Merge pull request #39 from metrumresearchgroup/develop

release/0.3.3

.Rbuildignore

@@ -6,13 +6,13 @@ inst/exdata/run102.RDS
 ^mrglogo\.pdf$
 ^.*\.tar\.gz$
 Makefile
-^.*\.html$
 inst/img
-inst/examples/img/
+inst/examples/img
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^docs$
 ^\.travis\.yml$
-vignettes
 \.drone\.yml
 _pkgdown\.yml
+vignettes/complete\.Rmd
+vignettes/*\.pdf

.gitignore

@@ -1,3 +1,4 @@
+docs
 test.R
 inst/examples/*.html
 Rplots.pdf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pmplots
 Type: Package
 Title: Plots for Pharmacometrics
-Version: 0.3.2
+Version: 0.3.3
 Authors@R: c(
        person("Kyle T", "Baron", "", "kyleb@metrumrg.com", c("aut", "cre")),
        person("Metrum Research Group", role =  c("cph"))
@@ -14,7 +14,6 @@ URL: https://github.com/metrumresearchgroup/pmplots/
 BugReports: https://github.com/metrumresearchgroup/pmplots/issues
 Encoding: UTF-8
 Language: en-US
-LazyData: true
 Imports: 
   dplyr (>= 0.7.2),
   rlang (>= 0.1.2),
@@ -23,7 +22,8 @@ Imports:
   tidyr, 
   purrr,
   forcats
-Suggests: testthat, GGally, latex2exp, knitr, cowplot, yaml, miniUI, shiny
+VignetteBuilder: knitr
+Suggests: testthat, GGally, latex2exp, knitr, cowplot, yaml, miniUI, shiny, rmarkdown
 Depends: ggplot2 (>= 3.0.0)
 RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)

Makefile

@@ -28,6 +28,11 @@ all:
 	make build
 	make install
 
+package:
+	make doc
+	make build-vignettes
+	make install
+
 spelling:
 	Rscript -e "spelling::spell_check_package()"
 
@@ -49,6 +54,9 @@ doc:
 build:
 	R CMD build --no-build-vignettes --md5 $(PKGDIR)
 
+build-vignettes:
+	R CMD build --md5 $(PKGDIR)
+
 install:
 	R CMD INSTALL --install-tests ${TARBALL}
 
@@ -58,16 +66,12 @@ install-build:
 check:
 	make doc
 	make build
-	R CMD check ${TARBALL} -o ${CHKDIR}
-
-checkk:
-	make doc
-	make build
-	R CMD check ${TARBALL} -o ${CHKDIR} --no-examples
+	R CMD check  --ignore-vignettes ${TARBALL} -o ${CHKDIR}
 
-testing:
+check-package:
 	make doc
-	make build
-	cp ${TARBALL} ../../qualification/pmplots_qualification/testing/${TARBALL}
-	cd ../../qualification/pmplots_qualification/testing/ && git commit -am "testing update" && git push
+	make build-vignettes
+	R CMD check ${TARBALL} -o ${CHKDIR}
 
+readme:
+	Rscript -e 'rmarkdown::render("README.Rmd")'

NEWS.md

@@ -1,3 +1,10 @@
+# pmplots 0.3.3
+
+- Add vignettes into package (#37)
+
+- Re-work README (#37)
+
+
 # pmplots 0.3.2
 
 - `pairs_plot()` and `eta_pairs()` now will properly call user-supplied

README.Rmd

@@ -0,0 +1,115 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = ".",
+  fig.path = "man/figures/README-",
+  warning = FALSE, 
+  message = FALSE,
+  fig.width = 5, 
+  fig.height = 4
+)
+```
+
+# pmplots <img align="right" src = "man/figures/metrum_pmplots_git_logo.png" width="135px">
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of pmplots is to create exploratory and diagnostic plots commonly 
+used in pharmacometrics.
+
+## Installation
+
+You can install the released version of pmplots from [MPN](https://mpn.metworx.com/docs/) with:
+
+```{r, eval = FALSE}
+mpn <- "https://mpn.metworx.com/snapshots/stable/2021-06-20"
+install.packages("pmplots", repos = mpn)
+```
+
+This installs from a specific, dated snapshot. Please check 
+https://mpn.metworx.com/docs/snapshots/ for the most recent snapshot date.
+
+You can install the development version from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("metrumresearchgroup/pmplots")
+```
+
+
+## Examples
+
+```{r, message = FALSE, warning = FALSE}
+library(pmplots)
+library(dplyr)
+
+data <- pmplots_data_obs()
+```
+
+
+The default pmplots behavior is to expect names following NONMEM convention, 
+for example `DV` refers to observed values, `PRED` refers to population 
+predicted values. With that convention, we can easily make observed versus 
+predicted plots
+
+```{r, dv_pred}
+dv_pred(data, yname = "MyDrug (ng/ml)")
+```
+
+```{r, dv_pred_log}
+dv_pred(data, loglog = TRUE)
+```
+
+
+## NPDE plots
+```{r, npde_time}
+npde_time(data)
+```
+
+```{r, npde_pred}
+npde_pred(data)
+```
+
+
+## QQ plots
+```{r, cwres_q}
+cwres_q(data)
+```
+
+
+## Exploratory plots
+
+```{r, cont_cat, fig.height = 5, fig.width = 7}
+id <- pmplots_data_id()
+cont_cat(id, x = "STUDYc", y = c("WT", "SCR", "AAG")) %>% pm_grid()
+```
+
+```{r, pairs, fig.width = 4.5, fig.width = 6}
+pairs_plot(id, y = c("WT//Weight (kg)", "SCR//Creat (mg/dL)", "BMI//BMI (kg/m2)"))
+```
+
+## Some faceted versions
+
+```{r, facet_example, fig.height = 5, fig.width = 7}
+wrap_cont_time(data, y = c("RES","WRES", "CWRES", "NPDE"), ncol = 2)
+```
+
+
+# Function and workflow overview
+
+A functions and features (code + output) listing is available at 
+[pmplots_complete.md](https://github.com/metrumresearchgroup/pmplots/blob/master/inst/examples/pmplots_complete.md).  
+
+# Suggested packages
+
+Consider installing the [cowplot](https://CRAN.R-project.org/package=cowplot) 
+package to help arranging plots on a page.  Also, consider installing
+[latex2exp](https://CRAN.R-project.org/package=latex2exp) to allow you to 
+use latex in axis titles.

