Update packages/ Add org-ref

elpa/ess-20180611.502/etc/ESSR/R/misc.R

@@ -0,0 +1,131 @@
+.ess_weave <- function(command, file, encoding = NULL){
+    cmd_symb <- substitute(command)
+    if (grepl('knit|purl', deparse(cmd_symb))) require(knitr)
+    od <- getwd()
+    on.exit(setwd(od))
+    setwd(dirname(file))
+    frame <- parent.frame()
+    if (is.null(encoding))
+        eval(bquote(.(cmd_symb)(.(file))), envir = frame)
+    else
+        eval(bquote(.(cmd_symb)(.(file), encoding = .(encoding))), envir = frame)
+}
+
+.ess_knit <- function(file, output = NULL){
+    library(knitr)
+    frame <- parent.frame()
+    od <- getwd()
+    on.exit(setwd(od))
+    setwd(dirname(file))
+    ## this bquote is really needed for data.table := operator to work correctly
+    eval(bquote(knit(.(file), output = .(output))), envir = frame)
+}
+
+.ess_sweave <- function(file, output = NULL){
+    od <- getwd()
+    frame <- parent.frame()
+    on.exit(setwd(od))
+    setwd(dirname(file))
+    eval(bquote(Sweave(.(file), output = .(output))), envir = frame)
+}
+
+## Users might find it useful. So don't prefix with .ess.
+htsummary <- function(x, hlength = 4, tlength = 4, digits = 3) {
+    ## fixme: simplify and generalize
+    snames <- c("mean", "sd", "min", "max", "nlev", "NAs")
+    d <- " "
+    num_sumr <- function(x){
+        c(f(mean(x, na.rm = TRUE)),
+          f(sd(x, na.rm = TRUE)),
+          f(min(x, na.rm = TRUE)),
+          f(max(x, na.rm = TRUE)),
+          d,
+          f(sum(is.na(x), na.rm = TRUE)))
+    }
+    f <- function(x) format(x, digits = digits)
+
+    if (is.data.frame(x) | is.matrix(x)) {
+        if (nrow(x) <= tlength + hlength){
+            print(x)
+        } else {
+            if (is.matrix(x))
+                x <- data.frame(unclass(x))
+            ## conversion needed, to avoid problems with derived classes suchs
+            ## as data.table
+            h <- as.data.frame(head(x, hlength))
+            t <- as.data.frame(tail(x, tlength))
+            for (i in 1:ncol(x)) {
+                h[[i]] <- f(h[[i]])
+                t[[i]] <- f(t[[i]])
+            }
+            ## summaries
+            sumr <- sapply(x, function(c){
+                if (is.logical(c))
+                    ## treat logical as numeric; it's harmless
+                    c <- as.integer(c)
+                if (is.numeric(c))
+                    num_sumr(c)
+                else if (is.factor(c)) c(d, d, d, d, nlevels(c), sum(is.na(c)))
+                else rep.int(d, length(snames))
+            })
+            sumr <- as.data.frame(sumr)
+            row.names(sumr) <- snames
+            dots <- rep("...", ncol(x))
+            empty <- rep.int(" ", ncol(x))
+            lines <- rep.int(" ", ncol(x))
+            df <- rbind(h, ... = dots, t, `_____` = lines, sumr, ` ` = empty)
+            print(df)
+        }
+    } else {
+        cat("head(", hlength, "):\n", sep = "")
+        print(head(x, hlength))
+        if (length(x) > tlength + hlength){
+            cat("\ntail(", tlength, "):\n", sep = "")
+            print(tail(x, tlength))
+        }
+        cat("_____\n")
+        if (is.numeric(x) || is.logical(x))
+            print(structure(num_sumr(x), names = snames), quote = FALSE)
+        else if (is.factor(x)){
+            cat("NAs: ", sum(is.na(x), na.rm = TRUE), "\n")
+            cat("levels: \n")
+            print(levels(x))
+        }
+    }
+    invisible(NULL)
+}
+
+.ess_vignettes <- function(all=FALSE) {
+    vs <- unclass(browseVignettes(all = all))
+    vs <- vs[sapply(vs, length) > 0]
+
+    mat2elist <- function(mat) {
+        if (!is.null(dim(mat))){
+            apply(mat, 1, function(r)
+                sprintf("(list \"%s\")",
+                        paste0(gsub("\"", "\\\\\"",
+                                    as.vector(r[c("Title", "Dir", "PDF",
+                                                  "File", "R")])),
+                               collapse = "\" \"")))
+        }
+    }
+    cat("(list \n",
+        paste0(mapply(function(el, name) {
+            sprintf("(list \"%s\"  %s)",
+                    name, paste0(mat2elist(el), collapse = "\n"))
+        },
+        vs, names(vs)), collapse = "\n"), ")\n")
+}
+
+.ess_Rd2txt <- function(rd) {
+    fun <- tools::Rd2txt
+    if (length(formals(fun)["stages"]))# newer R version
+        fun(rd, stages = c("build", "install", "render"))
+    else
+        fun(rd)
+}
+
+
+## Local Variables:
+## eval: (ess-set-style 'RRR t)
+## End: