Merge pull request #48 from philsf/release-0.6.2

Release 0.6.2

DESCRIPTION

@@ -1,11 +1,12 @@
 Package: philsfmisc
 Type: Package
 Title: philsf's miscellaneous R functions
-Version: 0.6.1
+Version: 0.6.2
 Authors@R: person("Felipe", "Figueiredo", email = "[email protected]", role = c("aut", "cre"))
 Description: Miscellaneous R functions for convenient data analyses.
 License: file LICENSE
 Encoding: UTF-8
 LazyData: true
 URL: https://github.com/philsf/philsfmisc
 Depends: R (>= 3.3.0)
+RoxygenNote: 6.1.0

NAMESPACE

@@ -1,2 +1,16 @@
-importFrom("stats", "qt", "sd")
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(cv2logsd)
+export(cv2logvar)
+export(format.float)
+export(format.interval)
+export(format.pct)
+export(geocv)
+export(geomean)
+export(geosd)
+export(is.within)
+export(logsd2cv)
+export(logvar2cv)
+export(predint)
+importFrom(stats,qt)
+importFrom(stats,sd)

NEWS.md

@@ -1,3 +1,8 @@
+# philsfmisc 0.6.2
+
+- Now uses `roxygen2` for function documentation creation ( #37 )
+- Styles updated for all templates ( #45 )
+
 # philsfmisc 0.6.1
 
 - Styles updated #41

R/cv2logsd.R

@@ -1,3 +1,18 @@
+#' Convert the CV from a log-normal variable to the log-transformed standard deviation.
+#'
+#' @description
+#'
+#' @param x A numeric value, vector or list.
+#'
+#' @return Returns log-transformed sd
+#'
+#' @examples
+#' cv2logsd(50)
+#' # [1] 0.2051523
+#'
+#' @author Felipe Figueiredo
+#' @export
+
 cv2logsd <- function(x) {
   SD <- sqrt( cv2logvar(x) )
   SD

R/cv2logvar.R

@@ -1,3 +1,18 @@
+#' Convert the CV from a log-normal variable to the log-transformed variance.
+#'
+#' @description
+#'
+#' @param x A numeric value, vector or list.
+#'
+#' @return Returns the log-transformed variance.
+#'
+#' @examples
+#' cv2logvar(50)
+#' # [1] 0.04208748
+#'
+#' @author Felipe Figueiredo
+#' @export
+
 cv2logvar <- function( x ) {
   VAR <- (log((x/100)^2 + 1))/(log(10)^2)
   VAR

R/format.float.R

@@ -1,3 +1,31 @@
+#' Format numbers for printing
+#'
+#' @description Format numbers, given a `digits` argument as significant decimal places.
+#'   Numbers are always assumed to be \code{\link[base]{double}}.
+#'
+#' @param x Value to be formatted.
+#'   Input can be a numeric or character value.
+#'
+#' @param digits Number of fixed digits, after decimal point
+#'
+#' @return Returns a character value.
+#'
+#' @examples
+#' format.float(0.5)
+#' format.float(0.672, 4)
+#' format.float(1.4927, 1)
+#' format.float(c(1.756, 1.823))
+#' # Input is character
+#' format.float("1.12543")
+#' format.float(c("1.756", "1.823"))
+#'
+#' # Useful for data frames
+#' DF <- data.frame(num = c(1.756, 1.823), char = c("1.756", "1.823"), stringsAsFactors = FALSE)
+#' transform(DF, num = format.float(num), char = format.float(char))
+#'
+#' @author Felipe Figueiredo
+#' @export format.float
+
 format.float <- function(x, digits = 2) {
   x <- suppressWarnings(as.numeric(x))
   x <- formatC(x, format = "f", digits = digits)

