368 lines
8.7 KiB
Plaintext
368 lines
8.7 KiB
Plaintext
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<%@meta language="R-vignette" content="--------------------------------
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DIRECTIVES FOR R:
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%\VignetteIndexEntry{matrixStats: Summary of functions}
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%\VignetteAuthor{Henrik Bengtsson}
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%\VignetteKeyword{matrix}
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%\VignetteKeyword{vector}
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%\VignetteKeyword{apply}
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%\VignetteKeyword{rows}
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%\VignetteKeyword{columns}
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%\VignetteKeyword{memory}
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%\VignetteKeyword{speed}
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%\VignetteEngine{R.rsp::rsp}
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%\VignetteTangle{FALSE}
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--------------------------------------------------------------------"%>
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<%
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pkgName <- "matrixStats"
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library(pkgName, character.only=TRUE)
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ns <- getNamespace(pkgName)
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env <- as.environment(sprintf("package:%s", pkgName))
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R.utils::use("R.utils")
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kable <- function(df, ...) {
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fcns <- as.character(df$Functions)
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fcns <- strsplit(fcns, split=",")
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fcns <- sapply(fcns, FUN=function(names) {
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names <- trim(names)
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ok <- sapply(names, FUN=exists, envir=ns, mode="function")
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names[ok] <- sprintf("%s()", names[ok])
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names[!ok] <- sprintf("~~%s()~~", names[!ok])
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names <- paste(names, collapse=", ")
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})
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df$Functions <- fcns
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df$Example <- sprintf("`%s`", df$Example)
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print(knitr::kable(df, ..., format="markdown"))
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}
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# Find all functions
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all <- ls(envir=env)
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keep <- sapply(all, FUN=function(name) {
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is.function(get(name, envir=env))
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})
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all <- all[keep]
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keep <- !grepl("[.]([^.]*)$", all)
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all <- all[keep]
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# Hidden functions
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skip <- c("rowAvgsPerColSet", "colAvgsPerRowSet")
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skip <- c(skip, "allocArray", "allocMatrix", "allocVector")
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all <- setdiff(all, skip)
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# Column and row functions
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crfcns <- grep("^(col|row)", all, value=TRUE)
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# Vector functions
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vfcns <- setdiff(all, crfcns)
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%>
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# <%@meta name="title"%>
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<% pkg <- R.oo::Package(pkgName) %>
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<%@meta name="author"%> on <%=format(as.Date(pkg$date), format="%B %d, %Y")%>
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<%
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fcns <- crfcns
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base <- gsub("^(col|row)", "", fcns)
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groups <- tapply(fcns, base, FUN=list)
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stopifnot(all(sapply(groups, FUN=length) == 2L))
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groups <- matrix(unlist(groups, use.names=FALSE), nrow=2L)
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%>
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<%---
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## Functions that apply to column and rows of matrices
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```
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<% print(fcns) %>
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```
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---%>
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<%
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fcns <- vfcns
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%>
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<%---
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## Functions that apply to vectors
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```
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<% print(fcns) %>
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```
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---%>
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## Location and scale estimators
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<%
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tbl <- NULL
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row <- data.frame(
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"Estimator" = "Weighted sample mean",
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"Functions" = "weightedMean, colWeightedMeans, rowWeightedMeans",
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"Example" = "weightedMean(x, w); rowWeightedMeans(x, w)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Mean",
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"Functions" = "mean2, colMeans2, rowMeans2",
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"Example" = "mean2(x); rowMeans2(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Median",
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"Functions" = "median, colMedians, rowMedians",
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"Example" = "median(x); rowMedians(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Weighted median",
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"Functions" = "weightedMedian, colWeightedMedians, rowWeightedMedians",
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"Example" = "weightedMedian(x, w); rowWeightedMedians(x, w)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Sample variance",
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"Functions" = "var, colVars, rowVars",
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"Example" = "var(x); rowVars(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Weighted sample variance",
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"Functions" = "weightedVar, colWeightedVars, rowWeightedVars",
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"Example" = "weightedVar(x, w), rowWeightedVars(x, w)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Sample variance by n-order differences",
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"Functions" = "varDiff, colVarDiffs, rowVarDiffs",
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"Example" = "varDiff(x); rowVarDiffs(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Sample standard deviation",
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"Functions" = "sd, colSds, rowSds",
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"Example" = "sd(x); rowSds(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Weighted sample deviation",
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"Functions" = "weightedSd, colWeightedSds, rowWeightedSds",
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"Example" = "weightedSd(x, w), rowWeightedSds(x, w)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Sample standard deviation by n-order differences",
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"Functions" = "sdDiff, colSdDiffs, rowSdDiffs",
