Merge pull request #7 from metrumresearchgroup/release/0.2.0

Release/0.2.0

.Rbuildignore

@@ -1,3 +1,4 @@
+_pkgdown\.yml
 Makefile
 ^test\.R$
 ^.*\.Rproj$

.gitignore

@@ -1,3 +1,4 @@
+.DS_Store
 README.html
 lastdose.Rcheck
 lastdose*.tar.gz

DESCRIPTION

@@ -1,15 +1,17 @@
 Package: lastdose
 Type: Package
 Title: Calculate Time and Amount of Last Dose
-Version: 0.1.0
-Author: Kyle Baron
-Maintainer: Kyle Baron <kylebtwin@imap.cc>
+Version: 0.2.0
+Authors@R: c(
+    person("Kyle T", "Baron", email = "kyleb@metrumrg.com", role=c("aut", "cre"), comment=c(ORCID="0000-0001-7252-5656"))
+    )
+Maintainer: Kyle T Baron  <kyleb@metrumrg.com>
 Description: Efficient calculation of time after last dose and last dose amount
     for analysis data sets.
 License: GPL (>=2)
 LinkingTo: Rcpp
-URL: https://github.com/kylebaron/lastdose
-BugReports: https://github.com/kylebaron/lastdose/issues
+URL: https://github.com/metrumresearchgroup/lastdose
+BugReports: https://github.com/metrumresearchgroup/lastdose/issues
 Suggests: testthat, Rcpp
 Encoding: UTF-8
 LazyData: true

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(find_comments,character)
+S3method(find_comments,data.frame)
+export(find_comments)
 export(lastdose)
 export(lastdose_df)
 export(lastdose_list)

NEWS.md

@@ -1,4 +1,9 @@
 
+# lastdose 0.2.0
+- Commented records are not considered when looking for doses in the data set, 
+  but `TAD` and `LDOS` are filled like any other observation record (relative
+  to the last non-commented dose) #9
+
 # lastdose 0.1.0
 
 - Update git origin

R/RcppExports.R

@@ -1,7 +1,7 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-lastdose_impl <- function(id, time, amt, evid, addl, ii, fill, back_calc, sort1) {
-    .Call(`_lastdose_lastdose_impl`, id, time, amt, evid, addl, ii, fill, back_calc, sort1)
+lastdose_impl <- function(id, time, amt, evid, addl, ii, fill, back_calc, sort1, comment) {
+    .Call(`_lastdose_lastdose_impl`, id, time, amt, evid, addl, ii, fill, back_calc, sort1, comment)
 }
 