R/format.interval.R

@@ -1,3 +1,24 @@
+#' Format intervals for printing
+#'
+#' @description Format intervals, given a `digits` argument as significant decimal places.
+#'
+#' @param interval Must be a vector of two values.
+#'   Values can be either numeric or character.
+#'
+#' @param digits Number of fixed digits, after decimal point.
+#'
+#' @return Returns a character value.
+#'
+#' @examples
+#' format.interval(c(1.756, 1.823))
+#' # format.interval(1.5, 1) # error: 1.5 is not an interval
+#'
+#' # Input is character
+#' format.interval(c("1.756", "1.823"))
+#'
+#' @author Felipe Figueiredo
+#' @export format.interval
+
 format.interval <- function(interval, digits = 2) {
   if (is.null(interval)) return(NULL) # if no argument passed, return
   if (anyNA(interval)) return(NA) # return NA in case of incomplete interval

R/format.pct.R

@@ -1,3 +1,25 @@
+#' Convenience function to format proportions as percentages
+#'
+#' @description
+#'
+#' @param p a numeric vector assumed to be a proportion.
+#' @param digits the number of decimal digits to be used in the output.
+#' @param pct.symbol (logical) whether or not to include the percent sign in the output.
+#'
+#' @return A character value formatted as percentages
+#'
+#' @examples
+#' format.pct(.1)
+#' format.pct(c(.42, .99), 0)
+#'
+#' m <- 10*matrix(c(1, 1.1, .9, 2), nrow = 2)
+#' format.pct(fisher.test(m)$p.value)
+#' format.pct(fisher.test(5*m)$p.value)
+#' format.pct(fisher.test(m)$conf.int)
+#'
+#' @author Felipe Figueiredo
+#' @export format.pct
+
 format.pct <- function(p, digits = 1, pct.symbol = FALSE) {
   symbol <- "%"
   if (!pct.symbol) symbol <- NULL

R/geocv.R

@@ -1,3 +1,21 @@
+#' Compute the CV of log-normally distributed data.
+#'
+#' @description
+#'
+#' @param x A numeric value, vector or list.
+#' @param na.rm (logical) whether or not to remove \code{NA} values from computation
+#'
+#' @return Returns the geometric CV (as percentage)
+#'
+#' @examples
+#' d <- c(10,100,1000)
+#' geocv(d)
+#' geocv(d) == logsd2cv(1)
+#'
+#' @author Felipe Figueiredo
+#' @export
+#' @importFrom stats sd
+
 geocv <- function(x, na.rm = TRUE) {
   logsd <- sd(log10(x), na.rm = na.rm)
   logsd2cv(logsd)

R/geomean.R

@@ -1,3 +1,21 @@
+#' Compute the geometric mean
+#'
+#' @description
+#'
+#' @param x A numeric value, vector or list.
+#'
+#' @details If any null values are present in \code{x} they are first replaced with \code{NA}.
+#'
+#' @return Returns the geometric mean of \code{x}.
+#'
+#' @examples
+#' d <- c(10,100,1000)
+#' geomean(d)
+#' geomean(c(d,0)) # na.rm is TRUE by default for sd()
+#'
+#' @author Felipe Figueiredo
+#' @export
+
 geomean <- function(x) {
   x[(x == 0)] <- NA # discard null values
   10^mean(log10(x), na.rm = T)

R/geosd.R

@@ -1,3 +1,21 @@
+#' Compute the "geometric standard deviation" of data
+#'
+#' @description The "geometric standard deviation" is not as well-defined as the geometric mean.
+#'  This function returns the analogous concept of \code{sd} in the same manner of the geometric mean.
+#'
+#' @param x A numeric value, vector or list.
+#'
+#' @return The anti-log of the \code{sd} of log-transformed data `x`.
+#'   Base 10 is assumed as a fixed default in this version.
+#'
+#' @examples
+#' d <- c(10,100,1000)
+#' geosd(d)
+#'
+#' @author Felipe Figueiredo
+#' @export
+#' @importFrom stats sd
+
 geosd <- function(x) {
   10^sd(log10(x))
 }