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"Example" = "sdDiff(x); rowSdDiffs(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Median absolute deviation (MAD)",
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"Functions" = "mad, colMads, rowMads",
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"Example" = "mad(x); rowMads(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Weighted median absolute deviation (MAD)",
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"Functions" = "weightedMad, colWeightedMads, rowWeightedMads",
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"Example" = "weightedMad(x, w), rowWeightedMads(x, w)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Median absolute deviation (MAD) by n-order differences",
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"Functions" = "madDiff, colMadDiffs, rowMadDiffs",
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"Example" = "madDiff(x); rowMadDiffs()"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Quantile",
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"Functions" = "quantile, colQuantiles, rowQuantiles",
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"Example" = "quantile(x, probs); rowQuantiles(x, probs)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Interquartile range (IQR)",
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"Functions" = "iqr, colIQRs, rowIQRs",
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"Example" = "iqr(x); rowIQRs(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Interquartile range (IQR) by n-order differences",
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"Functions" = "iqrDiff, colIQRDiffs, rowIQRDiffs",
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"Example" = "iqrDiff(x); rowIQRDiffs(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Range",
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"Functions" = "range, colRanges, rowRanges",
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"Example" = "range(x); rowRanges(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Minimum",
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"Functions" = "min, colMins, rowMins",
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"Example" = "min(x); rowMins(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Maximum",
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"Functions" = "max, colMaxs, rowMaxs",
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"Example" = "max(x); rowMaxs(x)"
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)
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tbl <- rbind(tbl, row)
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%>
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<% kable(tbl) %>
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## Testing for and counting values
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<%
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tbl <- NULL
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row <- data.frame(
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"Operator" = "Are there any missing values?",
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"Functions" = "anyMissing, colAnyMissings, rowAnyMissings",
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"Example" = "anyMissing(x); rowAnyMissings(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Operator" = "Does TRUE exists?",
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"Functions" = "any, colAnys, rowAnys",
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"Example" = "any(x); rowAnys(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Operator" = "Are all values TRUE?",
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"Functions" = "all, colAlls, rowAlls",
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"Example" = "all(x); rowAlls(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Operator" = "Does value exists?",
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"Functions" = "anyValue, colAnys, rowAnys",
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"Example" = "anyValue(x, value); rowAnys(x, value)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Operator" = "Do all elements have a given value?",
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"Functions" = "allValue, colAlls, rowAlls",
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"Example" = "allValue(x, value); rowAlls(x, value)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Operator" = "Number of occurrences of a value?",
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"Functions" = "count, colCounts, rowCounts",
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"Example" = "count(x, value); rowCounts(x, value)"
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)
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tbl <- rbind(tbl, row)
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%>
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<% kable(tbl) %>
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## Cumulative functions
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<%
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tbl <- NULL
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row <- data.frame(
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"Operator" = "Cumulative sum",
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"Functions" = "cumsum, colCumsums, rowCumsums",
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"Example" = "cumsum(x); rowCumsums(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Operator" = "Cumulative product",
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"Functions" = "cumprod, colCumprods, rowCumprods",
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"Example" = "cumprod(x); rowCumprods(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Operator" = "Cumulative minimum",
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"Functions" = "cummin, colCummins, rowCummins",
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"Example" = "cummin(x); rowCummins(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Operator" = "Cumulative maximum",
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"Functions" = "cummax, colCummaxs, rowCummaxs",
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"Example" = "cummax(x); rowCummaxs(x)"
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)
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tbl <- rbind(tbl, row)
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%>
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<% kable(tbl) %>
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## Binning
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<%
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tbl <- NULL
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row <- data.frame(
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"Estimator" = "Counts in disjoint bins",
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"Functions" = "binCounts",
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"Example" = "binCounts(x, bx)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Estimator" = "Sample means (and counts) in disjoint bins",
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"Functions" = "binMeans",
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"Example" = "binMeans(y, x, bx)"
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)
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tbl <- rbind(tbl, row)
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%>
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<% kable(tbl) %>
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## Miscellaneous
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<%
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tbl <- NULL
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row <- data.frame(
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"Operation" = "Sum",
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"Functions" = "sum2, colSums2, rowSums2",
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"Example" = "sum2(x); rowSums2(x)"
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)
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tbl <- rbind(tbl, row)
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row <- data.frame(
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"Operation" = "Lagged differences",
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"Functions" = c("diff2, colDiffs, rowDiffs"),
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"Example" = "diff2(x), rowDiffs(x)"
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)
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tbl <- rbind(tbl, row)
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%>
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<% kable(tbl) %>
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-------------------------------------------------------------
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<%=pkgName%> v<%=getVersion(pkg)%>. Release: [CRAN](https://cran.r-project.org/package=<%=pkgName%>), Development: [GitHub](<%=getUrl(pkg)%>).
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