From ceaa0bb64382abb7c9482d607818a9e6b97fcdf7 Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Tue, 14 Jan 2020 13:23:05 -0600 Subject: [PATCH 01/17] creating review branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 277fe47..b2f05ad 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: lastdose Type: Package Title: Calculate Time and Amount of Last Dose -Version: 0.1.0 +Version: 0.1.0.9000 Author: Kyle Baron Maintainer: Kyle Baron Description: Efficient calculation of time after last dose and last dose amount From 7fb0ff69386f646124a04a113046bec22e4ad46f Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Mon, 27 Jan 2020 16:41:54 -0600 Subject: [PATCH 02/17] release branch; reconcile test names as listed in issue --- tests/testthat/test-lastdose.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/testthat/test-lastdose.R b/tests/testthat/test-lastdose.R index b7c0139..bd1143d 100644 --- a/tests/testthat/test-lastdose.R +++ b/tests/testthat/test-lastdose.R @@ -73,7 +73,7 @@ test_that("required columns", { expect_error(lastdose(x)) }) -test_that("non-numeic data throws error", { +test_that("non-numeric data throws error", { for(col in c("ID","time", "addl", "ii", "evid", "ID", "amt")) { dd <- set1[seq(10),] dd[[col]] <- "A" @@ -102,7 +102,7 @@ test_that("error for missing values in ID,evid,ii,addl", { } }) -test_that("NA amt is error for dosing rec, ok otherwise", { +test_that("NA amt is error for dosing record, ok otherwise", { dd <- set1 dd$amt[5] <- NA_real_ expect_is(lastdose(dd), "data.frame") From d24a8bf894e5d22df6ffccd8e06166097a485bfa Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Mon, 27 Jan 2020 16:45:45 -0600 Subject: [PATCH 03/17] re-up docs --- DESCRIPTION | 8 ++++---- README.md | 4 ++-- docs/404.html | 4 ++-- docs/authors.html | 4 ++-- docs/index.html | 12 ++++++------ docs/news/index.html | 6 +++--- docs/reference/index.html | 4 ++-- docs/reference/lastdose.html | 6 +++--- 8 files changed, 24 insertions(+), 24 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b2f05ad..dc85bfe 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,15 +1,15 @@ Package: lastdose Type: Package Title: Calculate Time and Amount of Last Dose -Version: 0.1.0.9000 +Version: 0.2.0 Author: Kyle Baron -Maintainer: Kyle Baron +Maintainer: Kyle Baron 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 diff --git a/README.md b/README.md index 23cbe0c..a005e54 100644 --- a/README.md +++ b/README.md @@ -163,7 +163,7 @@ system.time(x2 <- lastdose(big)) ``` . user system elapsed - . 0.048 0.001 0.050 + . 0.047 0.002 0.049 ## Compare against the single profile @@ -172,7 +172,7 @@ system.time(x1 <- lastdose(df)) ``` . user system elapsed - . 0.001 0.001 0.000 + . 0 0 0 ``` r x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame() diff --git a/docs/404.html b/docs/404.html index 4633c53..62e79e0 100644 --- a/docs/404.html +++ b/docs/404.html @@ -67,7 +67,7 @@ lastdose - 0.1.0 + 0.2.0 @@ -88,7 +88,7 @@
  • - + diff --git a/docs/authors.html b/docs/authors.html index 94049d5..ef8c368 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -67,7 +67,7 @@ lastdose - 0.1.0 + 0.2.0 @@ -88,7 +88,7 @@
  • - + diff --git a/docs/index.html b/docs/index.html index 49be7e2..ec96eca 100644 --- a/docs/index.html +++ b/docs/index.html @@ -32,7 +32,7 @@ lastdose - 0.1.0 + 0.2.0 @@ -53,7 +53,7 @@
  • - + @@ -107,7 +107,7 @@

    Changelog

    - Source: NEWS.md + Source: NEWS.md
    diff --git a/docs/reference/index.html b/docs/reference/index.html index 4840d53..3441fa2 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -67,7 +67,7 @@ lastdose - 0.1.0 + 0.2.0
    @@ -88,7 +88,7 @@
  • - + diff --git a/docs/reference/lastdose.html b/docs/reference/lastdose.html index c7ef317..a88ca28 100644 --- a/docs/reference/lastdose.html +++ b/docs/reference/lastdose.html @@ -71,7 +71,7 @@ lastdose - 0.1.0 + 0.2.0 @@ -92,7 +92,7 @@
  • - + @@ -111,7 +111,7 @@

    Calculate last dose amount (LDOS) and time after last dose (TAD)

