Removed some links to functions in other packages

NEWS.md

@@ -1,7 +1,9 @@
 # FSA 0.8.20 ongoing
+* Fixed a bunch of bad links to other packages in the documentation.
 * `addRadCap()`: Removed. Moved to `RFishBC` package.
 * `bcFuns()`: Removed. Moved to `RFishBC` package.
 * `gConvert()`: Removed. Moved to `RFishBC` package.
+* `mrClosed()`: Modified. Fixed a bug that was related to `poiCI()` returning results from all four types. Now `mrClosed()` will use only one type. Thanks to Timothy Spiers for pointing out this bug.
 * `SMBassWB`: Modified. Fixed minor data entry error in row 404. Changed link in documentation from `alr3` to `alr4` package.
 
 

R/CIDists.R

@@ -12,7 +12,7 @@
 #'
 #' Note that Agresti and Coull (2000) suggest that the Wilson interval is the preferred method and is, thus, the default \code{type}.
 #'
-#' @note This is primarily a wrapper function for \code{\link[epitools]{binom.exact}}, \code{\link[epitools]{binom.wilson}}, and \code{\link[epitools]{binom.approx}} from the \pkg{epitools} package.
+#' @note This is primarily a wrapper function for \code{binom.exact}, \code{binom.wilson}, and \code{binom.approx} (documented in \code{\link[epitools]{binom.conf.int}}) from the \pkg{epitools} package.
 #'
 #' @param x A single or vector of numbers that contains the number of observed successes.
 #' @param n A single or vector of numbers that contains the sample size.
@@ -24,7 +24,7 @@
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
-#' @seealso See \code{\link{binom.test}}; \code{binconf} in \pkg{Hmisc}; \code{\link[epitools]{binom.exact}}, \code{\link[epitools]{binom.wilson}}, and \code{\link[epitools]{binom.approx}} in \pkg{epitools}, and functions in \pkg{binom}.
+#' @seealso See \code{\link{binom.test}}; \code{binconf} in \pkg{Hmisc}; \code{binom.exact}, \code{binom.wilson}, and \code{binom.approx} documented in \code{\link[epitools]{binom.conf.int}} in \pkg{epitools}, and functions in \pkg{binom}.
 #'
 #' @references Agresti, A. and B.A. Coull.  1998.  Approximate is better than \dQuote{exact} for interval estimation of binomial proportions.  American Statistician, 52:119-126.
 #'
@@ -100,7 +100,7 @@ binCI <- function(x,n,conf.level=0.95,type=c("wilson","exact","asymptotic"),
 #'
 #' @description Computes a confidence interval for the Poisson counts.
 #'
-#' @details Computes a CI for the Poisson counts using the \code{exact}, gamma distribution (\code{daly}`), Byar's (\code{byar}), or normal approximation (\code{asymptotic}) methods.  This is largely a wrapper to \code{\link[epitools]{pois.exact}}, \code{\link[epitools]{pois.daly}}, \code{\link[epitools]{pois.byar}}, and \code{\link[epitools]{pois.approx}} functions in \pkg{epitools}.
+#' @details Computes a CI for the Poisson counts using the \code{exact}, gamma distribution (\code{daly}`), Byar's (\code{byar}), or normal approximation (\code{asymptotic}) methods.  This is largely a wrapper to \code{pois.exact}, \code{pois.daly}, \code{pois.byar}, and \code{pois.approx} functions documented in \code{\link[epitools]{pois.conf.int}}in \pkg{epitools}.
 #'
 #' @param x A single number or vector that represents the number of observed successes.
 #' @param conf.level A number that indicates the level of confidence to use for constructing confidence intervals (default is \code{0.95}).
@@ -111,7 +111,7 @@ binCI <- function(x,n,conf.level=0.95,type=c("wilson","exact","asymptotic"),
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
-#' @seealso See \code{\link[epitools]{pois.exact}}, \code{\link[epitools]{pois.daly}}, \code{\link[epitools]{pois.byar}}, and \code{\link[epitools]{pois.approx}} in \pkg{epitools} for more description and references.
+#' @seealso See \code{pois.exact}, \code{pois.daly}, \code{pois.byar}, and \code{pois.approx} (documented in \code{\link[epitools]{pois.conf.int}) in \pkg{epitools} for more description and references.
 #'
 #' @keywords htest
 #'

