Merge pull request #22 from philsf/release-0.3.0

Release 0.3.0

R/geocv.R

@@ -0,0 +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)
+}

R/geomean.R

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

R/geosd.R

@@ -0,0 +1,3 @@
+geosd <- function(datavector) {
+  10^sd(log10(datavector))
+}

R/logsd2cv.R

@@ -0,0 +1,3 @@
+logsd2cv <- function(logsd, digits = 2, na.rm = TRUE) {
+  round(sqrt(exp(logsd^2) - 1)*100 , digits)
+}

README.md

@@ -17,6 +17,10 @@ To install the *development* version, use the following command:
 - `format.float`
 - `format.interval`
 - `is.within`
+- `geomean`
+- `geosd`
+- `geocv`
+- `logsd2cv`
 
 ## Report template
 

man/geocv.Rd

@@ -0,0 +1,58 @@
+\name{geocv}
+\alias{geocv}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{Compute the CV of log-normally distributed data.
+%%  ~~function to do ... ~~
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+geocv(x, digits = 2, 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~~
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\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{
+d <- c(10,100,1000)
+geocv(d)
+geocv(d) == logsd2cv(1)
+}
+% 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/geomean.Rd

@@ -0,0 +1,54 @@
+\name{geomean}
+\alias{geomean}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{Compute geometric mean
+%%  ~~function to do ... ~~
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+geomean(x)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{x}{vector of numeric.
+%%     ~~Describe \code{x} here~~
+}
+}
+\details{
+If any null values are present in \code{x} they are first replaced with \code{NA}.
+}
+\value{
+Returns the geometric mean of \code{x}.
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+Felipe Figueiredo
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+d <- c(10,100,1000)
+geomean(d)
+geomean(c(d,0)) # na.rm is TRUE by default for sd()
+
+}
+% 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/geosd.Rd

@@ -0,0 +1,56 @@
+\name{geosd}
+\alias{geosd}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{Compute the "geometric standard deviation" of data
+%%  ~~function to do ... ~~
+}
+\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.
+}
+\usage{
+geosd(x)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{x}{
+%%     ~~Describe \code{x} here~~
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+The anti-log of the \code{sd} of log-transformed data `x`.
+Base 10 is assumed as a fixed default in this version.
+
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\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}}, ~~~
+\code{\link{geomean}}
+}
+\examples{
+d <- c(10,100,1000)
+geosd(d)
+}
+% 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/logsd2cv.Rd

@@ -0,0 +1,52 @@
+\name{logsd2cv}
+\alias{logsd2cv}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{Convert the log-transformed standard deviation from a log-normal variable to the CV.
+%%  ~~function to do ... ~~
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+logsd2cv(x)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{x}{
+%%     ~~Describe \code{x} here~~
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\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{
+d <- c(10,100,1000)
+sd(log10(d)) # 1
+logsd2cv(1) # 131.08\%
+}
+% 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