    - Source: R/lastdose.R + Source: R/lastdose.R
    From 36940fd7326acdeec252d3d0494305366b99c3d6 Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Tue, 28 Jan 2020 12:38:32 -0600 Subject: [PATCH 04/17] clarify some of the documentation --- DESCRIPTION | 6 ++++-- R/lastdose.R | 17 ++++++++++++++--- man/lastdose.Rd | 16 +++++++++++++--- 3 files changed, 31 insertions(+), 8 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index dc85bfe..5919b93 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,10 @@ Package: lastdose Type: Package Title: Calculate Time and Amount of Last Dose Version: 0.2.0 -Author: Kyle Baron -Maintainer: Kyle Baron +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 Description: Efficient calculation of time after last dose and last dose amount for analysis data sets. License: GPL (>=2) diff --git a/R/lastdose.R b/R/lastdose.R index 4f70fe8..05af751 100644 --- a/R/lastdose.R +++ b/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 @@ -27,6 +27,17 @@ NULL #' #' @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). +#' +#' Additional notes regarding behavior: +#' #' - All functions require an input data set as a data frame #' - The data set should be formatted according to `NMTRAN` type #' conventions diff --git a/man/lastdose.Rd b/man/lastdose.Rd index 1effd2c..e1b9983 100644 --- a/man/lastdose.Rd +++ b/man/lastdose.Rd @@ -41,11 +41,21 @@ and the observation made immediately after (with no advance in time). See details.} } \description{ -Use \link{lastdose} to columns to the input data frame; \link{lastdose_list} -and \link{lastdose_df} returns calculated information as either -\code{list} or \code{data.frame} format without modifying the input data. +Use \link{lastdose} to add (or potentially replace) columns to the input +data frame; \link{lastdose_list} and \link{lastdose_df} returns calculated information +as either \code{list} or \code{data.frame} format without modifying the input data. } \details{ +When calling \link{lastdose} to modify the data frame, two columns will be +added (by default): \code{TAD} indicating the time after the most-recent dose +and \code{LDOS} indicating the amount of the most recent dose. This default +behavior can be modified with the \code{include_ldos} argument. + +When calling \link{lastdose_list} or \link{lastdose_df}, the respective items are +accessible with \code{tad} and \code{ldos} (note the lower case form here to +distinguish from the columns that might be added to the data frame). + +Additional notes regarding behavior: \itemize{ \item All functions require an input data set as a data frame \item The data set should be formatted according to \code{NMTRAN} type From d8973e7893936d0abb2c40456043d289b6640556 Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Tue, 28 Jan 2020 12:39:08 -0600 Subject: [PATCH 05/17] re-build pkgdown site --- README.md | 4 ++-- docs/404.html | 2 +- docs/authors.html | 4 ++-- docs/index.html | 8 ++++---- docs/news/index.html | 2 +- docs/reference/index.html | 2 +- docs/reference/lastdose.html | 24 +++++++++++++++--------- 7 files changed, 26 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index a005e54..1494a45 100644 --- a/README.md +++ b/README.md @@ -163,7 +163,7 @@ system.time(x2 <- lastdose(big)) ``` . user system elapsed - . 0.047 0.002 0.049 + . 0.045 0.001 0.047 ## Compare against the single profile @@ -172,7 +172,7 @@ system.time(x1 <- lastdose(df)) ``` . user system elapsed - . 0 0 0 + . 0.001 0.000 0.000 ``` r x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame() diff --git a/docs/404.html b/docs/404.html index 62e79e0..68b5ee1 100644 --- a/docs/404.html +++ b/docs/404.html @@ -119,7 +119,7 @@

    Page not found (404)

    -

    Developed by Kyle Baron.

    +

    Developed by Kyle T Baron.

    diff --git a/docs/authors.html b/docs/authors.html index ef8c368..5ed6d0e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -111,7 +111,7 @@

    Authors

    • -

      Kyle Baron. Maintainer. +

      Kyle T Baron. Author, maintainer. ORCID

    @@ -124,7 +124,7 @@

    Authors

    Compare against the single profile

    +. 0.001 0.000 0.000
    x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame()
 
 all.equal(x1,x3)
    @@ -252,7 +252,7 @@

    License

    Developers

      -
    • Kyle Baron
      Maintainer
      • +
    • Kyle T Baron
      Author, maintainer ORCID
    @@ -267,7 +267,7 @@

    Dev status

    -

    Developed by Kyle Baron.

    +

    Developed by Kyle T Baron.

    diff --git a/docs/news/index.html b/docs/news/index.html index 89bfab8..0db66c2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -133,7 +133,7 @@

    Contents

    -

    Developed by Kyle Baron.

    +

    Developed by Kyle T Baron.

    diff --git a/docs/reference/index.html b/docs/reference/index.html index 3441fa2..b1c7b5f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -146,7 +146,7 @@

    Contents

    -

    Developed by Kyle Baron.

    +

    Developed by Kyle T Baron.

    diff --git a/docs/reference/lastdose.html b/docs/reference/lastdose.html index a88ca28..9775aef 100644 --- a/docs/reference/lastdose.html +++ b/docs/reference/lastdose.html @@ -36,9 +36,9 @@ - + @@ -116,9 +116,9 @@

    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.

    lastdose(data, ..., include_ldos = TRUE)
@@ -173,8 +173,14 @@ 
    Arg
 
     
    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).
      
