<%@meta language="R-vignette" content="--------------------------------
  DIRECTIVES FOR R:

  %\VignetteIndexEntry{matrixStats: Summary of functions}
  %\VignetteAuthor{Henrik Bengtsson}
  %\VignetteKeyword{matrix}
  %\VignetteKeyword{vector}
  %\VignetteKeyword{apply}
  %\VignetteKeyword{rows}
  %\VignetteKeyword{columns}
  %\VignetteKeyword{memory}
  %\VignetteKeyword{speed}
  %\VignetteEngine{R.rsp::rsp}
  %\VignetteTangle{FALSE}
--------------------------------------------------------------------"%>
<%
pkgName <- "matrixStats"
library(pkgName, character.only=TRUE)
ns <- getNamespace(pkgName)
env <- as.environment(sprintf("package:%s", pkgName))

R.utils::use("R.utils")
kable <- function(df, ...) {
  fcns <- as.character(df$Functions)
  fcns <- strsplit(fcns, split=",")
  fcns <- sapply(fcns, FUN=function(names) {
    names <- trim(names)
    ok <- sapply(names, FUN=exists, envir=ns, mode="function")
    names[ok] <- sprintf("%s()", names[ok])
    names[!ok] <- sprintf("~~%s()~~", names[!ok])
    names <- paste(names, collapse=", ")
  })
  df$Functions <- fcns
  df$Example <- sprintf("`%s`", df$Example)
  print(knitr::kable(df, ..., format="markdown"))
}


# Find all functions
all <- ls(envir=env)
keep <- sapply(all, FUN=function(name) {
  is.function(get(name, envir=env))
})
all <- all[keep]
keep <- !grepl("[.]([^.]*)$", all)
all <- all[keep]

# Hidden functions
skip <- c("rowAvgsPerColSet", "colAvgsPerRowSet")
skip <- c(skip, "allocArray", "allocMatrix", "allocVector")
all <- setdiff(all, skip)

# Column and row functions
crfcns <- grep("^(col|row)", all, value=TRUE)

# Vector functions
vfcns <- setdiff(all, crfcns)
%>

# <%@meta name="title"%>

<% pkg <- R.oo::Package(pkgName) %>
<%@meta name="author"%> on <%=format(as.Date(pkg$date), format="%B %d, %Y")%>

<%
fcns <- crfcns
base <- gsub("^(col|row)", "", fcns)
groups <- tapply(fcns, base, FUN=list)
stopifnot(all(sapply(groups, FUN=length) == 2L))
groups <- matrix(unlist(groups, use.names=FALSE), nrow=2L)
%>
<%---
## Functions that apply to column and rows of matrices

```
<% print(fcns) %>
```
---%>

<%
fcns <- vfcns
%>
<%---
## Functions that apply to vectors

```
<% print(fcns) %>
```
---%>

## Location and scale estimators
<%
tbl <- NULL

row <- data.frame(
  "Estimator"   = "Weighted sample mean",
  "Functions"   = "weightedMean, colWeightedMeans, rowWeightedMeans",
  "Example"     = "weightedMean(x, w); rowWeightedMeans(x, w)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Mean",
  "Functions"   = "mean2, colMeans2, rowMeans2",
  "Example"     = "mean2(x); rowMeans2(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Median",
  "Functions"   = "median, colMedians, rowMedians",
  "Example"     = "median(x); rowMedians(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Weighted median",
  "Functions"   = "weightedMedian, colWeightedMedians, rowWeightedMedians",
  "Example"     = "weightedMedian(x, w); rowWeightedMedians(x, w)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Sample variance",
  "Functions"   = "var, colVars, rowVars",
  "Example"     = "var(x); rowVars(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Weighted sample variance",
  "Functions"   = "weightedVar, colWeightedVars, rowWeightedVars",
  "Example"     = "weightedVar(x, w), rowWeightedVars(x, w)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Sample variance by n-order differences",
  "Functions"   = "varDiff, colVarDiffs, rowVarDiffs",
  "Example"     = "varDiff(x); rowVarDiffs(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Sample standard deviation",
  "Functions"   = "sd, colSds, rowSds",
  "Example"     = "sd(x); rowSds(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Weighted sample deviation",
  "Functions"   = "weightedSd, colWeightedSds, rowWeightedSds",
  "Example"     = "weightedSd(x, w), rowWeightedSds(x, w)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Sample standard deviation by n-order differences",
  "Functions"   = "sdDiff, colSdDiffs, rowSdDiffs",
  "Example"     = "sdDiff(x); rowSdDiffs(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Median absolute deviation (MAD)",
  "Functions"   = "mad, colMads, rowMads",
  "Example"     = "mad(x); rowMads(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Weighted median absolute deviation (MAD)",
  "Functions"   = "weightedMad, colWeightedMads, rowWeightedMads",
  "Example"     = "weightedMad(x, w), rowWeightedMads(x, w)"
)
tbl <- rbind(tbl, row)


