Dockerize App

.Rbuildignore

@@ -0,0 +1,4 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^Dockerfile$
+^\.dockerignore$

.dockerignore

@@ -0,0 +1,9 @@
+.RData
+.Rhistory
+.git
+.gitignore
+manifest.json
+rsconnect/
+.Rproj.user
+
+

.gitignore

@@ -0,0 +1,9 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store
+
+
+data/deadcounter.rds
+data/efscounter.rds

Dockerfile

@@ -0,0 +1,27 @@
+FROM --platform=linux/amd64 rocker/verse:4.4.1
+RUN apt-get update && apt-get install -y  libcairo2-dev libcurl4-openssl-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libssl-dev libtiff-dev libxml2-dev make pandoc zlib1g-dev && rm -rf /var/lib/apt/lists/*
+RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
+RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site
+RUN R -e 'install.packages("remotes")'
+RUN Rscript -e 'remotes::install_version("bslib",upgrade="never", version = "0.5.0")'
+RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.7.5.1")'
+RUN Rscript -e 'remotes::install_version("rmarkdown",upgrade="never", version = "2.23")'
+RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.2")'
+RUN Rscript -e 'remotes::install_version("waiter",upgrade="never", version = "0.2.5")'
+RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.1.0")'
+RUN Rscript -e 'remotes::install_version("shinyBS",upgrade="never", version = "0.61.1")'
+RUN Rscript -e 'remotes::install_version("nftbart",upgrade="never", version = "2.1")'
+RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.4.1")'
+RUN Rscript -e 'remotes::install_version("ggplot2",upgrade="never", version = "3.4.3")'
+RUN Rscript -e 'remotes::install_version("flextable",upgrade="never", version = "0.9.6")'
+RUN Rscript -e 'remotes::install_version("fastDummies",upgrade="never", version = "1.7.3")'
+RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.33")'
+RUN mkdir /build_zone
+ADD . /build_zone
+WORKDIR /build_zone
+RUN R -e 'remotes::install_local(upgrade="never")'
+RUN rm -rf /build_zone
+EXPOSE 80
+ENV RDS_DATA /efsdata
+
+CMD R -e "remotes::install_local(upgrade=\"never\");options('shiny.port'=80,shiny.host='0.0.0.0');library(nmdp.asom);nmdp.asom::run_app()"

NAMESPACE

@@ -1,23 +1,2 @@
 # Generated by roxygen2: do not edit by hand
 
-export(run_app)
-import(bslib)
-import(flextable)
-import(ggplot2)
-import(nftbart)
-import(shiny)
-import(shinyBS)
-import(shinyjs)
-import(waiter)
-importFrom(golem,activate_js)
-importFrom(golem,add_resource_path)
-importFrom(golem,bundle_resources)
-importFrom(golem,favicon)
-importFrom(golem,with_golem_options)
-importFrom(shiny,HTML)
-importFrom(shiny,NS)
-importFrom(shiny,column)
-importFrom(shiny,shinyApp)
-importFrom(shiny,tagAppendAttributes)
-importFrom(shiny,tagList)
-importFrom(shiny,tags)

R/app_ui.R

@@ -9,14 +9,16 @@ waiter::waiter_set_theme(html = waiter::spin_3()
 
 options(mc.cores = 8)
 
+data_directory = Sys.getenv("RDS_DATA", "data")
+
 # load data:
-zcta_hhinc     <- readRDS(file = "data/zcta_hhinc.RDS")
-patdat_default <- readRDS(file = "data/patdat_default.RDS")
-xtest_names    <- readRDS(file = "data/xtest_vnames.RDS")
-dat_fmtfun     <- readRDS(file = "data/dat_fmtfun.RDS")
-
-nft_os  <- readRDS(file = "data/deadcounter.rds")
-nft_efs <- readRDS(file = "data/efscounter.rds")
+zcta_hhinc     <- readRDS(file = paste0(data_directory, "/zcta_hhinc.RDS"))
+patdat_default <- readRDS(file = paste0(data_directory, "/patdat_default.RDS"))
+xtest_names    <- readRDS(file = paste0(data_directory, "/xtest_vnames.RDS"))
+dat_fmtfun     <- readRDS(file = paste0(data_directory, "/dat_fmtfun.RDS"))
+ 
+nft_os  <- readRDS(file = paste0(data_directory, "/deadcounter.rds"))
+nft_efs <- readRDS(file = paste0(data_directory, "/efscounter.rds"))
 
 #' The application User-Interface
 #'

README.Rmd

@@ -2,10 +2,10 @@
 title: "README for nmdp.asom"
 author: "Lisa Rein"
 date: "2024-08-23"
-output: html_document
+output: md_document
 ---
 
-```{r }
+```
 
 # set working directory to R project for nmdp.asom app
 # working directory should be wherever app.R is housed:
@@ -25,7 +25,10 @@ list.files(paste0(mydir, "/data"))
 # To run the app:
 # Note the model objects are large and the initial load could take a long time:
 library(shiny)
+# Run and time startup
+Sys.time()
 shiny::runApp()
+Sys.time()
 
 # you should see a message in the console if the app is successfully loading: 'Loading nmdp.asom'
 

README.md

@@ -0,0 +1,44 @@
+```         
+# set working directory to R project for nmdp.asom app
+# working directory should be wherever app.R is housed:
+mydir <- "Z:/consulting/Logan_Brent/nmdp.asom"
+setwd(mydir)
+
+list.files(mydir)
+
+# make sure that model objects deadcounter.rds and efscounter.rds are saved in data folder:
+list.files(paste0(mydir, "/data"))
+
+# To run the app:
+# Note the model objects are large and the initial load could take a long time:
+library(shiny)
+# Run and time startup
+Sys.time()
+shiny::runApp()
+Sys.time()
+
+# you should see a message in the console if the app is successfully loading: 'Loading nmdp.asom'
+
+# Dependent packages should automatically be installed/loaded but just in case,
+# app dependencies (also noted in NAMESPACE):
+# import(bslib)
+# import(flextable)
+# import(ggplot2)
+# import(nftbart)
+# import(shiny)
+# import(shinyBS)
+# import(shinyjs)
+# import(waiter)
+# importFrom(golem,activate_js)
+# importFrom(golem,add_resource_path)
+# importFrom(golem,bundle_resources)
+# importFrom(golem,favicon)
+# importFrom(golem,with_golem_options)
+# importFrom(shiny,HTML)
+# importFrom(shiny,NS)
+# importFrom(shiny,column)
+# importFrom(shiny,shinyApp)
+# importFrom(shiny,tagAppendAttributes)
+# importFrom(shiny,tagList)
+# importFrom(shiny,tags)
+```

nmdp.asom.Rproj

@@ -1,23 +1,23 @@
-Version: 1.0
-
-RestoreWorkspace: No
-SaveWorkspace: No
-AlwaysSaveHistory: No
-
-EnableCodeIndexing: No
-UseSpacesForTab: Yes
-NumSpacesForTab: 4
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
-LineEndingConversion: Posix
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
-
-QuitChildProcessesOnExit: Yes
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: No
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+
+QuitChildProcessesOnExit: Yes