R/FSAUtils.R

@@ -1024,7 +1024,7 @@ validn <- function(object) {
 #' 
 #' @note This function is largely an implementation of the code suggested by Russell Senior on R-help in November, 1999.
 #' 
-#' @seealso See \code{\link[psych]{geometric.mean}} in \pkg{psych} and \code{\link[DescTools]{Gmean}} for geometric mean calculators. See \code{\link[DescTools]{Gsd}} for geometric standard deviation calculators.
+#' @seealso See \code{\link[psych]{geometric.mean}} in \pkg{psych} and \code{\link[DescTools]{Gmean}} for geometric mean calculators. See \code{Gsd} (documented with \code{\link[DescTools]{Gmean}}) from \pkg{DescTools} for geometric standard deviation calculators.
 #' 
 #' @keywords misc
 #' 

R/SMBassWB.R

@@ -43,7 +43,7 @@
 #'
 #' @source Data from the linear growth modeling software distributed in support of Weisberg, S. 1993. Using hard-part increment data to estimate age and environmental effects. Canadian Journal of Fisheries and Aquatic Sciences 50:1229-1237.
 #'
-#' @seealso See \code{\link[alr4]{wblake2}} from \pkg{alr4} for the same dataset with only the \code{agecap}, \code{lencap}, and \code{radcap} variables.
+#' @seealso See \code{\link[alr4]{wblake}} from \pkg{alr4} for the same dataset with only the \code{agecap}, \code{lencap}, and \code{radcap} variables.
 #' @keywords datasets
 #'
 #' @examples

R/Summarize.R

@@ -29,7 +29,7 @@
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
-#' @seealso See \code{\link[base]{summary}} for related one dimensional functionality. See \code{\link[base]{tapply}}, \code{\link[doBy]{summaryBy}} in \pkg{doBy}, \code{\link[psych]{describe}} in \pkg{psych}, \code{\link[prettyR]{describe}} in \pkg{prettyR}, and \code{\link[fBasics]{basicStats}} in \pkg{fBasics} for similar \dQuote{by} functionality.
+#' @seealso See \code{\link[base]{summary}} for related one dimensional functionality. See \code{\link[base]{tapply}}, \code{summaryBy} in \pkg{doBy}, \code{\link[psych]{describe}} in \pkg{psych}, \code{\link[prettyR]{describe}} in \pkg{prettyR}, and \code{basicStats} in \pkg{fBasics} for similar \dQuote{by} functionality.
 #'
 #' @keywords misc
 #'

R/bootstrap.R

@@ -44,7 +44,7 @@
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
-#' @seealso \code{\link[car]{bootCase}} in \pkg{car}.
+#' @seealso \code{\link[car]{Boot}} in \pkg{car}.
 #'
 #' @references S. Weisberg (2005). \emph{Applied Linear Regression}, third edition. New York: Wiley, Chapters 4 and 11.
 #' 
@@ -186,7 +186,7 @@ plot.bootCase <- function(x,...){ #nocov start
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
-#' @seealso \code{\link[car]{Boot}} and related methods in \pkg{car} and \code{\link[nlstools]{summary.nlsBoot}} in \pkg{nlstools}.
+#' @seealso \code{\link[car]{Boot}} and related methods in \pkg{car} and \code{summary.\link[nlstools]{nlsBoot}} in \pkg{nlstools}.
 #'
 #' @aliases confint.nlsboot htest.nlsboot predict.nlsbooot
 #'

