Merge pull request #30 from RConsortium/pkglite_fix

Streamline pkglite bundle

.Rbuildignore

@@ -22,3 +22,4 @@ $run_dev.*
 ^app\.R$
 ^rsconnect$
 ^LICENSE\.md$
+^datasets$

.Renviron

@@ -0,0 +1 @@
+RENV_PATHS_CELLAR="renv/cellar"

R/app_teal.R

@@ -1,23 +1,24 @@
 #' @importFrom teal init modules module
 #' @importFrom shiny tags
 create_teal <- function() {
-  adsl  <- haven::read_xpt(app_sys("adam", "adsl.xpt"))
+  adam_path <- get_golem_config("adam_path")
+  adsl  <- haven::read_xpt(file.path(adam_path, "adsl.xpt"))
   adsl <- adsl %>%
     dplyr::mutate(
       TRT01P = factor(TRT01P, levels = c("Placebo", "Xanomeline Low Dose",  "Xanomeline High Dose")),
       AGEGR1 = factor(AGEGR1, levels = c("<65", "65-80", ">80")),
       RACE = factor(RACE, levels = c("WHITE", "BLACK OR AFRICAN AMERICAN", "AMERICAN INDIAN OR ALASKA NATIVE"))
     )
-  adas  <- haven::read_xpt(app_sys("adam", "adadas.xpt")) %>%
+  adas  <- haven::read_xpt(file.path(adam_path, "adadas.xpt")) %>%
     dplyr::filter(
       EFFFL == "Y",
       ITTFL == 'Y',
       PARAMCD == 'ACTOT',
       ANL01FL == 'Y'
     )
-  adtte <- haven::read_xpt(app_sys("adam", "adtte.xpt")) %>%
+  adtte <- haven::read_xpt(file.path(adam_path, "adtte.xpt")) %>%
     dplyr::filter(PARAMCD == "TTDE")
-  adlb <- haven::read_xpt(app_sys("adam", "adlbc.xpt")) %>%
+  adlb <- haven::read_xpt(file.path(adam_path, "adlbc.xpt")) %>%
     subset(TRTPN %in% c(0, 81) & PARAMCD == "GLUC" & !is.na(AVISITN)) %>%
     dplyr::mutate(TRTPN = ifelse(TRTPN == 0, 99, TRTPN)) # change treatment order for pairwise comparison
 
@@ -63,7 +64,7 @@ create_teal <- function() {
       )
 
     ),
-    header = "Pilot2 app (draft)",
+    header = "Pilot2 Shiny Application",
     footer = tags$p(class="text-muted", "Source: R Consortium")
   )
 

R/tm_g_kmplot.R

@@ -21,7 +21,7 @@ srv_g_kmplot <- function(input, output, session, datasets) {
   output$plot <- renderPlot({
     adsl <- datasets$get_data("ADSL", filtered = TRUE)
     adtte <- datasets$get_data("ADTTE", filtered = TRUE)
-    anl <- adsl %>% 
+    anl <<- adsl %>% 
       dplyr::filter(
         SAFFL == "Y",
         STUDYID == "CDISCPILOT01"

dev/03_deploy.R

@@ -17,6 +17,18 @@
 ## Check the package before sending to prod
 devtools::check()
 
+# Build
+## Buld the package tarball and send to the renv cellar directory
+
+## Linux version
+devtools::build(path = "renv/cellar")
+
+## Windows version
+
+
+# Install to renv library
+renv::install("renv/cellar/pilot2wrappers_0.2.0.tar.gz")
+
 # Deploy
 
 ## Local, CRAN or Package Manager ---- 

inst/golem-config.yml

@@ -2,6 +2,7 @@ default:
   golem_name: pilot2wrappers
   golem_version: 0.0.0.9000
   app_prod: no
+  adam_path: "datasets/adam"
 production:
   app_prod: yes
 dev:

renv/.gitignore

@@ -1,4 +1,3 @@
-cellar/
 library/
 local/
 lock/

vignettes/adrg-prepare.Rmd

@@ -50,7 +50,7 @@ pkg_desc
 
 ## Pack Shiny Application
 
-The code below assembles the application's code and supporting files into a custom text file using `{pkglite}` and saved into `ectd/r0pkg.txt`. Please note that the size of this text file is approximately 37 megabytes due to the included data sets within the application.
+The code below assembles the application's code and supporting files into a custom text file using `{pkglite}` and saved into `ectd/r1pk1.txt`. Please note that the size of this text file is approximately 37 megabytes due to the included data sets within the application.
 
 ```{r}
 # specification for app.R file
@@ -75,6 +75,8 @@ renv_spec2 <- file_spec(
   recursive = FALSE
 )
 
+golem_spec <- file_auto("dev")
+
 file_ectd2 <- file_spec(
   ".",
   pattern = "^DESCRIPTION$|^NAMESPACE$|^README$|^README\\.md$|^NEWS$|^NEWS\\.md$|^LICENSE$|\\.Rbuildignore$|\\.Rprofile$",
@@ -90,16 +92,17 @@ path$home %>%
     file_auto("inst"), 
     app_spec, 
     renv_spec,
-    renv_spec2
+    renv_spec2,
+    golem_spec
   ) %>%
-  pack(output = "ectd/r0pkg.txt")
+  pack(output = "ectd/r1pkg.txt")
 ```
 
 ## Application Installation (Dry run) 
 
-To unpack the application source code and supporting files from the custom `ectd/r0pkg.txt` bundle and run the Shiny applicaton, perform the following steps in your preferred R development environment, such as RStudio or a R console session:
+To unpack the application source code and supporting files from the custom `ectd/r1pkg.txt` bundle and run the Shiny applicaton, perform the following steps in your preferred R development environment, such as RStudio or a R console session:
 
-1. Ensure that the working directory is set to the same location as the downloaded `r0pkg.txt` file, and run the following code: `pkglite::unpack(input = "r0pkg.txt", install = FALSE)`. You should see a series of messages indicating the application files being written to a subdirectory called `pilot2wrappers`.
+1. Ensure that the working directory is set to the same location as the downloaded `r1pkg.txt` file, and run the following code: `pkglite::unpack(input = "r0pkg.txt", install = FALSE)`. You should see a series of messages indicating the application files being written to a subdirectory called `pilot2wrappers`.
 1. Launch a new R session in the `pilot2wrappers` subdirectory. 
 1. Ensure that the package library is restored with `{renv}` by running the following code: `renv::restore()`. After confirmation, the packages used by the application will be downloaded and installed in a project-specific library.
 1. To run the application, you have the following choices. If you are using RStudio to view the application, open the `app.R` file and click the Run App button at the top of the file window. If you are using an R console, run the following code: `golem:::run_dev()`.