###
###
### From spida-test
### 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"
#' @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
}
#mat2arr( zza)
#' @export
dropLast <- function( mat ,drop = FALSE, keep = NULL) {
# NEW: 2013-08-20, G. Monette
# utility function to drop totals from tab
ind.last <- dim(mat)
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(mat), 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(mat),ind.keep,drop=drop)
# print(call)
do.call( `[`,call)
}
#' @export
Tab <- function(...,keep = "All") {
# 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
dropLast(tab(...), keep = keep)
}
#' @export
pab <- Tab # legacy
#' Table of frequencies or relative frequencies bordered with totals and
#' including NAs
#'
#' Generates a table of frequencies or relative frequencies or relative
#' percentages %% ~~ A concise (1-5 lines) description of what the function
#' does. ~~
#'
#' %% ~~ If necessary, more details than the description above ~~
#'
#' @aliases tab tab.formula tab.data.frame tab.default Tab
#' @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
#' @param pr margins to be scaled to sum to 1
#' @param total.margins if FALSE, generate table without margins
#' @param weights 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 = "".
#' @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.
#' @note %% ~~further notes~~
#' @author Georges Monette
#' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
#' @references %% ~put references to the literature/web site here ~
#' @keywords ~kwd1 ~kwd2
#' @examples
#'
#' titanic <- as.data.frame(Titanic)
#' head(titanic)
#' tab(titanic, ~ Sex + Age, weights = Freq)
#'
#' tab(titanic, ~ Sex + Survived + Age, weights = Freq)
#'
#' round(tab(titanic, ~ Sex + Survived + Age,
#' pct = c(1,3), weights = Freq),2)
#'
#' round(Tab(titanic, ~ Sex + Survived + Age,
#' pct = c(1,3), weights = Freq),2)
#'
#' round(Tab(titanic, ~ Sex + Survived + Age,
#' pct = c(1,3), weights = Freq, keep = ""),2)
#'
#' @export
tab <- function(x,...) UseMethod("tab")
#' @export
tab.table <- function(x,...) {
data <- as.data.frame(x)
wt <- data$Freq
data$Freq <- NULL
tab(data, ..., weights = wt)
}
#' @export
tab.matrix <- function(x,...) tab(as.table(x),...)
#' @export
tab.array <- function(x,...) tab(as.table(x),...)
#' @export
tab.formula <- function( fmla, data = sys.frame(sys.parent()), ... ) tab.data.frame(data,fmla,...)
#' @export
tab.data.frame <- function (dd, fmla,
total.margins = TRUE,
useNA = "ifany",
pct = NULL, pr = NULL,
test = FALSE,
weights = NULL,
na.rm = NULL,
all.label = "All")
{
# 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(dd),collapse="+"))))
fmla <- eval(fmla)
environment(fmla) <- parent.frame()
}
if (is.null(weights) && (length(fmla) >2 )) {
weights <- model.frame(fmla[-3], dd, na.action = NULL)[[1]]
xx <- model.frame(fmla[-2], dd, na.action = NULL)
} else {
xx = model.frame(fmla, dd, na.action = NULL)
weights <- eval(substitute(weights), dd, environment(fmla))
}
if(!is.null(weights) && any(is.na(weights))) {
warning("NAs in weights set to -Inf")
weights[ is.na(weights) ] <- -Inf
}
# disp(weights)
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) )
do.call("tab", xx)
}
#' @export
tab.default <- function (..., total.margins = TRUE,
pct = NULL, pr = NULL,
useNA = "ifany",
test = FALSE,
weights = NULL,
na.rm = NULL,
all.label = "All")
{
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(useNA=="ifany") for (ii in 1:length(aa)) aa[[ii]] <- factor(aa[[ii]], exclude = NULL) # table uses 'ifany' correctly when a number but not for factors
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)
} else if ( length(dim(ret)) > 3) {
test.out <- .mat2arr(apply( ret, 3:length(dim(ret)), chisq.test))
}
}
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
if( test ) ret <- unclass(ret) # so attributes will print
ret
}
#' Transform a frequency table into relative frequencies relative to a margin.
#'
#' %% ~~ A concise (1-5 lines) description of what the function does. ~~
#'
#' %% ~~ If necessary, more details than the description above ~~
#'
#' @param x %% ~~Describe \code{x} here~~
#' @param MARGIN %% ~~Describe \code{MARGIN} here~~
#' @return %% ~Describe the value returned %% If it is a LIST, use %%
#' @note %% ~~further notes~~
#' @author %% ~~who you are~~
#' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
#' @references %% ~put references to the literature/web site here ~
#' @keywords ~kwd1 ~kwd2
#' @examples
#'
#' ##---- Should be DIRECTLY executable !! ----
#' ##-- ==> Define data, use random,
#' ##-- or do help(data=index) for the standard data sets.
#'
#' ## The function is currently defined as
#' function (x, MARGIN = NULL)
#' {
#' debug <- F
#' x <- atotal(x)
#' if (is.null(MARGIN))
#' 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)
#' perm <- c(MARGIN, setdiff(1:n, MARGIN))
#' perm.inverse <- order(perm)
#' if (debug)
#' print(perm)
#' if (debug)
#' print(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)
#' print(dim(ret))
#' if (debug)
#' print(dn)
#' dimnames(ret) <- dn
#' ret
#' }
#'
#' @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
}
# environment(acond) <- as.environment("package:spida.beta")
#' Relative proportions
#'
#' %% ~~ A concise (1-5 lines) description of what the function does. ~~
#'
#' %% ~~ If necessary, more details than the description above ~~
#'
#' @param x %% ~~Describe \code{x} here~~
#' @param MARGIN %% ~~Describe \code{MARGIN} here~~
#' @return %% ~Describe the value returned %% If it is a LIST, use %%
#' @note %% ~~further notes~~
#' @author %% ~~who you are~~
#' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
#' @references %% ~put references to the literature/web site here ~
#' @keywords ~kwd1 ~kwd2
#' @examples
#'
#' ##---- Should be DIRECTLY executable !! ----
#' ##-- ==> Define data, use random,
#' ##-- or do help(data=index) for the standard data sets.
#'
#' ## The function is currently defined as
#' function (x, MARGIN = NULL)
#' {
#' debug <- F
#' x <- atotal(x)
#' if (is.null(MARGIN))
#' 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)
#' perm <- c(MARGIN, setdiff(1:n, MARGIN))
#' perm.inverse <- order(perm)
#' if (debug)
#' print(perm)
#' if (debug)
#' print(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)
#' print(dim(ret))
#' if (debug)
#' print(dn)
#' dimnames(ret) <- dn
#' ret
#' }
#'
#' @export
aprop <- acond # older name
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.