R/capHistConvert.R

@@ -13,7 +13,7 @@
 #' 21 \tab 1 \tab 1 \tab 0 \tab 0 \cr
 #' }
 #'
-#' The \dQuote{frequency} format data.frame (this format is used in \code{\link[Rcapture:Rcapture-package]{Rcapture}}) has unique capture histories in separate columns, as in the \dQuote{individual} format, but also includes a column with the frequency of individuals that had the capture history of that row. It will not contain a fish identifier variable. The same data from above looks like:
+#' The \dQuote{frequency} format data.frame (this format is used in \pkg{Rcapture}) has unique capture histories in separate columns, as in the \dQuote{individual} format, but also includes a column with the frequency of individuals that had the capture history of that row. It will not contain a fish identifier variable. The same data from above looks like:
 #'
 #' \tabular{ccccc}{
 #' event1 \tab event2 \tab event3 \tab event4 \tab freq \cr
@@ -84,7 +84,7 @@
 #'
 #' @return A data frame of the proper type given in \code{out.type} is returned. See details.
 #'
-#' @note The formats as used here are simple in the sense that one is only allowed to have the individual fish identifier or the frequency variable in addition to the capture history information. More complex analyses may use a number of covariates. For these more complex analyses, one should work directly with the \code{\link[Rcapture:Rcapture-package]{Rcapture}}, \code{\link[RMark:ABeginnersGuide]{RMark}}, or \pkg{marked} packages.
+#' @note The formats as used here are simple in the sense that one is only allowed to have the individual fish identifier or the frequency variable in addition to the capture history information. More complex analyses may use a number of covariates. For these more complex analyses, one should work directly with the \pkg{Rcapture}, \code{\link[RMark:ABeginnersGuide]{RMark}}, or \pkg{marked} packages.
 #' 
 #' This function also assumes that all unmarked captured fish are marked and returned to the population (i.e., no losses at the time of marking are allowed).
 #' 
@@ -94,7 +94,7 @@
 #'
 #' @section IFAR Chapter: 9-Abundance from Capture-Recapture Data.
 #'
-#' @seealso See \code{\link{capHistSum}} to summarize \dQuote{individual} capture histories into a format usable in \code{\link{mrClosed}} and \code{\link{mrOpen}}. Also see \code{\link[Rcapture:Rcapture-package]{Rcapture}}, \code{\link[RMark:ABeginnersGuide]{RMark}}, or \pkg{marked} packages for handling more complex analyses.
+#' @seealso See \code{\link{capHistSum}} to summarize \dQuote{individual} capture histories into a format usable in \code{\link{mrClosed}} and \code{\link{mrOpen}}. Also see \pkg{Rcapture}, \code{\link[RMark:ABeginnersGuide]{RMark}}, or \pkg{marked} packages for handling more complex analyses.
 #' 
 #' @references Ogle, D.H. 2016. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
 #' 

R/comparisonsDVR.R

@@ -2,10 +2,10 @@
 #'
 #' @description Tests for significant differences among all pairs of slopes in a dummy variable regression where the dummy variables all stem from one factor.
 #'
-#' @details In a dummy variable regression the coefficient for the interaction between the covariate (x) and a dummy variable tests for a difference in slopes between the level of the dummy variable and the reference level. Thus, all dummy variables from a particular linear model fit only compare slopes with the reference level. Other slope comparisons may be found by changing the reference level, which requires refitting the model. This function automates this sequential process and produces a data.frame that shows the estimated difference, an unadjusted confidence interval for the difference, and the unadjusted and adjusted (for multiple comparisons) p-values for testing that the difference in slopes is equal to zero for each pair of levels. The adjusted p-values may be computed with any of the methods coded in \code{\link[stats]{p.adjust}} (see \code{\link[stats]{p.adjust.methods}}).
+#' @details In a dummy variable regression the coefficient for the interaction between the covariate (x) and a dummy variable tests for a difference in slopes between the level of the dummy variable and the reference level. Thus, all dummy variables from a particular linear model fit only compare slopes with the reference level. Other slope comparisons may be found by changing the reference level, which requires refitting the model. This function automates this sequential process and produces a data.frame that shows the estimated difference, an unadjusted confidence interval for the difference, and the unadjusted and adjusted (for multiple comparisons) p-values for testing that the difference in slopes is equal to zero for each pair of levels. The adjusted p-values may be computed with any of the methods coded in \code{\link[stats]{p.adjust}} (see \code{p.adjust.methods} there).
 #' 
 #' @param mdl A \code{lm} object.
-#' @param method A string indicating the method of p-value adjustment to use. See details and \code{\link[stats]{p.adjust.methods}}.
+#' @param method A string indicating the method of p-value adjustment to use. See details and \code{p.adjust.methods} (documented in \code{\link[stats]{p.adjust}}.
 #' @param conf.level A single number that represents the level of confidence to use for constructing confidence intervals.
 #' @param x A \code{compSlopes} object (i.e., returned from \code{compSlopes}).
 #' @param order.slopes A logical indicating whether the slopes should be ordered from smallest to largest upon output.