README.md

@@ -1,37 +1,116 @@
-pmplots
-================
 
-## Browse source code at 
-https://github.com/metrumresearchgroup/pmplots
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# pmplots <img align="right" src = "man/figures/metrum_pmplots_git_logo.png" width="135px">
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of pmplots is to create exploratory and diagnostic plots
+commonly used in pharmacometrics.
 
 ## Installation
 
-TODO(devin) pmplots is available on MPN
+You can install the released version of pmplots from
+[MPN](https://mpn.metworx.com/docs/) with:
+
+``` r
+mpn <- "https://mpn.metworx.com/snapshots/stable/2021-06-20"
+install.packages("pmplots", repos = mpn)
+```
+
+This installs from a specific, dated snapshot. Please check
+<https://mpn.metworx.com/docs/snapshots/> for the most recent snapshot
+date.
+
+You can install the development version from
+[GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("metrumresearchgroup/pmplots")
+```
+
+## Examples
+
+``` r
+library(pmplots)
+library(dplyr)
+
+data <- pmplots_data_obs()
+```
+
+The default pmplots behavior is to expect names following NONMEM
+convention, for example `DV` refers to observed values, `PRED` refers to
+population predicted values. With that convention, we can easily make
+observed versus predicted plots
+
+``` r
+dv_pred(data, yname = "MyDrug (ng/ml)")
+```
+
+![](man/figures/README-dv_pred-1.png)<!-- -->
+
+``` r
+dv_pred(data, loglog = TRUE)
+```
+
+![](man/figures/README-dv_pred_log-1.png)<!-- -->
+
+## NPDE plots
+
+``` r
+npde_time(data)
+```
+
+![](man/figures/README-npde_time-1.png)<!-- -->
+
+``` r
+npde_pred(data)
+```
+
+![](man/figures/README-npde_pred-1.png)<!-- -->
+
+## QQ plots
+
+``` r
+cwres_q(data)
+```
+
+![](man/figures/README-cwres_q-1.png)<!-- -->
+
+## Exploratory plots
+
+``` r
+id <- pmplots_data_id()
+cont_cat(id, x = "STUDYc", y = c("WT", "SCR", "AAG")) %>% pm_grid()
+```
+
+![](man/figures/README-cont_cat-1.png)<!-- -->
 
-## News
+``` r
+pairs_plot(id, y = c("WT//Weight (kg)", "SCR//Creat (mg/dL)", "BMI//BMI (kg/m2)"))
+```
 
-News can be found [here](news.md)
+![](man/figures/README-pairs-1.png)<!-- -->
 
-## Function and workflow overview
+## Some faceted versions
 
-A functions and features (code + output) listing is available at 
-[pmplots_complete.md](https://github.com/metrumresearchgroup/pmplots/blob/master/inst/examples/pmplots_complete.md).  
+``` r
+wrap_cont_time(data, y = c("RES","WRES", "CWRES", "NPDE"), ncol = 2)
+```
 
-## Vignettes
+![](man/figures/README-facet_example-1.png)<!-- -->
 
-- [Get started](https://metrumresearchgroup.github.io/pmplots/articles/start.html)
-- [Customize your plot](https://metrumresearchgroup.github.io/pmplots/articles/customize.html)
-- [Residual plots](https://metrumresearchgroup.github.io/pmplots/articles/residual_plots.html)
-- [NPDE plots](https://metrumresearchgroup.github.io/pmplots/articles/npde_plots.html)
-- [Dependent variable plots](https://metrumresearchgroup.github.io/pmplots/articles/dv.html)
-- [ETA plots](https://metrumresearchgroup.github.io/pmplots/articles/eta.html)
-- [Vectorized plots](https://metrumresearchgroup.github.io/pmplots/articles/list_plots.html)
-- [Wrapped or faceted plots](https://metrumresearchgroup.github.io/pmplots/articles/wrapped_plots.html)
+# Function and workflow overview
 
-## Suggested packages
+A functions and features (code + output) listing is available at
+[pmplots\_complete.md](https://github.com/metrumresearchgroup/pmplots/blob/master/inst/examples/pmplots_complete.md).
 
-Consider installing the [cowplot](https://CRAN.R-project.org/package=cowplot) 
-package to help arranging plots on a page.  Also, consider installing
-[latex2exp](https://CRAN.R-project.org/package=latex2exp) to allow you to 
-use latex in axis titles.
+# Suggested packages
 
+Consider installing the
+[cowplot](https://CRAN.R-project.org/package=cowplot) package to help
+arranging plots on a page. Also, consider installing
+[latex2exp](https://CRAN.R-project.org/package=latex2exp) to allow you
+to use latex in axis titles.

_pkgdown.yml

@@ -1,2 +1,5 @@
-development:
-  mode: auto
+title: pmplots
+navbar:
+  right:
+  - icon: fa-github fa-lg
+    href: https://github.com/metrumresearchgroup/pmplots