+
      Additional notes regarding behavior:
        
 
      • All functions require an input data set as a data frame
        • 
 
      • The data set should be formatted according to NMTRAN type
 conventions
        • 
@@ -230,7 +236,7 @@ 
        Contents
        
 
       
        
       
        
-  
        Developed by Kyle Baron.
        
+  
        Developed by Kyle T Baron.
        
 
        
 
 
        

From 244c73d0d9debd53fccc4fbe4b55901bf55d4c94 Mon Sep 17 00:00:00 2001
From: Kyle Baron 
Date: Wed, 29 Jan 2020 23:51:42 -0600
Subject: [PATCH 06/17] handle commented records #8

---
 NAMESPACE                      |  3 ++
 R/RcppExports.R                |  4 +--
 R/lastdose.R                   | 50 ++++++++++++++++++++++++++++++++--
 man/find_comments.Rd           | 33 ++++++++++++++++++++++
 man/lastdose.Rd                |  7 ++++-
 src/RcppExports.cpp            |  9 +++---
 src/lastdose.cpp               | 40 ++++++++++++++++++++-------
 tests/testthat/test-lastdose.R | 27 ++++++++++++++++++
 8 files changed, 154 insertions(+), 19 deletions(-)
 create mode 100644 man/find_comments.Rd

diff --git a/NAMESPACE b/NAMESPACE
index d6d4adb..a28e19c 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/RcppExports.R b/R/RcppExports.R
index a733eb4..992d871 100644
--- a/R/RcppExports.R
+++ b/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)
 }
 
diff --git a/R/lastdose.R b/R/lastdose.R
index 05af751..9795297 100644
--- a/R/lastdose.R
+++ b/R/lastdose.R
@@ -21,6 +21,9 @@ 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`.
 #' @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.
@@ -89,7 +92,11 @@ 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)==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)
@@ -157,7 +164,8 @@ lastdose_list <- function(data, fill = -99, back_calc = TRUE,
     col_ii,
     fill,
     back_calc,
-    sort1
+    sort1,
+    comments
   )
   ans
 }
@@ -172,3 +180,41 @@ lastdose_df <- function(data,...) {
     fix.empty.names=FALSE, row.names=NULL
   )
 }
+
+#' Find commented records
+#'
+#'
+#' @param x a data frame or character vector
+#' @param ... not used
+#'
+#' @return
+#' A logical vector
+#'
+#' @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=='.')
+}
+
diff --git a/man/find_comments.Rd b/man/find_comments.Rd
new file mode 100644
index 0000000..87db55e
--- /dev/null
+++ b/man/find_comments.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/lastdose.R
+\name{find_comments}
+\alias{find_comments}
+\alias{find_comments.data.frame}
+\alias{find_comments.character}
+\title{Find commented records}
+\usage{
+find_comments(x, ...)
+
+\method{find_comments}{data.frame}(x, ...)
+
+\method{find_comments}{character}(x, ...)
+}
+\arguments{
+\item{x}{a data frame or character vector}
+
+\item{...}{not used}
+}
+\value{
+A logical vector
+}
+\description{
+Find commented records
+}
+\examples{
+comment <- c(NA, "C", "C", NA, ".", NA, "Comment")
+dv <- rnorm(length(comment))
+df <- data.frame(C = comment , DV = dv)
+
+find_comments(df)
+
+}
diff --git a/man/lastdose.Rd b/man/lastdose.Rd
index e1b9983..2b6aba6 100644
--- a/man/lastdose.Rd
+++ b/man/lastdose.Rd
@@ -12,7 +12,8 @@ lastdose_list(
   data,
   fill = -99,
   back_calc = TRUE,
-  addl_ties = c("obs_first", "dose_first")
+  addl_ties = c("obs_first", "dose_first"),
+  comments = find_comments(data)
 )
 
 lastdose_df(data, ...)
@@ -39,6 +40,10 @@ is assumed to happen before the dose and the observation is a trough
 concentration; if \code{dose_first} then the dose is assumed to be administered
 and the observation made immediately after (with no advance in time). See
 details.}
+
+\item{comments}{a logcial vector with length equal to the number of rows
+in \code{data} indicating which records are to be ignored when looking for \code{TAD}
+and \code{LDOS}.}
 }
 \description{
 Use \link{lastdose} to add (or potentially replace) columns to the input
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index d0d1bcf..b315baa 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -6,8 +6,8 @@
 using namespace Rcpp;
 
