Merge pull request #34 from philsf/release-0.6.0

Release 0.6.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: philsfmisc
 Type: Package
 Title: philsf's miscellaneous R functions
-Version: 0.5.1
+Version: 0.6.0
 Authors@R: person("Felipe", "Figueiredo", email = "[email protected]", role = c("aut", "cre"))
 Description: Miscellaneous R functions for convenient data analyses.
 License: GPL-2

R/cv2logsd.R

@@ -1,4 +1,4 @@
-cv2logsd <- function(CV) {
-  SD <- sqrt( cv2logvar(CV) )
+cv2logsd <- function(x) {
+  SD <- sqrt( cv2logvar(x) )
   SD
 }

R/cv2logvar.R

@@ -1,4 +1,4 @@
-cv2logvar <- function( CV ) {
-  VAR <- (log((CV/100)^2 + 1))/(log(10)^2)
+cv2logvar <- function( x ) {
+  VAR <- (log((x/100)^2 + 1))/(log(10)^2)
   VAR
 }

R/format.float.R

@@ -1,5 +1,5 @@
-format.float <- function(value, digits = 2) {
-  value <- suppressWarnings(as.numeric(value))
-  value <- formatC(value, format = "f", digits = digits)
-  value
+format.float <- function(x, digits = 2) {
+  x <- suppressWarnings(as.numeric(x))
+  x <- formatC(x, format = "f", digits = digits)
+  x
 }

R/format.pct.R

@@ -0,0 +1,5 @@
+format.pct <- function(p, digits = 1, pct.symbol = TRUE) {
+  symbol <- "%"
+  if (!pct.symbol) symbol <- NULL
+  paste0(format.float(p*100, digits), symbol)
+}

R/geocv.R

@@ -1,4 +1,4 @@
-geocv <- function(datavector, digits = 2, na.rm = TRUE) {
-  logsd <- sd(log10(datavector), na.rm = na.rm)
-  logsd2cv(logsd, digits = digits, na.rm = na.rm)
+geocv <- function(x, na.rm = TRUE) {
+  logsd <- sd(log10(x), na.rm = na.rm)
+  logsd2cv(logsd)
 }

R/geomean.R

@@ -1,4 +1,4 @@
-geomean <- function(datavector) {
-  datavector[(datavector == 0)] <- NA # discard null values
-  10^mean(log10(datavector), na.rm = T)
+geomean <- function(x) {
+  x[(x == 0)] <- NA # discard null values
+  10^mean(log10(x), na.rm = T)
 }

R/geosd.R

@@ -1,3 +1,3 @@
-geosd <- function(datavector) {
-  10^sd(log10(datavector))
+geosd <- function(x) {
+  10^sd(log10(x))
 }

R/logsd2cv.R

@@ -1,3 +1,3 @@
-logsd2cv <- function(logsd, digits = 2, na.rm = TRUE) {
-  round(sqrt(exp((log(10)^2)*logsd^2) - 1)*100 , digits)
+logsd2cv <- function(x) {
+  sqrt(exp((log(10)^2)*x^2) - 1)*100
 }

R/logvar2cv.R

@@ -1,3 +1,3 @@
-logvar2cv <- function(var, digits = 2, na.rm = TRUE) {
-  round(sqrt(exp((log(10)^2)*var) - 1)*100 , digits)
+logvar2cv <- function(x) {
+  sqrt(exp((log(10)^2)*x) - 1)*100
 }

README.md

@@ -16,11 +16,15 @@ To install the *development* version, use the following command:
 
 - `format.float`
 - `format.interval`
+- `format.pct`
 - `is.within`
 - `geomean`
 - `geosd`
 - `geocv`
 - `logsd2cv`
+- `logvar2cv`
+- `cv2logsd`
+- `cv2logvar`
 - `predint`
 
 ## Report template

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

@@ -48,6 +48,29 @@ kable(history)
 
 ---
 
+# Assinaturas
+
+```{r, echo=FALSE}
+sig.field <- "__________________________"
+date.field <- "_____________"
+Stat <- c("Elaborador", "Nome", "Função", sig.field, date.field)
+Reviewer <- c("Revisado por", "", "", sig.field, date.field)
+Approver <- c("Verificado por", "", "", sig.field, date.field)
+Final.Approver <- c("Aprovação final", "", "", sig.field, date.field)
+
+sigs <- rbind(
+  Stat
+  , Reviewer
+  , Approver
+  , Final.Approver
+  )
+rownames(sigs) <- NULL
+colnames(sigs) <- c("Papel", "Nome", "Função", "Assinatura", "Data")
+
+# pander(sigs, split.cells = c(9, 14, 14, 16, 8), split.table = Inf)
+kable(sigs)
+```
+
 # Lista de abreviaturas
 
 # Introdução

man/format.float.Rd

@@ -11,11 +11,11 @@ Format numbers, given a `digits` argument as significant decimal places.
 {Numbers are always assumed to be \code{\link[base]{double}}.}
 }
 \usage{
-format.float(x)
+format.float(x, digits)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
-  \item{value}{
+  \item{x}{
   Value to be formatted.
   Input can be a numeric or character value.
   }
@@ -62,7 +62,7 @@ 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 = F)
+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))
 }
 % Add one or more standard keywords, see file 'KEYWORDS' in the

man/format.interval.Rd

@@ -53,7 +53,7 @@ Felipe Figueiredo
 \examples{
 format.interval(c(1.756, 1.823))
 
-format.interval(1.5, 1) # error: 1.5 is not an interval
+# format.interval(1.5, 1) # error: 1.5 is not an interval
 
 # Input is character
 format.interval(c("1.756", "1.823"))

man/format.pct.Rd

@@ -0,0 +1,51 @@
+\name{format.pct}
+\alias{format.pct}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+Convenience function to format proportions as percentages
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+format.pct(p, digits = 1, pct.symbol = TRUE)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{p}{a numeric vector assumed to be a proportion.}
+  \item{digits}{the number of decimal digits to be used in the output.}
+  \item{pct.symbol}{(logical) whether or not to include the percent sign in the output.}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+A character value formatted as percentages}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+%%  ~~who you are~~
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\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)
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }% use one of  RShowDoc("KEYWORDS")
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

man/geocv.Rd

@@ -8,15 +8,12 @@
 %%  ~~ A concise (1-5 lines) description of what the function does. ~~
 }
 \usage{
-geocv(x, digits = 2, na.rm = TRUE)
+geocv(x, na.rm = TRUE)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{x}{
 %%     ~~Describe \code{x} here~~
-}
-  \item{digits}{
-%%     ~~Describe \code{digits} here~~
 }
   \item{na.rm}{
 %%     ~~Describe \code{na.rm} here~~

man/predint.Rd

@@ -4,7 +4,7 @@
 \title{Prediction Intervals for given data
 %%  ~~function to do ... ~~
 }
-\description{Compute a prediction of a vector, which is assumed normally distributed with unknown mean and variance.
+\description{Compute a prediction interval of a vector, which is assumed normally distributed with unknown mean and variance.
 %%  ~~ A concise (1-5 lines) description of what the function does. ~~
 }
 \usage{