
d <- dim(arr)
}
if(is.character(FUN))
FUN <- get(FUN, mode = "function")
else if(mode(FUN) != "function") {
farg <- substitute(FUN)
if(mode(farg) == "name")
FUN <- get(farg, mode = "function")
else stop(paste("\"", farg, "\" is not a function", sep = ""))
}
if (is.null(d)) {
ret <- structure(c(arr,FUN(arr,...)), names = c(names(arr), label), class = cls)
if (dim1) {
dn[[1]] <- c(dn[[1]],label)
ret <- structure( ret, dim = length(ret), dimnames = dn)
}
return (ret)
}
n <- length(d)
ret <- arr
ind <- 1:n
for ( i in n:1) {
new <- apply(ret,ind[-i],FUN,...)
ret <- abind( ret, new, i, label)
}
class( ret ) <- cls
ret
}
###
### abind
###
#' Bind comformable arrays
#'
#' \code{abind} binds two conformable arrays along a dimension.
#'
#' Warning: abind::abind should be preferred to spida2::abind.
#'
#' dim( arr1 ) and dim( arr2 ) must be equal except in the dth dimension. If
#' the length of dim( arr2 ) is 1 less than that of dim( arr1 ), then 'arr2' is
#' treated as if it had dropped the dth dimension with size 1.
#'
#' If length(dim(arr2)) == length(dim(arr1)) - 1, then arr2 is treated as if it
#' dropped a dimension of size 1 in the dth dimension. 'facename' is used as
#' the name of the dimnames list for this dimension.
#' @param arr1 first array
#' @param arr2 second array
#' @param d dimension along which arr1 and arr2 are joined, or, if the
#' \code{length(dim(arr1)) == length(dim(arr2)) + 1} the dimension in arr1 that
#' is extended by arr2.
#' @param facename Name for the new array dimension
#' @return The returned value, ret, is an array with dimension dim(arr1) except
#' for the dth dimension where dim(ret)[d] == dim(arr1)[d] + dim(arr2)[d].
#'
#' @author Georges Monette
#' @seealso \code{\link[base]{aperm}}, to permute arrays
#' @export
abind <- function(arr1,arr2,d,facename="") {
d1 <- dim(arr1)
n1 <- length(d1)
dn1 <- dimnames(arr1)
d2 <- dim(arr2)
n2 <- length(d2)
dn2 <- dimnames(arr2)
# warning('spida2::abind is deprecated. Consider using abind::abind')
arenull <- is.null(dn1) & is.null(dn2)
if (is.null(dn1)){
dn1 <- lapply( as.list(d1), function(x) seq(1,x))
dimnames(arr1) <- dn1
}
if ( n1 != n2 ) {
d2 <- d1
d2[d] <- 1
dn2 <- dn1
dn2[[d]] <- facename
dimnames(arr2) <- NULL
dim(arr2) <- d2
dimnames(arr2) <- dn2
n2 <- n1
}
if (is.null(dn2)){
dn2 <- lapply( as.list(d2), function(x) seq(1,x))
dimnames(arr2) <- dn2
}
# check input for consistency
# ... later
#
perm <- 1:n1
perm[c(d,n1)] <- c(n1,d) # perm is an involution
#
# permute arr1
#
arr.p1 <- aperm(arr1,perm)
#
# permute arr2 if length of dimension same as arr1
#
arr.p2 <- aperm(arr2,perm)
dret <- d1[perm]
dret[n1] <- dret[n1] + d2[d]
dnret <- dn1
dnret[[d]] <- c(dnret[[d]],dn2[[d]])
ret <- c(arr.p1, arr.p2)
dim(ret) <- dret
#
# permute response back
#
ret <- aperm(ret, perm)
dimnames(ret) <- dnret
ret
}
#' tab without marginal totals
#'
#' Version of \code{\link{tab}}, with the option to drop selected margins without
#' necessarily dropping
#' the marginal average proportions denoted by "All".
#'
#' @param \dots arguments to the \code{\link{tab}} function.
#' @param names_to_drop (default "Total") names of margins to drop
#' @aliases Tab pab
#' @seealso \code{\link{tab}}
#' @export
tab_ <- function(..., names_to_drop = "Total") {
# New version of Tab that handles pct and pr
# To keep the "All" and not the "Total" rows,
# specify keep = "All"
# BUGS: would be more efficient if it
# called tab(...,total.margins=FALSE)
# when pct or pr arguments are not given
as.table(dropLastTotal(
tab(..., total.margins = FALSE),
names_to_drop = names_to_drop))
}
#' tab without marginal totals and 'All'
#'
#' Version of \code{\link{tab}}, with the option to drop selected margins without
#' necessarily dropping
#' the marginal average proportions denoted by "All".
#'
#' @param \dots arguments to the \code{\link{tab}} function.