row <- data.frame(
  "Estimator"   = "Median absolute deviation (MAD) by n-order differences",
  "Functions"   = "madDiff, colMadDiffs, rowMadDiffs",
  "Example"     = "madDiff(x); rowMadDiffs()"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Quantile",
  "Functions"   = "quantile, colQuantiles, rowQuantiles",
  "Example"     = "quantile(x, probs); rowQuantiles(x, probs)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Interquartile range (IQR)",
  "Functions"   = "iqr, colIQRs, rowIQRs",
  "Example"     = "iqr(x); rowIQRs(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Interquartile range (IQR) by n-order differences",
  "Functions"   = "iqrDiff, colIQRDiffs, rowIQRDiffs",
  "Example"     = "iqrDiff(x); rowIQRDiffs(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Range",
  "Functions"   = "range, colRanges, rowRanges",
  "Example"     = "range(x); rowRanges(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Minimum",
  "Functions"   = "min, colMins, rowMins",
  "Example"     = "min(x); rowMins(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Maximum",
  "Functions"   = "max, colMaxs, rowMaxs",
  "Example"     = "max(x); rowMaxs(x)"
)
tbl <- rbind(tbl, row)

%>
<% kable(tbl) %>



## Testing for and counting values
<%
tbl <- NULL

row <- data.frame(
  "Operator"   = "Are there any missing values?",
  "Functions"   = "anyMissing, colAnyMissings, rowAnyMissings",
  "Example"     = "anyMissing(x); rowAnyMissings(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Operator"   = "Does TRUE exists?",
  "Functions"   = "any, colAnys, rowAnys",
  "Example"     = "any(x); rowAnys(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Operator"   = "Are all values TRUE?",
  "Functions"   = "all, colAlls, rowAlls",
  "Example"     = "all(x); rowAlls(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Operator"   = "Does value exists?",
  "Functions"   = "anyValue, colAnys, rowAnys",
  "Example"     = "anyValue(x, value); rowAnys(x, value)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Operator"   = "Do all elements have a given value?",
  "Functions"   = "allValue, colAlls, rowAlls",
  "Example"     = "allValue(x, value); rowAlls(x, value)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Operator"   = "Number of occurrences of a value?",
  "Functions"   = "count, colCounts, rowCounts",
  "Example"     = "count(x, value); rowCounts(x, value)"
)
tbl <- rbind(tbl, row)

%>
<% kable(tbl) %>


## Cumulative functions
<%
tbl <- NULL

row <- data.frame(
  "Operator"   = "Cumulative sum",
  "Functions"   = "cumsum, colCumsums, rowCumsums",
  "Example"     = "cumsum(x); rowCumsums(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Operator"   = "Cumulative product",
  "Functions"   = "cumprod, colCumprods, rowCumprods",
  "Example"     = "cumprod(x); rowCumprods(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Operator"   = "Cumulative minimum",
  "Functions"   = "cummin, colCummins, rowCummins",
  "Example"     = "cummin(x); rowCummins(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Operator"   = "Cumulative maximum",
  "Functions"   = "cummax, colCummaxs, rowCummaxs",
  "Example"     = "cummax(x); rowCummaxs(x)"
)
tbl <- rbind(tbl, row)

%>
<% kable(tbl) %>


## Binning

<%
tbl <- NULL

row <- data.frame(
  "Estimator"   = "Counts in disjoint bins",
  "Functions"   = "binCounts",
  "Example"     = "binCounts(x, bx)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Estimator"   = "Sample means (and counts) in disjoint bins",
  "Functions"   = "binMeans",
  "Example"     = "binMeans(y, x, bx)"
)
tbl <- rbind(tbl, row)

%>
<% kable(tbl) %>


## Miscellaneous

<%
tbl <- NULL

row <- data.frame(
  "Operation"   = "Sum",
  "Functions"   = "sum2, colSums2, rowSums2",
  "Example"     = "sum2(x); rowSums2(x)"
)
tbl <- rbind(tbl, row)

row <- data.frame(
  "Operation"   = "Lagged differences",
  "Functions"   = c("diff2, colDiffs, rowDiffs"),
  "Example"     = "diff2(x), rowDiffs(x)"
)
tbl <- rbind(tbl, row)

%>
<% kable(tbl) %>


-------------------------------------------------------------
<%=pkgName%> v<%=getVersion(pkg)%>.  Release: [CRAN](https://cran.r-project.org/package=<%=pkgName%>), Development: [GitHub](<%=getUrl(pkg)%>).
