For submission to CRAN

R/comparators.R

@@ -24,9 +24,9 @@
 #' (\code{TRUE}/\code{FALSE} or \code{1}/\code{0}) result. The result should 
 #' not contain missing values. 
 #' 
-#' The `jaro_winkler`, `lcs` and `jaccard` functions use the corresponding 
+#' The \code{jaro_winkler}, \code{lcs} and \code{jaccard} functions use the corresponding 
 #' methods from \code{\link{stringdist}} except that they are transformed from
-#' a distnce to a similarity score.
+#' a distance to a similarity score.
 #' 
 #' @return 
 #' The functions return a comparison function (see details).

R/data.R

@@ -4,13 +4,13 @@
 #' Contains fictional records of 7 persons.
 #'
 #' \itemize{
-#'   \item id the id of the person; this contains no errors and can be used to 
+#'   \item \code{id} the id of the person; this contains no errors and can be used to 
 #'     validate the linkage. 
-#'   \item lastname the lastname of the person; contains errors.
-#'   \item firstname the firstname of the persons; contains errors.
-#'   \item address the address; contains errors.
-#'   \item sex the sex; contains errors and missing values.
-#'   \item postcode the postcode; contains no errors. 
+#'   \item \code{lastname} the last name of the person; contains errors.
+#'   \item \code{firstname} the first name of the persons; contains errors.
+#'   \item \code{address} the address; contains errors.
+#'   \item \code{sex} the sex; contains errors and missing values.
+#'   \item \code{postcode} the postcode; contains no errors. 
 #' }
 #'
 #' @docType data

R/filter_pairs_for_deduplication.R

@@ -4,7 +4,7 @@
 #' 
 #' In case of deduplication one tries to link a data set to itself. Therefore, 
 #' comparisons only have to be made for records for which the index of the
-#' records from the first data set is larger than the index fron the record from
+#' records from the first data set is larger than the index from the record from
 #' the second data set. 
 #' 
 #' @param pairs a \code{pairs} object, such as generated by 

R/pair_blocking.R

@@ -22,7 +22,7 @@
 #' @return 
 #' When \code{large} is \code{FALSE}, a \code{data.frame} with two columns, 
 #' \code{x} and \code{y}, is returned. Columns \code{x} and \code{y} are 
-#' rownumbers from \code{data.frame}s \code{x} and \code{y} respectively. 
+#' row numbers from \code{data.frame}s \code{x} and \code{y} respectively. 
 #' When \code{large} is \code{TRUE}, an object of type \code{ldat} is returned. 
 #'
 #' @examples

R/predict_problink_em.R

@@ -1,12 +1,12 @@
 
 #' Calculate weights and probabilities for pairs
 #' 
-#' @param object an object of type `problink_em` as produced by 
+#' @param object an object of type \code{problink_em} as produced by 
 #'   \code{\link{problink_em}}.
 #' @param pairs a object with pairs for which to calculate weights.
-#' @param newdata an alternative name for the `pairs` argument. Specify 
-#'   `newdata` or `pairs`. 
-#' @param type a character vector of length one speicifying what to calculate. 
+#' @param newdata an alternative name for the \code{pairs} argument. Specify 
+#'   \code{newdata} or \code{pairs}. 
+#' @param type a character vector of length one specifying what to calculate. 
 #'   See results for more information.
 #' @param binary convert comparison vectors to binary vectors using the 
 #'   comparison function in comparators. 
@@ -15,12 +15,12 @@
 #' @param ... unused.
 #'   
 #' @return 
-#' In case of `type == "weights"` returns a vector (\code{\link{lvec}} or
-#' regular R-vector depending on the type of `pairs`). with the linkage weights. 
-#' In case of `type == "mpost"` returns a vector with the posterior m-probabilities
-#' (probability that a pair is a match). In case of `type == "probs"` returns a
+#' In case of \code{type == "weights"} returns a vector (\code{\link{lvec}} or
+#' regular R-vector depending on the type of \code{pairs}). with the linkage weights. 
+#' In case of \code{type == "mpost"} returns a vector with the posterior m-probabilities
+#' (probability that a pair is a match). In case of \code{type == "probs"} returns a
 #' data.frame or \code{\link{ldat}} with the m- and u-probabilities and posterior
-#' m- and u probabilities. In case `type == "all"` returns a `data.frame` or 
+#' m- and u probabilities. In case \code{type == "all"} returns a \code{data.frame} or 
 #' \code{\link{ldat}} with both probabilities and weights. 
 #' 
 #' @import ldat

R/problink_em.R

@@ -9,7 +9,7 @@
 #'   should be lists with numeric values. The names of the elements in the list
 #'   should correspond to the names in \code{by_x} in \code{\link{compare_pairs}}. 
 #' @param p0 the initial estimate of the probability that a pair is a match.
-#' @param tol when the change in the m and u-probabilities is smaller than tol
+#' @param tol when the change in the m and u-probabilities is smaller than \code{tol}
 #'   the algorithm is stopped. 
 #'   
 #' @return 

R/score_problink.R

@@ -18,7 +18,7 @@
 #' \code{...} argument that causes the calculation of multiple scores (such
 #' are \code{type = "all"}). In that case the text given by \code{var} is 
 #' prepended to the names of the variables returned by 
-#' \code{\link{predict.problink_em}} (with a seperator '\code{_}'). 
+#' \code{\link{predict.problink_em}} (with a separator '\code{_}'). 
 #' 
 #' When \code{add = FALSE} the scores are returned as is. 
 #' 

cran-comments.md

@@ -4,14 +4,17 @@ This is a new package.
 
 ## Test environments
 * local ubuntu 18.04 install, R 3.4.4
+* local ubuntu 18.04 install, R 3.4.4 + valgrind
 * R-devel on windows using the R-builder
 * R with valgrind and sanitizers on rhub
 * R-devel on rhub
 
 
 ## R CMD check results
 
-0 errors | 0 warnings | 0 notes
+0 errors | 0 warnings | 1 notes
+
+1 note because it is a new package
 
 
 ## Reverse dependencies

vignettes/deduplication.Rmd

@@ -4,7 +4,7 @@ author: "Jan van der Laan"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteIndexEntry{Deduplication using reclin}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

vignettes/introduction_to_reclin.Rmd

@@ -4,7 +4,7 @@ author: "Jan van der Laan"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteIndexEntry{Introduction to reclin}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---