#' @param names_to_drop (default "Total") names of margins to drop
#' @aliases Tab pab
#' @seealso \code{\link{tab}}
#' @export
tab__ <- function(..., names_to_drop = c("All","Total")) {
# New version of Tab that handles pct and pr
# To keep the "All" and not the "Total" rows,
# specify keep = "All"
# BUGS: would be more efficient if it
# called tab(...,total.margins=FALSE)
# when pct or pr arguments are not given
as.table(dropLastTotal(
tab(..., total.margins = FALSE),
names_to_drop = names_to_drop))
}
#' @export
pab <- tab_ # legacy
#' @export
Tab <- tab_ # future?
#' Return a table as as data frame
#'
#' @param data a data frame
#' @param fmla a one-sided or two-sided formula
#' @param \dots other arguments to \code{\link{tab}}
#'
#' @details The right hand side of 'fmla' is used for the dimensions of the table. The
#' left-hand side, if present, is summed to generate the values in the cells of the table. If there is no
#' left-hand side, cell frequencies are shown.
#'
#' \code{tab_df(data, fmla)} is similar in effect to \code{as.data.frame(tab_(data, fmla))} except
#' that the former uses the name in the LHS of \code{fmla} as a variable name for counts while the latter
#' uses 'Freq'. Also, \code{tab_df} preserved ordered factors.
#'
#' @export
tab_df <- function(data, fmla, ...){
if(missing(fmla)) ret <- as.data.frame( tab_(data, ...))
else if (length(fmla) >2 ) {
nam <- as.character(fmla)[2]
ret <- as.data.frame(tab_(data, fmla, ...))
ret[[nam]] <- ret$Freq
ret$Freq <- NULL
} else ret <- as.data.frame(tab_(data, fmla, ...))
nams.fac <- intersect(names(data)[sapply(data,is.factor)], names(ret))
for( nn in nams.fac) {
if(is.ordered(data[[nn]])) ret[[nn]] <- ordered(ret[[nn]],levels = levels(data[[nn]]))
else ret[[nn]] <- factor(ret[[nn]], levels = levels(data[[nn]]))
}
ret
}
#' Display matrix
#'
#' Transform a matrix of test results for display
#'
#' @param x matrix
#' @export
.mat2arr <- function(x) {
ret <- as.list(x)
dim(ret) <- NULL
nams <- expand.grid( dimnames(x))
for ( ii in 1:length(nams)) {
nams[[ii]] <- paste( names(nams)[ii] , nams[[ii]], sep = " = ")
}
nams <- c( nams, sep = ", ")
nams <- do.call( paste, nams)
names(ret) <- nams
ret
}
#' Add faces to an array of data frames
#'
#' Add union of rows in elements of an array of data frames to marginal
#' faces of the array
#'
#' @param arr an array of data frames
#' @param label character string to label faces, default "All"
#' @export
add_faces <- function(arr, label = 'All', ...) {
if(is.null(dim(arr))) {
nn <- names(arr)
dim(arr) <- length(arr)
dimnames(arr)[[1]] <- nn
}
d <- dim(arr)
cls <- class(arr)
n <- length(d)
ret <- arr
ind <- 1:n
for ( i in n:1) {
new <- apply(ret,ind[-i], function(x) do.call(rbind, x))
ret <- abind( ret, new, i, label)
}
class( ret ) <- cls
ret
}
#' Create an array of data frames splitting on a formula with marginal faces
#'
#' Like a table but each element consists of the rows of the data frame
#' for a particular combination of levels of the formula
#'
#' @param dd data frame
#' @param fmla formula whose RHS creates a table and
#' LHS adds variables to the resulting data frames
#' @param all adds all variables in the data frame
#' @examples
#' tabf(mtcars, ~ cyl + carb)[1,1]
#' tabf(mtcars, ~ cyl + carb) %>% dimnames
#' tabf(mtcars, ~ cyl + carb + gear ) %>% Apply(dim) %>% Apply(paste, collapse = ' ')
#'
#' @export
tabf <- function(dd, fmla, all = TRUE, ...) {
# returns an array of data frames
# that can be processed through
# Apply (version of lapply for dimensioned lists)
mm <- model.frame(fmla, dd, na.action = NULL)
mp <- if(length(fmla) == 3)
model.frame(fmla[-2],mm, na.action = NULL) else mm
if(all) mm <- dd
ret <- split(mm, mp)
tt <- tab__(mp)
dim(ret) <- dim(tt)
add_faces(ret)
}
#' Version of lapply that can return an array of lists
#'
#' Returns an array of lists similar to its input
#'
#' @param X list of array of lists, as in \code{\link{lapply}}
#' @param fun function to be applied to each element of X
#' @param ... same as \code{\link{lapply}}
#' @export
Apply <- function(X, fun, ...) {
X[] <- lapply(X, fun,...)
X
}
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