R/dunnTest.R

@@ -2,7 +2,7 @@
 #'
 #' @description Performs Dunn's (1964) test of multiple comparisons following a significant Kruskal-Wallis test, possibly with a correction to control the experimentwise error rate. This is largely a wrapper for the \code{\link[dunn.test]{dunn.test}} function in \pkg{dunn.test}. Please see and cite that package.
 #' 
-#' @details This function performs \dQuote{Dunn's} test of multiple comparisons following a Kruskal-Wallis test. Unadjusted one- or two-sided p-values for each pairwise comparison among groups are computed following Dunn's description as implemented in the \code{\link[dunn.test]{dunn.test}} function from \pkg{dunn.test}. These p-values may be adjusted using methods in the \code{\link[dunn.test]{p.adjustment.methods}} function in \pkg{dunn.test}.
+#' @details This function performs \dQuote{Dunn's} test of multiple comparisons following a Kruskal-Wallis test. Unadjusted one- or two-sided p-values for each pairwise comparison among groups are computed following Dunn's description as implemented in the \code{\link[dunn.test]{dunn.test}} function from \pkg{dunn.test}. These p-values may be adjusted using methods in the \code{p.adjustment.methods} function in \pkg{dunn.test}.
 #'
 #' This function is largely a wrapper for the \code{\link[dunn.test]{dunn.test}} function in \pkg{dunn.test}. Changes here are the possible use of formula notation, results not printed by the main function (but are printed in a more useful format (in my opinion) by the \code{print} function), the p-values are adjusted by default with the \dQuote{holm} method, and two-sided p-values are returned by default. See \code{\link[dunn.test]{dunn.test}} function in \pkg{dunn.test} for a more details underlying these computations.
 #' 
@@ -25,7 +25,7 @@
 #' @param x A numeric vector of data values or a formula of the form x~g.
 #' @param g A factor vector or a (non-numeric) vector that can be coerced to a factor vector.
 #' @param data A data.frame that minimally contains \code{x} and \code{g}.
-#' @param method A single string that identifies the method used to control the experimentwise error rate. See the list of methods in \code{\link[dunn.test]{p.adjustment.methods}} in \pkg{dunn.test}.
+#' @param method A single string that identifies the method used to control the experimentwise error rate. See the list of methods in \code{p.adjustment.methods} (documented with \code{\link[dunn.test]{dunn.test}}) in \pkg{dunn.test}.
 #' @param two.sided A single logical that indicates whether a two-sided p-value should be returned (\code{TRUE}; default) or not. See details.
 #' @param altp Same as \code{two.sided}. Allows similar code with the \code{\link[dunn.test]{dunn.test}} function in \pkg{dunn.test}. \code{two.sided} is maintained because it pre-dates \code{altp}.
 #' @param dunn.test.results A single logical that indicates whether the results that would have been printed by \code{\link[dunn.test]{dunn.test}} function in \pkg{dunn.test} are shown.

R/knitUtil.R

@@ -40,13 +40,13 @@
 #'  \itemize{
 #'    \item \code{kCounts} returns a numeric value if the count is less than zero or greater than ten and returns a character string of the number \sQuote{name}. See the examples.
 #'    \item \code{kPvalue} returns a character string of the supplied p-value rounded to the requested number of digits or a character string that indicates what the p-value is less than the value with a \sQuote{5} in the \code{digits}+1 place. See the examples. 
-#'    \item \code{purl2} is a modification of \code{\link[knitr]{purl}} from \pkg{knitr} that creates a file with the same name as \code{file} but with lines removed that contain certain words (those found in \code{ItemsToRemove} and \code{moreItems}). 
+#'    \item \code{purl2} is a modification of \code{purl} from \pkg{knitr} that creates a file with the same name as \code{file} but with lines removed that contain certain words (those found in \code{ItemsToRemove} and \code{moreItems}). 
 #'    \item \code{reproInfo} returns Markdown, LaTeX, or R code that prints \dQuote{reproducibility information} at the bottom of the knitted document.
 #'  }
 #'
 #' @author Derek H. Ogle, \email{derek@@derekogle.com}
 #'
-#' @seealso See \code{\link{formatC}} for functionality similar to \code{kPvalue}. See \code{\link[knitr]{purl}} and \code{\link[knitr]{knit}} in \pkg{knitr} for functionality similar to \code{purl2}.
+#' @seealso See \code{\link{formatC}} for functionality similar to \code{kPvalue}. See \code{purl} and \code{\link[knitr]{knit}} in \pkg{knitr} for functionality similar to \code{purl2}.
 #'
 #' @keywords manip
 #'