R/lastdose.R

@@ -4,9 +4,9 @@ NULL
 
 #' Calculate last dose amount (LDOS) and time after last dose (TAD)
 #'
-#' Use [lastdose] to columns to the input data frame; [lastdose_list]
-#' and [lastdose_df] returns calculated information as either
-#' `list` or `data.frame` format without modifying the input data.
+#' Use [lastdose] to add (or potentially replace) columns to the input
+#' data frame; [lastdose_list] and [lastdose_df] returns calculated information
+#' as either `list` or `data.frame` format without modifying the input data.
 #'
 #' @param data data set as data frame; see `details`
 #' @param back_calc if `TRUE`, then the time before the first dose
@@ -21,12 +21,32 @@ NULL
 #' concentration; if `dose_first` then the dose is assumed to be administered
 #' and the observation made immediately after (with no advance in time). See
 #' details.
+#' @param comments a logcial vector with length equal to the number of rows
+#' in `data` indicating which records are to be ignored when looking for `TAD`
+#' and `LDOS`.  See all the `fill_comments_na` argument.
 #' @param ... arguments passed to [lastdose_list]
 #' @param include_ldos `logical`; if `FALSE` then the `LDOS` data is not
 #' appended to the data set.  Only used for the [lastdose] function.
 #'
 #' @details
 #'
+#' When calling [lastdose] to modify the data frame, two columns will be
+#' added (by default): `TAD` indicating the time after the most-recent dose
+#' and `LDOS` indicating the amount of the most recent dose.  This default
+#' behavior can be modified with the `include_ldos` argument.
+#'
+#' When calling [lastdose_list] or [lastdose_df], the respective items are
+#' accessible with `tad` and `ldos` (note the lower case form here to
+#' distinguish from the columns that might be added to the data frame).
+#'
+#' **Handling of commented records**: Dosing records that have been "commented"
+#' (as indicated with the `comments` argument) will never be considered as
+#' actual doses when determining `TAD` and `LDOS`.  But commented records (doses
+#' and non-doses) will be assigned `TAD` and `LDOS` according to the last
+#' non-commented dosing record.
+#'
+#' **Additional notes**:
+#'
 #' - All functions require an input data set as a data frame
 #' - The data set should be formatted according to `NMTRAN` type
 #'   conventions
@@ -78,7 +98,14 @@ lastdose <- function(data,..., include_ldos = TRUE) {
 #' @rdname lastdose
 #' @export
 lastdose_list <- function(data, fill = -99, back_calc = TRUE,
-                          addl_ties = c("obs_first", "dose_first")) {
+                          addl_ties = c("obs_first", "dose_first"),
+                          comments = find_comments(data)) {
+  if(length(comments)==1) {
+    comments <- rep(comments,nrow(data))
+  }
+  if(!length(comments)==nrow(data)) {
+    stop("'comments' must be have length equal to the number of rows in 'data'",call.=FALSE)
+  }
   addl_ties <- match.arg(addl_ties)
   sort1 <- addl_ties == "obs_first"
   x <- as.data.frame(data)
@@ -146,7 +173,8 @@ lastdose_list <- function(data, fill = -99, back_calc = TRUE,
     col_ii,
     fill,
     back_calc,
-    sort1
+    sort1,
+    comments
   )
   ans
 }
@@ -161,3 +189,54 @@ lastdose_df <- function(data,...) {
     fix.empty.names=FALSE, row.names=NULL
   )
 }
+
+#' Find commented records
+#'
+#' This function uses specific criteria for finding comment records that may
+#' not match up with your coding conventions.  See details below as well as
+#' unit tests.
+#'
+#' @param x a data frame or character vector
+#' @param ... not used
+#'
+#' @return
+#' A logical vector
+#'
+#' @details
+#' For the data frame method, comments are found in a column with name `C`
+#' with type `character`.  If a `C` column is found that is not character,
+#' a warning is generated and no comments are found.
+#'
+#' For the character method or when an appropriate `C` column is found when
+#' using the data frame method, a position or row is considered a comment
+#' when it is either `NA` or when it is equal to `.`.
+#'
+#' @examples
+#' comment <- c(NA, "C", "C", NA, ".", NA, "Comment")
+#' dv <- rnorm(length(comment))
+#' df <- data.frame(C = comment , DV = dv)
+#'
+#' find_comments(df)
+#'
+#'
+#' @export
+find_comments <- function(x,...) UseMethod("find_comments")
+#' @rdname find_comments
+#'
+#' @export
+find_comments.data.frame <- function(x,...) {
+  if(!is.character(x[["C"]])) {
+    if(exists("C", x)) {
+      warning("looking for comment records; found column 'C' but is wasn't character.")
+    }
+    return(vector(mode="logical", nrow(x)))
+  }
+  find_comments.character(x[["C"]])
+}
+
+#' @rdname find_comments
+#' @export
+find_comments.character <- function(x,...) {
+  !(is.na(x)|x=='.')
+}
+

README.md

@@ -163,7 +163,7 @@ system.time(x2 <- lastdose(big))
 ```
 
     .    user  system elapsed 
-    .   0.048   0.001   0.050
+    .   0.045   0.002   0.047
 
 ## Compare against the single profile
 
@@ -172,7 +172,7 @@ system.time(x1 <- lastdose(df))
 ```
 
     .    user  system elapsed 
-    .   0.001   0.001   0.000
+    .   0.000   0.000   0.001
 
 ``` r
 x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame()

_pkgdown.yml

@@ -0,0 +1,2 @@
+development:
+  mode: auto