 // lastdose_impl
-Rcpp::List lastdose_impl(Rcpp::NumericVector id, Rcpp::NumericVector time, Rcpp::NumericVector amt, Rcpp::NumericVector evid, Rcpp::NumericVector addl, Rcpp::NumericVector ii, Rcpp::NumericVector fill, Rcpp::LogicalVector back_calc, Rcpp::LogicalVector sort1);
-RcppExport SEXP _lastdose_lastdose_impl(SEXP idSEXP, SEXP timeSEXP, SEXP amtSEXP, SEXP evidSEXP, SEXP addlSEXP, SEXP iiSEXP, SEXP fillSEXP, SEXP back_calcSEXP, SEXP sort1SEXP) {
+Rcpp::List lastdose_impl(Rcpp::NumericVector id, Rcpp::NumericVector time, Rcpp::NumericVector amt, Rcpp::NumericVector evid, Rcpp::NumericVector addl, Rcpp::NumericVector ii, Rcpp::NumericVector fill, Rcpp::LogicalVector back_calc, Rcpp::LogicalVector sort1, Rcpp::LogicalVector comment);
+RcppExport SEXP _lastdose_lastdose_impl(SEXP idSEXP, SEXP timeSEXP, SEXP amtSEXP, SEXP evidSEXP, SEXP addlSEXP, SEXP iiSEXP, SEXP fillSEXP, SEXP back_calcSEXP, SEXP sort1SEXP, SEXP commentSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
@@ -20,13 +20,14 @@ BEGIN_RCPP
     Rcpp::traits::input_parameter< Rcpp::NumericVector >::type fill(fillSEXP);
     Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type back_calc(back_calcSEXP);
     Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type sort1(sort1SEXP);
-    rcpp_result_gen = Rcpp::wrap(lastdose_impl(id, time, amt, evid, addl, ii, fill, back_calc, sort1));
+    Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type comment(commentSEXP);
+    rcpp_result_gen = Rcpp::wrap(lastdose_impl(id, time, amt, evid, addl, ii, fill, back_calc, sort1, comment));
     return rcpp_result_gen;
 END_RCPP
 }
 
 static const R_CallMethodDef CallEntries[] = {
-    {"_lastdose_lastdose_impl", (DL_FUNC) &_lastdose_lastdose_impl, 9},
+    {"_lastdose_lastdose_impl", (DL_FUNC) &_lastdose_lastdose_impl, 10},
     {NULL, NULL, 0}
 };
 
diff --git a/src/lastdose.cpp b/src/lastdose.cpp
index e2a0ae0..3462b43 100644
--- a/src/lastdose.cpp
+++ b/src/lastdose.cpp
@@ -4,20 +4,35 @@
 
 class  record {
 public:
-  record(double time_, double amt_, int evid_,bool from_data_);
+  record(double time_, double amt_, int evid_,bool from_data_,bool comment_);
+  bool is_dose();
   double time;
   double amt;
   int evid;
   bool from_data;
   int pos;
+  bool comment;
 };
 
-record::record(double time_, double amt_, int evid_,bool from_data_) {
+record::record(double time_, double amt_, int evid_,bool from_data_,bool comment_) {
   time = time_;
   amt = amt_;
   evid = evid_;
   from_data = from_data_;
   pos = -1;
+  comment = comment_;
+}
+
+bool record::is_dose() {
+  return (evid==1 || evid==4) && (!comment);
+}
+
+bool is_dose(const int evid) {
+  return evid==1 || evid==4;
+}
+
+bool is_dose(const int evid, const bool comment) {
+  return (evid==1 || evid==4) && (!comment);
 }
 
 typedef std::vector recs;
@@ -41,7 +56,8 @@ Rcpp::List lastdose_impl(Rcpp::NumericVector id,
                          Rcpp::NumericVector ii,
                          Rcpp::NumericVector fill,
                          Rcpp::LogicalVector back_calc,
-                         Rcpp::LogicalVector sort1) {
+                         Rcpp::LogicalVector sort1,
+                         Rcpp::LogicalVector comment) {
 
