Merge pull request #55 from philsf/release-0.6.3

Release 0.6.3

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: philsfmisc
 Type: Package
 Title: philsf's miscellaneous R functions
-Version: 0.6.2
+Version: 0.6.3
 Authors@R: person("Felipe", "Figueiredo", email = "[email protected]", role = c("aut", "cre"))
 Description: Miscellaneous R functions for convenient data analyses.
 License: file LICENSE
@@ -10,3 +10,5 @@ LazyData: true
 URL: https://github.com/philsf/philsfmisc
 Depends: R (>= 3.3.0)
 RoxygenNote: 6.1.0
+Imports: 
+    stringr

NAMESPACE

@@ -14,3 +14,4 @@ export(logvar2cv)
 export(predint)
 importFrom(stats,qt)
 importFrom(stats,sd)
+importFrom(stringr,str_remove)

NEWS.md

@@ -1,3 +1,10 @@
+# philsfmisc 0.6.3
+
+- Revert the default of pct.symbol to FALSE (#49)
+- Percentage intervals are now correctly formatted (#35, #53)
+  - adds depencency: stringr
+- All functions now have description and details sections (#33)
+
 # philsfmisc 0.6.2
 
 - Now uses `roxygen2` for function documentation creation ( #37 )

R/cv2logsd.R

@@ -1,6 +1,8 @@
-#' Convert the CV from a log-normal variable to the log-transformed standard deviation.
+#' Convert the CV to the log10 sd (log-normal variable).
 #'
-#' @description
+#' \code{cv2logsd} converts the CV from a log-normal variable to the log10-transformed standard deviation.
+#'
+#' This function converts the CV to the log10-transformed standard deviation, by taking the square root of \code{cv2logvar}.
 #'
 #' @param x A numeric value, vector or list.
 #'

R/cv2logvar.R

@@ -1,6 +1,8 @@
-#' Convert the CV from a log-normal variable to the log-transformed variance.
+#' Convert the CV to the log10 var (log-normal variable).
 #'
-#' @description
+#' \code{cv2logsd} converts the CV from a log-normal variable to the log10-transformed variance.
+#'
+#' This function converts the CV to the log10-transformed variance by inverting the formula used in \code{logvar2cv}.
 #'
 #' @param x A numeric value, vector or list.
 #'

R/format.float.R

@@ -1,7 +1,10 @@
 #' Format numbers for printing
 #'
-#' @description Format numbers, given a `digits` argument as significant decimal places.
+#' \code{format.float} prepares numbers for results printing.
+#'
+#' This function formats numbers with the given number of decimal digits.
 #'   Numbers are always assumed to be \code{\link[base]{double}}.
+#'   If there is a percent sign in \code{x}, it is removed prior to formatting.
 #'
 #' @param x Value to be formatted.
 #'   Input can be a numeric or character value.
@@ -18,15 +21,20 @@
 #' # Input is character
 #' format.float("1.12543")
 #' format.float(c("1.756", "1.823"))
+#' # Input is percentage
+#' format.float("10%", 1)
+#' format.float("15 %", 1)
 #'
 #' # 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
+#' @importFrom stringr str_remove
 #' @export format.float
 
 format.float <- function(x, digits = 2) {
+  x <- stringr::str_remove(x, "%")
   x <- suppressWarnings(as.numeric(x))
   x <- formatC(x, format = "f", digits = digits)
   x

R/format.interval.R

@@ -1,6 +1,10 @@
 #' Format intervals for printing
 #'
-#' @description Format intervals, given a `digits` argument as significant decimal places.
+#' \code{format.interval} prepares intervals for results printing.
+#'
+#' This function formats a given interval with the given number of decimal digits.
+#'   \code{interval} is always assumed to be a two valued vector of \code{\link[base]{double}}.
+#'   If there is a percent sign in any of \code{interval} values, it is removed prior to formatting by \code{format.float}.
 #'
 #' @param interval Must be a vector of two values.
 #'   Values can be either numeric or character.
@@ -16,6 +20,9 @@
 #' # Input is character
 #' format.interval(c("1.756", "1.823"))
 #'
+#' # Input is percentage
+#' format.interval(c("10%", "15%"), 1)
+#'
 #' @author Felipe Figueiredo
 #' @export format.interval
 

