cran release

asancpt · Aug 14, 2017 · 9eceda0 · 9eceda0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,9 @@
 Package: caffsim
 Title: Simulation of Plasma Caffeine Concentrations by Using Population Pharmacokinetic Model
-Version: 0.1.0
-Date: 2017-08-13
+Version: 0.2.0
+Date: 2017-08-14
 Authors@R: person("Sungpil", "Han", email = "[email protected]", role = c("aut", "cre"))
-Description: Simulate plasma caffeine concentrations using population pharmacokinetic model.
+Description: Simulate plasma caffeine concentrations using population pharmacokinetic model described in Lee, Kim, Perera, McLachlan and Bae (2015) <doi:10.1007/s00431-015-2581-x>.
 Depends:
     R (>= 3.3.2)
 Encoding: UTF-8
@@ -16,3 +16,5 @@ URL: https://github.com/asancpt/caffsim
 BugReports: https://github.com/asancpt/caffsim/issues
 RoxygenNote: 6.0.1
 Maintainer: Sungpil Han <[email protected]>
+
+
diff --git a/Makefile b/Makefile
@@ -1,5 +1,5 @@
 rd2pdf:
-	rm caffsim.pdf;R CMD rd2pdf ../caffsim
+	rm caffsim.pdf;R CMD Rd2pdf ../caffsim
 
 pkgdown:
 	rm -rf docs;Rscript -e "Sys.setlocale('LC_ALL', 'C'); pkgdown::build_site()" 
@@ -8,4 +8,4 @@ roxygen:
 	Rscript -e "library(caffsim);roxygen2::roxygenise()" 
 
 CRAN:
-	make roxygen; make rd2pdf; Rscript -e "devtools::build()"; R CMD CHECK --as-cran ../caffsim_*.tar.gz; mv ../caffsim_*.tar.gz releases
+	make roxygen; make rd2pdf; Rscript -e "devtools::build()"; R CMD check --as-cran ../caffsim_*.tar.gz; mv ../caffsim_*.tar.gz releases
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(UnitTable)
 export(caffConcTime)
 export(caffConcTimeMulti)
 export(caffDataset)

diff --git a/R/Plot.R b/R/Plot.R
@@ -7,7 +7,7 @@
 #' @return The concentration-time curve
 #' @export
 #' @examples 
-#' \donttest{caffPlot(caffConcTime(Weight = 20, Dose = 200, N = 20))}
+#' caffPlot(caffConcTime(Weight = 20, Dose = 200, N = 20))
 #' @import dplyr
 #' @import ggplot2
 #' @seealso \url{https://asancpt.github.io/caffsim}
@@ -36,7 +36,7 @@ caffPlot <- function(caffConcTimeData, log = FALSE){
 #' @return The concentration-time curve
 #' @export
 #' @examples 
-#' \donttest{caffPlotMulti(ConcTimeMulti(Weight = 20, Dose = 200, N = 20, Tau = 8, Repeat = 4))}
+#' caffPlotMulti(caffConcTimeMulti(Weight = 20, Dose = 200, N = 20, Tau = 8, Repeat = 4))
 #' @import dplyr
 #' @import ggplot2
 #' @seealso \url{https://asancpt.github.io/caffsim}

diff --git a/R/data.R b/R/data.R
@@ -8,5 +8,6 @@
 #'   \item{Parameter}{Pharmacokinetic parameters in full name}
 #' }
 #' @seealso \url{https://asancpt.github.io/caffsim}
+#' @export
 
 "UnitTable"
diff --git a/README.md b/README.md
@@ -38,14 +38,14 @@ knitr::kable(head(MyDataset), format = "markdown")
 
 
 
-|      Tmax|      Cmax|      AUC| Half_life|       CL|        V|        Ka|        Ke|
-|---------:|---------:|--------:|---------:|--------:|--------:|---------:|---------:|
-| 0.7506950| 10.904556| 99.33949|  5.768755| 2.013298| 16.75934|  5.118124| 0.1201299|
-| 0.9756280|  9.535194| 78.96550|  5.015262| 2.532751| 18.32960|  3.430260| 0.1381782|
-| 0.8869807| 14.091555| 81.22170|  3.319075| 2.462396| 11.79347|  3.331590| 0.2087931|
-| 0.6458470| 12.058570| 95.70897|  5.032268| 2.089668| 15.17427|  5.975385| 0.1377113|
-| 0.2466091|  8.607292| 72.15405|  5.635830| 2.771847| 22.54208| 20.959415| 0.1229632|
-| 0.2747344| 12.558457| 67.17518|  3.511209| 2.977290| 15.08498| 16.252669| 0.1973679|
+|      Tmax|     Cmax|       AUC| Half_life|       CL|        V|       Ka|        Ke|
+|---------:|--------:|---------:|---------:|--------:|--------:|--------:|---------:|
+| 1.5932082| 10.78304| 101.26248|  5.279877| 1.975065| 15.04777| 1.760984| 0.1312531|
+| 2.0916257| 12.86940| 175.74298|  7.871994| 1.138025| 12.92717| 1.416190| 0.0880336|
+| 0.4921188| 11.86278| 124.11671|  6.901047| 1.611387| 16.04654| 9.302930| 0.1004195|
+| 0.6908504| 10.17830|  48.35470|  2.769650| 4.136103| 16.53038| 4.400363| 0.2502121|
+| 2.0047057| 10.22826|  98.64327|  5.085895| 2.027508| 14.87979| 1.236351| 0.1362592|
+| 1.1338165| 14.59544|  85.88897|  3.186989| 2.328588| 10.70878| 2.296390| 0.2174466|
 
