fix empty documentation of some arguments

.gitignore

@@ -26,3 +26,7 @@ vignettes/*.pdf
 /.svn
 .Rproj.user
 *.Rproj
+# twutz 2401
+/tmp/
+/tests/testthat/Rplots.pdf
+

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: logitnorm
 Title: Functions for the Logitnormal Distribution
-Version: 0.8.38
+Version: 0.8.39
 Author: Thomas Wutzler
 Maintainer: Thomas Wutzler <[email protected]>
 Description: Density, distribution, quantile and random generation function for the logitnormal distribution. Estimation of the mode and the first two moments. Estimation of distribution parameters.

NEWS.md

@@ -1,26 +1,29 @@
-# logitnorm 0.8.38
-- Reworked twCoefLogitnormMLEFlat
+# version 0.8.39
+fix empty documentation of some arguments
+
+# version 0.8.38
+- Reworked twCoefversionMLEFlat
 - Migrated from RUnit to testthat
 
-# logitnorm 0.8.37
+# version 0.8.37
 
 - Density returns 0 instead of NAN outside (0,1)
-- Changed first argument name of dlogitnorm from q to x
-- Document argument n of rlogitnorm
+- Changed first argument name of dversion from q to x
+- Document argument n of rversion
 
-# logitnorm 0.8.36
+# version 0.8.36
 Remove the library call to MASS.
 
-# logitnorm 0.8.35
+# version 0.8.35
 Avoid writing file reports during testing and installation.
 
-# logitnorm 0.8.33
+# version 0.8.33
 
 ## New features
 
 ### density on log-scale 
 
-Thanks to @madeleine-empirical the density function `dlogitnorm` now has `log` an argument that allows computing the density directly at log-scale.
+Thanks to @madeleine-empirical the density function `dversion` now has `log` an argument that allows computing the density directly at log-scale.
 
 
 ## Further changes

R/logitnorm.R

@@ -5,7 +5,8 @@
 
 logit <- function(
   ### Transforming (0,1) to normal scale (-Inf Inf)
-  p,...
+  p      ##<< percentile
+  ,...   ##<< further arguments to qlogis
 ){ 
   ##details<<
   ## function \eqn{logit(p) = log \left( \frac{p}{1-p} \right) = log(p) - log(1-p)}
@@ -16,7 +17,8 @@ logit <- function(
 
 invlogit <- function(
   ### Transforming (-Inf,Inf) to original scale (0,1)
-  q,...
+  q,   ##<< quantile
+  ...  ##<< further arguments to plogis
 ){
   ##details<<
   ## function \eqn{f(z) = \frac{e^{z}}{e^{z} + 1} \! = \frac{1}{1 + e^{-z}} \!}
@@ -42,8 +44,9 @@ rlogitnorm <- function(
 plogitnorm <- function(
   ### Distribution function for logitnormal distribution	
   q  ##<< vector of quantiles
-  , mu = 0, sigma = 1	##<< distribution parameters
-  , ...
+  , mu = 0    ##<< location distribution parameter
+  , sigma = 1	##<< scale distribution parameter
+  , ...       ##<< further arguments to pnorm
 ){
   ##seealso<< \code{\link{logitnorm}}
   ql <- qlogis(q)
@@ -54,7 +57,8 @@ plogitnorm <- function(
 dlogitnorm <- function(
   ### Density function of logitnormal distribution	
   x		##<< vector of quantiles
-  , mu = 0, sigma = 1	##<< distribution parameters
+  , mu = 0         ##<< scale distribution parameter
+  , sigma = 1	     ##<< location distribution parameter
   , log = FALSE    ##<< if TRUE, the log-density is returned
   , ...	##<< further arguments passed to \code{\link{dnorm}}: \code{mean}, 
   ## and \code{sd} for mu and sigma respectively.  
@@ -89,8 +93,9 @@ dlogitnorm <- function(
 qlogitnorm <- function(
   ### Quantiles of logitnormal distribution.	
   p ##<< vector of probabilities
-  , mu = 0, sigma = 1	##<< distribution parameters
-  , ...
+  , mu = 0    ##<< location distribution parameter
+  , sigma = 1	##<< scale distribution parameter
+  , ...       ##<< further arguments to plogis
 ){
   ##seealso<< \code{\link{logitnorm}}
   qn <- qnorm(p,mean = mu,sd = sigma,...)
@@ -166,7 +171,6 @@ twCoefLogitnorm <- function(
   median					##<< numeric vector: the median of the density function
   , quant					##<< numeric vector: the upper quantile value
   , perc = 0.975				##<< numeric vector: the probability for which the quantile was specified
-  , ... 
 ){
   ##seealso<< \code{\link{logitnorm}}
   # twCoefLogitnorm
@@ -397,7 +401,7 @@ twCoefLogitnormE <- function(
   , theta0 = c(mu = 0,sigma = 1)	##<< starting parameters
   , returnDetails = FALSE	##<< if TRUE, the full output of optim is returned 
   ## with attribute resOptim
-  , ... 
+  , ...                   ##<< further arguments to optim
 ){
   ##seealso<< \code{\link{logitnorm}}
   # twCoefLogitnormE

cran-comments.md

@@ -1,11 +1,9 @@
 ## Note
-Added random seeds to tests to avoid accidental failing,
-and markdown dependency to Suggests.
+Fixed empty Rd comments for some arguments.
 