   bool use_comp1 = sort1[0];
   bool use_fill = !back_calc[0];
@@ -106,7 +122,7 @@ Rcpp::List lastdose_impl(Rcpp::NumericVector id,
       }
       // Deal with missing dose
       bool missing_amt = Rcpp::NumericVector::is_na(amt[j]);
-      if(((evid[j]==1) || (evid[j]==4))) {
+      if(is_dose(evid[j],comment[j])) {
         if(!found_dose) {
           found_dose = true;
           tofd[i] = time[j];
@@ -122,13 +138,12 @@ Rcpp::List lastdose_impl(Rcpp::NumericVector id,
       }
       if(missing_amt) amt[j] = 0;
       // done with missing dose
-      record this_rec(time[j],amt[j],evid[j],true);
-      this_rec.from_data = true;
+      record this_rec(time[j],amt[j],evid[j],true,comment[j]);
       this_rec.pos = crow;
       this_id.push_back(this_rec);
-      if(has_addl && (addl[j] > 0) && ((evid[j]==1) || (evid[j]==4))) {
+      if(has_addl && (addl[j] > 0) && this_rec.is_dose()) {
         for(int k = 0; k < addl[j]; ++k) {
-          record addl_rec(0.0,amt[j],evid[j],false);
+          record addl_rec(0.0,amt[j],evid[j],false,false);
           addl_rec.time = time[j] + ii[j]*double(k+1);
           if(addl_rec.time >= (max_time)) break;
           this_id.push_back(addl_rec);
@@ -145,13 +160,18 @@ Rcpp::List lastdose_impl(Rcpp::NumericVector id,
     bool had_dose = false;
     bool no_dose = tofd[i] == -1;
     last_time = 0;
-    for(recs::const_iterator it = this_id.begin(); it !=this_id.end(); ++it) {
-      if((it->evid ==1) || (it->evid==4)) {
+    for(recs::iterator it = this_id.begin(); it !=this_id.end(); ++it) {
+      if(it->is_dose()) {
         had_dose = true;
         last_dose = it->amt;
         last_time = it->time;
       }
       if(it->from_data) {
+        if(it->comment) {
+          tad[it->pos] = NA_REAL;
+          ldos[it->pos] = NA_REAL;
+          continue;
+        }
         if(had_dose) {
           tad[it->pos] = it->time - last_time;
         } else {
diff --git a/tests/testthat/test-lastdose.R b/tests/testthat/test-lastdose.R
index bd1143d..9a430d6 100644
--- a/tests/testthat/test-lastdose.R
+++ b/tests/testthat/test-lastdose.R
@@ -110,3 +110,30 @@ test_that("NA amt is error for dosing record, ok otherwise", {
   dd$amt[10] <- NA_real_
   expect_error(lastdose(dd))
 })
+
+test_that("commented records", {
+  com <- c(".", NA ,"C", "A","Comment")
+  ans <- find_comments(com)
+  expect_identical(ans, c(FALSE,FALSE,TRUE,TRUE,TRUE))
+  df <- data.frame(C = com, DV=stats::rnorm(length(com)))
+  ans2 <- find_comments(com)
+  expect_identical(ans,ans2)
+  df2 <- df
+  df2[["C"]] <- sample(c(0,1),nrow(df),replace=TRUE)
+  expect_warning(find_comments(df2))
+  set1[["time"]] <- ifelse(set1[["ID"]]==2, set1[["time"]] + 25, set1[["time"]])
+  set1[["C"]] <- NA_character_
+  set1[["ID"]] <- 1
+  set1[["ii"]] <- 0
+  set1[["addl"]] <- 0
+  set1[["C"]][10] <- "C"
+  ans <- lastdose(set1)
+  expect_true(is.na(ans$TAD[10]))
+  expect_true(is.na(ans$LDOS[10]))
+  diff <- ans[["time"]] - ans[["TAD"]]
+  expect_equal(sum(diff,na.rm=TRUE),0)
+  expect_error(lastdose(set1, comments = c(FALSE, TRUE,FALSE)))
+})
+
+
+

From cf22368a429d853ef9b0cf4269e839516854706f Mon Sep 17 00:00:00 2001
From: Kyle Baron 
Date: Wed, 29 Jan 2020 23:54:18 -0600
Subject: [PATCH 07/17] ignore DS_Store

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 4928367..ff68e31 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
+.DS_Store
 README.html
 lastdose.Rcheck
 lastdose*.tar.gz

From 1a80a36f63d3590a5ea8b6931599684f2c2932d4 Mon Sep 17 00:00:00 2001
From: Kyle Baron 
Date: Wed, 29 Jan 2020 23:55:10 -0600
Subject: [PATCH 08/17] rebuild readme and site

---
 README.md                         |   4 +-
 docs/index.html                   |   4 +-
 docs/reference/find_comments.html | 183 ++++++++++++++++++++++++++++++
 docs/reference/index.html         |   6 +
 docs/reference/lastdose.html      |   9 +-
 5 files changed, 201 insertions(+), 5 deletions(-)
 create mode 100644 docs/reference/find_comments.html

diff --git a/README.md b/README.md
index 1494a45..cad38ec 100644
--- a/README.md
+++ b/README.md
@@ -163,7 +163,7 @@ system.time(x2 <- lastdose(big))
 ```
 
     .    user  system elapsed 
-    .   0.045   0.001   0.047
+    .   0.047   0.001   0.048
 
 ## Compare against the single profile
 
@@ -172,7 +172,7 @@ system.time(x1 <- lastdose(df))
 ```
 