R/format.pct.R

@@ -1,6 +1,9 @@
-#' Convenience function to format proportions as percentages
+#' Format proportions as percentages for printing
 #'
-#' @description
+#' \code{format.pct} prepares proportions as percentages for results printing, possibly with a percent sign.
+#'
+#' This function multiplies the proportion by 100, formats with the given number of decimal digits.
+#' It also (optionally) includes a percent sign.
 #'
 #' @param p a numeric vector assumed to be a proportion.
 #' @param digits the number of decimal digits to be used in the output.
@@ -20,7 +23,7 @@
 #' @author Felipe Figueiredo
 #' @export format.pct
 
-format.pct <- function(p, digits = 1, pct.symbol = FALSE) {
+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

@@ -1,6 +1,9 @@
 #' Compute the CV of log-normally distributed data.
 #'
-#' @description
+#' \code{geocv} computes the CV of log-normal data.
+#'
+#' This function first log10-transforms the original data \code{x}.
+#' It then passes the standard deviation of the result to \code{logsd2cv}.
 #'
 #' @param x A numeric value, vector or list.
 #' @param na.rm (logical) whether or not to remove \code{NA} values from computation

R/geomean.R

@@ -1,6 +1,9 @@
 #' Compute the geometric mean
 #'
-#' @description
+#' \code{geomean} computes the anti-log of the \code{mean} of log10-transformed data.
+#'
+#' This function first log10-transforms the original data \code{x}.
+#' It then back-transforms the \code{mean} of the results from the log10 scale.
 #'
 #' @param x A numeric value, vector or list.
 #'

R/geosd.R

@@ -1,7 +1,9 @@
-#' Compute the "geometric standard deviation" of data
+#' Compute the "geometric standard deviation" of log-normal 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.
+#' \code{geosd} computes the anti-log of the standard deviation of log10-transformed data.
+#'
+#' The "geometric standard deviation" is not as well-defined as the geometric mean.
+#' Here we apply the analogous concept of the geometric mean to the \code{sd}.
 #'
 #' @param x A numeric value, vector or list.
 #'

R/is.within.R

@@ -1,9 +1,11 @@
-#' Check if number is within given interval
+#' Test if number is within given interval
 #'
-#' @description
+#' \code{is.within} tests if object \code{x} is within \code{interval}.
 #'
-#' @param value A numeric value, vector or list.
-#' @param interval The (numeric) interval within which \code{value} is being tested.
+#' This function tests if the given value is contained within a (possibly open) given interval.
+#'
+#' @param x A numeric x, vector or list.
+#' @param interval The (numeric) interval within which \code{x} 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
@@ -19,7 +21,7 @@
 #' @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]
+is.within <- function(x, interval, open.interval = FALSE) {
+  if (open.interval) return( x > interval[1] & x < interval[2] )
+  x >= interval[1] & x <= interval[2]
 }

R/logsd2cv.R

@@ -1,8 +1,11 @@
-#' Convert the log-transformed standard deviation from a log-normal variable to the CV.
+#' Convert the log10 standard deviation to the CV (log-normal variable).
 #'
-#' @description
+#' \code{logsd2cv} the log10-transformed \code{sd} from a log-normal variable to the CV.
 #'
-#' @param x A numeric value, vector or list.
+#' This function converts the log10-transformed standard deviation of a log-normal variable to the CV.
+#'
+#' @param x The log10-transformed \code{sd} of data.
+#'   A numeric value, vector or list.
 #'
 #' @return Returns the geometric CV (as percentage)
 #'

R/logvar2cv.R

@@ -1,8 +1,11 @@
-#' Convert the log-transformed variance from a log-normal variable to the CV.
+#' Convert the log10 variance to the CV (log-normal variable).
 #'
-#' @description
+#' \code{logvar2cv} converts the log10-transformed \code{var} of a log-normal variable to the CV.
 #'
-#' @param x A numeric value, vector or list.
+#' This function converts the log10-transformed variance of a log-normal variable to the CV.
+#'
+#' @param x The log10-transformed \code{var} of data.
+#'   A numeric value, vector or list.
 #'
 #' @return Returns the geometric CV (as percentage)
 #'

R/predint.R

@@ -1,6 +1,8 @@
 #' Prediction Intervals for given data
 #'
-#' @description Compute a prediction interval of a vector, which is assumed
+#' \code{predint} computes a prediction interval of Normal data.
+#'
+#' This function computes a prediction interval of a vector, which is assumed
 #'  normally distributed with unknown mean and variance.
 #'
 #' @param datavector A numeric value, vector or list.