 ## Test environments
-* local R 4.0.3 on Mint 20 64bit
+* local R 4.3.2 on Mint 21.2 64bit
 * r-hub.io
-* winbuilder
 
 ## R CMD check results
 There were no ERRORs nor WARNINGs nor NOTEs

inst/WORDLIST

@@ -0,0 +1,36 @@
+Logitnormal
+README
+RUnit
+Rmd
+dlogitnorm
+dversion
+github
+invlogit
+logitnormal
+md
+mle
+modeLogitnorm
+momentsLogitnorm
+optim
+perc
+plogis
+plogitnorm
+pnorm
+precisions
+qlogis
+qlogitnorm
+quant
+resOptim
+rlogitnorm
+rversion
+sigmaFac
+testthat
+twCoefLogitnorm
+twCoefLogitnormCi
+twCoefLogitnormE
+twCoefLogitnormMLE
+twCoefLogitnormMLEFlat
+twCoefLogitnormN
+twCoefversionMLEFlat
+twSigmaLogitnorm
+vectorized

man/dlogitnorm.Rd

@@ -6,9 +6,8 @@
     ...)}
 \arguments{
   \item{x}{vector of quantiles}
-  \item{mu}{distribution parameters}
-  \item{sigma}{
-}
+  \item{mu}{scale distribution parameter}
+  \item{sigma}{location distribution parameter}
   \item{log}{if TRUE, the log-density is returned}
   \item{\dots}{further arguments passed to \code{\link{dnorm}}: \code{mean},
 and \code{sd} for mu and sigma respectively.  }

man/invlogit.Rd

@@ -4,10 +4,8 @@
 \description{Transforming (-Inf,Inf) to original scale (0,1)}
 \usage{invlogit(q, ...)}
 \arguments{
-  \item{q}{
-}
-  \item{\dots}{
-}
+  \item{q}{quantile}
+  \item{\dots}{further arguments to plogis}
 }
 \details{function \eqn{f(z) = \frac{e^{z}}{e^{z} + 1} \! = \frac{1}{1 + e^{-z}} \!}}
 

man/logit.Rd

@@ -4,10 +4,8 @@
 \description{Transforming (0,1) to normal scale (-Inf Inf)}
 \usage{logit(p, ...)}
 \arguments{
-  \item{p}{
-}
-  \item{\dots}{
-}
+  \item{p}{percentile}
+  \item{\dots}{further arguments to qlogis}
 }
 \details{function \eqn{logit(p) = log \left( \frac{p}{1-p} \right) = log(p) - log(1-p)}}
 

man/plogitnorm.Rd

@@ -5,11 +5,9 @@
 \usage{plogitnorm(q, mu = 0, sigma = 1, ...)}
 \arguments{
   \item{q}{vector of quantiles}
-  \item{mu}{distribution parameters}
-  \item{sigma}{
-}
-  \item{\dots}{
-}
+  \item{mu}{location distribution parameter}
+  \item{sigma}{scale distribution parameter}
+  \item{\dots}{further arguments to pnorm}
 }
 
 

man/qlogitnorm.Rd

@@ -5,11 +5,9 @@
 \usage{qlogitnorm(p, mu = 0, sigma = 1, ...)}
 \arguments{
   \item{p}{vector of probabilities}
-  \item{mu}{distribution parameters}
-  \item{sigma}{
-}
-  \item{\dots}{
-}
+  \item{mu}{location distribution parameter}
+  \item{sigma}{scale distribution parameter}
+  \item{\dots}{further arguments to plogis}
 }
 
 

man/twCoefLogitnorm.Rd

@@ -2,14 +2,11 @@
 \alias{twCoefLogitnorm}
 \title{twCoefLogitnorm}
 \description{Estimating coefficients of logitnormal distribution from median and upper quantile	}
-\usage{twCoefLogitnorm(median, quant, perc = 0.975, 
-    ...)}
+\usage{twCoefLogitnorm(median, quant, perc = 0.975)}
 \arguments{
   \item{median}{numeric vector: the median of the density function}
   \item{quant}{numeric vector: the upper quantile value}
   \item{perc}{numeric vector: the probability for which the quantile was specified}
-  \item{\dots}{
-}
 }
 
 \value{numeric matrix with columns \code{c("mu","sigma")}

man/twCoefLogitnormE.Rd

@@ -14,8 +14,7 @@ specified}
   \item{theta0}{starting parameters}
   \item{returnDetails}{if TRUE, the full output of optim is returned
 with attribute resOptim}
-  \item{\dots}{
-}
+  \item{\dots}{further arguments to optim}
 }
 
 \value{named numeric matrix with estimated parameters of the logitnormal