     .    user  system elapsed 
-    .   0.001   0.000   0.000
+    .       0       0       0
 
 ``` r
 x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame()
diff --git a/docs/index.html b/docs/index.html
index c314533..b9c68e9 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -181,14 +181,14 @@ 
        
 
        Timing result
        
 
        system.time(x2 <- lastdose(big))
        
 
+.   0.047   0.001   0.048

    Compare against the single profile

    +. 0 0 0
    x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame()
 
 all.equal(x1,x3)
    diff --git a/docs/reference/find_comments.html b/docs/reference/find_comments.html new file mode 100644 index 0000000..93f374b --- /dev/null +++ b/docs/reference/find_comments.html @@ -0,0 +1,183 @@ + + + + + + + + +Find commented records — find_comments • lastdose + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Find commented records

    + Source: R/lastdose.R + +
    + +
    +

    Find commented records

    +
    + + 
    find_comments(x, ...)
+
+# S3 method for data.frame
+find_comments(x, ...)
+
+# S3 method for character
+find_comments(x, ...)
    + +

    Arguments

    + + + + + + + + + + +
    x

    a data frame or character vector

    ...

    not used

    + +

    Value

    + +

    A logical vector

    + +

    Examples

    + 
    comment <- c(NA, "C", "C", NA, ".", NA, "Comment")
+dv <- rnorm(length(comment))
+df <- data.frame(C = comment , DV = dv)
+
+find_comments(df)
    #> Warning: looking for comment records; found column 'C' but is wasn't character.
    #> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE
    
+
    +
    + +
    + + +
    +
    +

    Developed by Kyle T Baron.

    +
    + +
    +

    Site built with pkgdown 1.4.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index b1c7b5f..69c5b44 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -126,6 +126,12 @@

    find_comments()

    + +

    Find commented records

    + +

    lastdose() lastdose_list() lastdose_df()

    diff --git a/docs/reference/lastdose.html b/docs/reference/lastdose.html index 9775aef..9d1a0ab 100644 --- a/docs/reference/lastdose.html +++ b/docs/reference/lastdose.html @@ -127,7 +127,8 @@

    Calculate last dose amount (LDOS) and time after last dose (TAD)

    data, fill = -99, back_calc = TRUE, - addl_ties = c("obs_first", "dose_first") + addl_ties = c("obs_first", "dose_first"), + comments = find_comments(data) ) lastdose_df(data, ...) @@ -168,6 +169,12 @@

    Arg 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.

    + + + 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.

    From 3a54adff0fb86a18b8f371cdc7f27ab0ed1c1e5f Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Thu, 30 Jan 2020 00:00:27 -0600 Subject: [PATCH 09/17] add details to find_comments function and re-document #8 --- R/lastdose.R | 13 +++++++++++++ README.md | 4 ++-- docs/index.html | 4 ++-- docs/reference/find_comments.html | 18 ++++++++++++++++-- man/find_comments.Rd | 14 +++++++++++++- 5 files changed, 46 insertions(+), 7 deletions(-) diff --git a/R/lastdose.R b/R/lastdose.R index 9795297..bbed4ad 100644 --- a/R/lastdose.R +++ b/R/lastdose.R @@ -183,6 +183,9 @@ lastdose_df <- function(data,...) { #' 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 @@ -190,6 +193,15 @@ lastdose_df <- function(data,...) { #' @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)) @@ -197,6 +209,7 @@ lastdose_df <- function(data,...) { #' #' find_comments(df) #' +#' #' @export find_comments <- function(x,...) UseMethod("find_comments") #' @rdname find_comments diff --git a/README.md b/README.md index cad38ec..c4dc827 100644 --- a/README.md +++ b/README.md @@ -163,7 +163,7 @@ system.time(x2 <- lastdose(big)) ``` . user system elapsed - . 0.047 0.001 0.048 + . 0.049 0.001 0.051 ## Compare against the single profile @@ -172,7 +172,7 @@ system.time(x1 <- lastdose(df)) ``` . user system elapsed - . 0 0 0 + . 0.000 0.000 0.001 ``` r x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame() diff --git a/docs/index.html b/docs/index.html index b9c68e9..68c7d5c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -181,14 +181,14 @@

    Timing result

    system.time(x2 <- lastdose(big))
    +. 0.049 0.001 0.051

    Compare against the single profile

    +. 0.000 0.000 0.001
    x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame()
 
 all.equal(x1,x3)
    diff --git a/docs/reference/find_comments.html b/docs/reference/find_comments.html index 93f374b..107a45a 100644 --- a/docs/reference/find_comments.html +++ b/docs/reference/find_comments.html @@ -36,7 +36,9 @@ - + @@ -114,7 +116,9 @@

    Find commented records

    -

    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.