R/is.within.R

@@ -1,3 +1,24 @@
+#' Check if number is within given interval
+#'
+#' @description
+#'
+#' @param value A numeric value, vector or list.
+#' @param interval The (numeric) interval within which \code{value} is being tested.
+#' @param open.interval logical: should \code{interval} be regarded as an open interval?
+#'
+#' @return The default method for \code{is.within} applied to an atomic vector returns
+#'  a logical vector of the same length as its argument x, containing TRUE for those elements contained within \code{interval}, and FALSE otherwise.
+#'
+#' @examples
+#' is.within(1.5, c(0,5)) # TRUE
+#' is.within(6, c(0,5)) # FALSE
+#'
+#' is.within(c(1.5, 6), c(0,5)) # vector: TRUE, TRUE
+#' is.within(list(1.5, 6), c(0,5)) # list: TRUE, FALSE
+#'
+#' @author Felipe Figueiredo
+#' @export is.within
+
 is.within <- function(value, interval, open.interval = FALSE) {
   if (open.interval) return( value > interval[1] & value < interval[2] )
   value >= interval[1] & value <= interval[2]

R/logsd2cv.R

@@ -1,3 +1,19 @@
+#' Convert the log-transformed standard deviation from a log-normal variable to the CV.
+#'
+#' @description
+#'
+#' @param x A numeric value, vector or list.
+#'
+#' @return Returns the geometric CV (as percentage)
+#'
+#' @examples
+#' d <- c(10,100,1000)
+#' sd(log10(d)) # 1
+#' logsd2cv(1) # 1413.21\%
+#'
+#' @author Felipe Figueiredo
+#' @export
+
 logsd2cv <- function(x) {
   sqrt(exp((log(10)^2)*x^2) - 1)*100
 }

R/logvar2cv.R

@@ -1,3 +1,19 @@
+#' Convert the log-transformed variance from a log-normal variable to the CV.
+#'
+#' @description
+#'
+#' @param x A numeric value, vector or list.
+#'
+#' @return Returns the geometric CV (as percentage)
+#'
+#' @examples
+#' d <- c(10,100,1000)
+#' var(log10(d)) # 1
+#' logvar2cv(1) # 1413.21\%
+#'
+#' @author Felipe Figueiredo
+#' @export
+
 logvar2cv <- function(x) {
   sqrt(exp((log(10)^2)*x) - 1)*100
 }

R/predint.R

@@ -1,3 +1,23 @@
+#' Prediction Intervals for given data
+#'
+#' @description Compute a prediction interval of a vector, which is assumed
+#'  normally distributed with unknown mean and variance.
+#'
+#' @param datavector A numeric value, vector or list.
+#' @param alpha the significance level required
+#'
+#' @return a vector of two values
+#'   A vector with values giving lower and upper prediction limits for each parameter.
+#'
+#' @examples
+#' x <- rnorm(30)
+#' predint(x)
+#'
+#' @author Felipe Figueiredo
+#' @export
+#' @importFrom stats sd
+#' @importFrom stats qt
+
 predint <- function(datavector, alpha = 0.05) {
   datavector <- datavector[!is.na(datavector)] # discard NA values
   N <- length(datavector)

inst/rmarkdown/templates/Relatorio/skeleton/skeleton.Rmd

@@ -7,6 +7,7 @@ output:
     fig_caption: yes
     fig_height: 6
     fig_width: 6
+    keep_md: yes
     number_sections: yes
     toc: yes
   pdf_document:
@@ -18,7 +19,7 @@ output:
     fig_width: 6
     reference_docx: misc/style.docx
     toc: yes
-subtitle: 'CÓDIGO: analise_dados_XX_aaaa'
+subtitle: 'RELATÓRIO: analise_dados_XX_aaaa'
 toc-title: "Sumário"
 ---
 
@@ -29,8 +30,6 @@ options(scipen = 999)
 library(pander)
 library(knitr)
 library(philsfmisc)
-
-
 ```
 
 ---