 ### Create a dataset for concentration-time curve
 
@@ -57,14 +57,14 @@ knitr::kable(head(MyConcTime), format = "markdown")
 
 
 
-| Subject| Time|     Conc|
-|-------:|----:|--------:|
-|       1|  0.0| 0.000000|
-|       1|  0.1| 5.117929|
-|       1|  0.2| 7.721610|
-|       1|  0.3| 9.025087|
-|       1|  0.4| 9.656359|
-|       1|  0.5| 9.940279|
+| Subject| Time|      Conc|
+|-------:|----:|---------:|
+|       1|  0.0|  0.000000|
+|       1|  0.1|  6.577377|
+|       1|  0.2|  9.164757|
+|       1|  0.3| 10.103392|
+|       1|  0.4| 10.362305|
+|       1|  0.5| 10.342533|
 
 ### Create a concentration-time curve
 
@@ -111,14 +111,14 @@ knitr::kable(head(MyDatasetMulti), format = "markdown")
 
 
 
-|     TmaxS|     CmaxS|      AUCS|       AI|     Aavss|     Cavss|   Cmaxss|    Cminss|
-|---------:|---------:|---------:|--------:|---------:|---------:|--------:|---------:|
-| 0.9236100| 12.730981| 122.83645| 1.334606| 144.26677| 10.236371| 18.89986| 4.7384847|
-| 2.2515756| 12.207227| 158.30692| 1.464930| 173.90274| 13.192243| 22.17966| 7.0392348|
-| 0.2178431| 12.469114|  83.51313| 1.185915| 107.70968|  6.959427| 15.29319| 2.3974994|
-| 0.6228740|  7.487806|  43.61323| 1.108450|  85.86370|  3.634436|  9.36417| 0.9161845|
-| 4.0027303|  9.990159| 146.93629| 1.413289| 162.32568| 12.244691| 21.27733| 6.2221419|
-| 0.7494883|  9.448188|  55.46029| 1.103058|  84.19326|  4.621691| 12.08503| 1.1291008|
+|     TmaxS|     CmaxS|      AUCS|       AI|    Aavss|     Cavss|   Cmaxss|   Cminss|
+|---------:|---------:|---------:|--------:|--------:|---------:|--------:|--------:|
+| 0.5158465| 14.957443| 137.90585| 1.335630| 144.5057| 11.492154| 21.19963| 5.327244|
+| 0.6093528| 14.631043| 132.44702| 1.316633| 140.0501| 11.037252| 20.70942| 4.980344|
+| 2.4233186| 11.047738| 117.37331| 1.272119| 129.4152|  9.781109| 19.18918| 4.104760|
+| 0.7263908|  9.032753|  76.01314| 1.263379| 127.2897|  6.334428| 12.54797| 2.615900|
+| 0.7195809|  7.929042|  70.60036| 1.297770| 135.5795|  5.883363| 11.23971| 2.578924|
+| 0.5069677| 11.059353|  76.27684| 1.179214| 105.9351|  6.356403| 14.12180| 2.146198|
 
 ### Create a dataset for concentration-time curve
 
@@ -132,12 +132,12 @@ knitr::kable(head(MyConcTimeMulti), format = "markdown")
 
 | Subject| Time|     Conc|
 |-------:|----:|--------:|
-|       1|  0.0| 0.000000|
-|       1|  0.2| 2.974553|
-|       1|  0.4| 5.015058|
-|       1|  0.6| 6.390925|
-|       1|  0.8| 7.294470|
-|       1|  1.0| 7.862957|
+|       1|  0.0|  0.00000|
+|       1|  0.2| 12.94468|
+|       1|  0.4| 12.37024|
+|       1|  0.6| 11.81864|
+|       1|  0.8| 11.29163|
+|       1|  1.0| 10.78813|
 
 ### Create a concentration-time curve
 

diff --git a/assets/figures/MyPlotMultiMyConcTimeMulti-1.png b/assets/figures/MyPlotMultiMyConcTimeMulti-1.png
diff --git a/assets/figures/MyPlotMultiPub-1.png b/assets/figures/MyPlotMultiPub-1.png
diff --git a/assets/figures/MyPlotMyConcTime-1.png b/assets/figures/MyPlotMyConcTime-1.png
diff --git a/assets/figures/MyPlotPub-1.png b/assets/figures/MyPlotPub-1.png
diff --git a/caffsim.pdf b/caffsim.pdf
diff --git a/docs/assets/figures/MyPlotMultiMyConcTimeMulti-1.png b/docs/assets/figures/MyPlotMultiMyConcTimeMulti-1.png
diff --git a/docs/assets/figures/MyPlotMultiPub-1.png b/docs/assets/figures/MyPlotMultiPub-1.png
diff --git a/docs/assets/figures/MyPlotMyConcTime-1.png b/docs/assets/figures/MyPlotMyConcTime-1.png
diff --git a/docs/assets/figures/MyPlotPub-1.png b/docs/assets/figures/MyPlotPub-1.png