    find_comments(x, ...)
@@ -141,6 +145,14 @@ 
    Arg
     
    Value
    
 
     
    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")
@@ -148,6 +160,7 @@ 
    Examp
 df <- data.frame(C = comment , DV = dv)
 
 find_comments(df)
    #> Warning: looking for comment records; found column 'C' but is wasn't character.
    #> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE
    
+
 
    
   
   
    x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame()
 
 all.equal(x1,x3)
    diff --git a/docs/reference/lastdose.html b/docs/reference/lastdose.html index 9d1a0ab..e0e37a3 100644 --- a/docs/reference/lastdose.html +++ b/docs/reference/lastdose.html @@ -174,7 +174,7 @@

    Arg 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.

    +and LDOS. See all the fill_comments_na argument.

    @@ -187,7 +187,12 @@

    Details

    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).

    -

    Additional notes regarding behavior:

      +

      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

        • diff --git a/man/lastdose.Rd b/man/lastdose.Rd index f4ac70a..5d405ed 100644 --- a/man/lastdose.Rd +++ b/man/lastdose.Rd @@ -13,8 +13,7 @@ lastdose_list( fill = -99, back_calc = TRUE, addl_ties = c("obs_first", "dose_first"), - comments = find_comments(data), - fill_comments_na = FALSE + comments = find_comments(data) ) lastdose_df(data, ...) @@ -45,11 +44,6 @@ details.} \item{comments}{a logcial vector with length equal to the number of rows in \code{data} indicating which records are to be ignored when looking for \code{TAD} and \code{LDOS}. See all the \code{fill_comments_na} argument.} - -\item{fill_comments_na}{if \code{TRUE}, then \code{TAD} and \code{LDOS} will be filled with -\code{NA} when the comment indicator is \code{TRUE}; otherwise, commented records -are filled in with the time since and amount of the dose on the last -non-commented dosing record (the default).} } \description{ Use \link{lastdose} to add (or potentially replace) columns to the input @@ -70,8 +64,7 @@ distinguish from the columns that might be added to the data frame). (as indicated with the \code{comments} argument) will never be considered as actual doses when determining \code{TAD} and \code{LDOS}. But commented records (doses and non-doses) will be assigned \code{TAD} and \code{LDOS} according to the last -non-commented dosing record by default. The behavior can be modified by -setting through the \code{fill_comments_na} argument. +non-commented dosing record. \strong{Additional notes}: \itemize{ diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index d4b2aa7..b315baa 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -6,8 +6,8 @@ using namespace Rcpp; // lastdose_impl -Rcpp::List lastdose_impl(Rcpp::NumericVector id, Rcpp::NumericVector time, Rcpp::NumericVector amt, Rcpp::NumericVector evid, Rcpp::NumericVector addl, Rcpp::NumericVector ii, Rcpp::NumericVector fill, Rcpp::LogicalVector back_calc, Rcpp::LogicalVector sort1, Rcpp::LogicalVector comment, bool fill_comment_na); -RcppExport SEXP _lastdose_lastdose_impl(SEXP idSEXP, SEXP timeSEXP, SEXP amtSEXP, SEXP evidSEXP, SEXP addlSEXP, SEXP iiSEXP, SEXP fillSEXP, SEXP back_calcSEXP, SEXP sort1SEXP, SEXP commentSEXP, SEXP fill_comment_naSEXP) { +Rcpp::List lastdose_impl(Rcpp::NumericVector id, Rcpp::NumericVector time, Rcpp::NumericVector amt, Rcpp::NumericVector evid, Rcpp::NumericVector addl, Rcpp::NumericVector ii, Rcpp::NumericVector fill, Rcpp::LogicalVector back_calc, Rcpp::LogicalVector sort1, Rcpp::LogicalVector comment); +RcppExport SEXP _lastdose_lastdose_impl(SEXP idSEXP, SEXP timeSEXP, SEXP amtSEXP, SEXP evidSEXP, SEXP addlSEXP, SEXP iiSEXP, SEXP fillSEXP, SEXP back_calcSEXP, SEXP sort1SEXP, SEXP commentSEXP) { BEGIN_RCPP Rcpp::RObject rcpp_result_gen; Rcpp::RNGScope rcpp_rngScope_gen; @@ -21,14 +21,13 @@ BEGIN_RCPP Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type back_calc(back_calcSEXP); Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type sort1(sort1SEXP); Rcpp::traits::input_parameter< Rcpp::LogicalVector >::type comment(commentSEXP); - Rcpp::traits::input_parameter< bool >::type fill_comment_na(fill_comment_naSEXP); - rcpp_result_gen = Rcpp::wrap(lastdose_impl(id, time, amt, evid, addl, ii, fill, back_calc, sort1, comment, fill_comment_na)); + rcpp_result_gen = Rcpp::wrap(lastdose_impl(id, time, amt, evid, addl, ii, fill, back_calc, sort1, comment)); return rcpp_result_gen; END_RCPP } static const R_CallMethodDef CallEntries[] = { - {"_lastdose_lastdose_impl", (DL_FUNC) &_lastdose_lastdose_impl, 11}, + {"_lastdose_lastdose_impl", (DL_FUNC) &_lastdose_lastdose_impl, 10}, {NULL, NULL, 0} }; diff --git a/src/lastdose.cpp b/src/lastdose.cpp index 0d8b6cd..58c456d 100644 --- a/src/lastdose.cpp +++ b/src/lastdose.cpp @@ -57,8 +57,7 @@ Rcpp::List lastdose_impl(Rcpp::NumericVector id, Rcpp::NumericVector fill, Rcpp::LogicalVector back_calc, Rcpp::LogicalVector sort1, - Rcpp::LogicalVector comment, - bool fill_comment_na) { + Rcpp::LogicalVector comment) { bool use_comp1 = sort1[0]; bool use_fill = !back_calc[0]; @@ -167,13 +166,7 @@ Rcpp::List lastdose_impl(Rcpp::NumericVector id, last_dose = it->amt; last_time = it->time; } - if(it->from_data) { - if(it->comment && fill_comment_na) { - tad[it->pos] = NA_REAL; - ldos[it->pos] = NA_REAL; - continue; - } - if(had_dose) { + if(it->from_data) { if(had_dose) { tad[it->pos] = it->time - last_time; } else { tad[it->pos] = (use_fill || no_dose) ? fill[0] : (it->time - tofd[i]); diff --git a/tests/testthat/test-lastdose.R b/tests/testthat/test-lastdose.R index 5c5929e..3aa4f03 100644 --- a/tests/testthat/test-lastdose.R +++ b/tests/testthat/test-lastdose.R @@ -130,11 +130,6 @@ test_that("commented records", { ans <- lastdose(set1) diff <- ans[["time"]] - ans[["TAD"]] expect_equal(sum(diff),0) - ans <- lastdose(set1, fill_comments_na = TRUE) - expect_true(is.na(ans$TAD[10])) - expect_true(is.na(ans$LDOS[10])) - diff <- ans[["time"]] - ans[["TAD"]] - expect_equal(sum(diff,na.rm=TRUE),0) expect_error(lastdose(set1, comments = c(FALSE, TRUE,FALSE))) }) From 5cca89abdae93aec5b916665598a9861dc2dec82 Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Sat, 1 Feb 2020 07:41:35 -0600 Subject: [PATCH 13/17] site; add _pkgdown.yml --- _pkgdown.yml | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 _pkgdown.yml diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..c4e25ab --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,2 @@ +development: + mode: auto From cd84466312b2e4ab2be2fd6daf1badb12449986d Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Sat, 1 Feb 2020 07:45:22 -0600 Subject: [PATCH 14/17] update news --- NEWS.md | 5 +++++ docs/news/index.html | 8 ++++++++ 2 files changed, 13 insertions(+) diff --git a/NEWS.md b/NEWS.md index ada024b..61c1f81 100644 --- a/NEWS.md +++ b/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 no-commented dose) #9 + # lastdose 0.1.0 - Update git origin diff --git a/docs/news/index.html b/docs/news/index.html index 0db66c2..5b3ae49 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -110,6 +110,13 @@

        Changelog

        Source: NEWS.md +
        +

        +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 no-commented dose) #9
          • +
        +

        lastdose 0.1.0

        @@ -123,6 +130,7 @@

        Contents

        From 4ba6c87c7da7785fc9fada9bdaa30473fcef422f Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Tue, 4 Feb 2020 06:26:08 -0600 Subject: [PATCH 15/17] tweak news --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 61c1f81..23a781b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,7 @@ # 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 no-commented dose) #9 + to the last non-commented dose) #9 # lastdose 0.1.0 From 4b4e1cea58f2980a6dce7113c1a7a8e595ffdd47 Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Tue, 4 Feb 2020 06:26:43 -0600 Subject: [PATCH 16/17] rebuild pkgdown --- README.md | 4 ++-- docs/index.html | 4 ++-- docs/news/index.html | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 265151a..053c2f6 100644 --- a/README.md +++ b/README.md @@ -163,7 +163,7 @@ system.time(x2 <- lastdose(big)) ``` . user system elapsed - . 0.045 0.002 0.048 + . 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 0.000 0.000 + . 0.000 0.000 0.001 ``` r x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame() diff --git a/docs/index.html b/docs/index.html index 32f0870..22f729f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -181,14 +181,14 @@

        Timing result

        system.time(x2 <- lastdose(big))
        +. 0.045 0.002 0.047

        x3 <- filter(x2, big[["ID"]]==1) %>% as.data.frame()
 
 all.equal(x1,x3)
        diff --git a/docs/news/index.html b/docs/news/index.html index 5b3ae49..e4706fe 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -114,7 +114,7 @@

        Changelog

        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 no-commented dose) #9
          • +
        • 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
        From 9d543dfe1c7e3f54c6104291a74b276d95c5d29f Mon Sep 17 00:00:00 2001 From: Kyle Baron Date: Tue, 4 Feb 2020 06:40:19 -0600 Subject: [PATCH 17/17] add pkgdown file to rbuildignore --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index 30ba539..82703ce 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,4 @@ +_pkgdown\.yml Makefile ^test\.R$ ^.*\.Rproj$