Merge pull request #4 from kaybenleroll/create-simple-hier-models

create simple hier models

.dockerignore

@@ -2,11 +2,16 @@
 
 *.qmd
 *.html
+*.log
+*.R
 
 data/*
 precompute/*
+.git/*
 
+stan_code/*
 stan_models/*
+img/*
 
 *_cache/*
 *_files/*

.gitignore

@@ -1,15 +1,18 @@
-.Rhistory
-.RData
-
 .Rproj.user/
-
-temp.R
+.vscode/
 
 *_cache/*
 *_files/*
 
-output.log
-
 *.rmarkdown
 *.dot
 
+.Rhistory
+.RData
+
+*.log
+
+temp*.R
+
+precompute_*.bz2
+

Dockerfile

@@ -1,4 +1,7 @@
-FROM rocker/tidyverse:4.2.3
+FROM rocker/tidyverse:4.3.1
+
+COPY build/Rprofile.site /usr/local/lib/R/etc/
+COPY build/Renviron.site /usr/local/lib/R/etc/
 
 ENV TZ=Europe/Dublin
 
@@ -17,23 +20,38 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
     libglpk-dev \
     libgsl-dev \
     libnlopt-dev \
+    libomp-dev \
     p7zip-full \
     pbzip2 \
     rsyslog \
   && apt-get clean \
   && rm -rf /var/lib/apt/lists/* \
   && mkdir -p $HOME/.R \
   && echo "" > $HOME/.R/Makevars \
+  && echo "CC=clang"                                               >> $HOME/.R/Makevars \
   && echo "CXX=clang++"                                            >> $HOME/.R/Makevars \
   && echo "CXXFLAGS=-Os"                                           >> $HOME/.R/Makevars \
   && echo "CXXFLAGS+= -Wno-unused-variable -Wno-unused-function"   >> $HOME/.R/Makevars \
   && echo "CXXFLAGS+= -Wno-unknown-pragmas -Wno-macro-redefined"   >> $HOME/.R/Makevars \
   && echo ""                                                       >> $HOME/.R/Makevars \
+  && echo "CC11=clang"                                             >> $HOME/.R/Makevars \
+  && echo "CXX11=clang++"                                          >> $HOME/.R/Makevars \
+  && echo "CXX11FLAGS=-Os"                                         >> $HOME/.R/Makevars \
+  && echo "CXX11FLAGS+= -Wno-unused-variable -Wno-unused-function" >> $HOME/.R/Makevars \
+  && echo "CXX11FLAGS+= -Wno-unknown-pragmas -Wno-macro-redefined" >> $HOME/.R/Makevars \
+  && echo ""                                                       >> $HOME/.R/Makevars \
+  && echo "CC14=clang"                                             >> $HOME/.R/Makevars \
   && echo "CXX14=clang++"                                          >> $HOME/.R/Makevars \
   && echo "CXX14FLAGS=-Os"                                         >> $HOME/.R/Makevars \
   && echo "CXX14FLAGS+= -Wno-unused-variable -Wno-unused-function" >> $HOME/.R/Makevars \
   && echo "CXX14FLAGS+= -Wno-unknown-pragmas -Wno-macro-redefined" >> $HOME/.R/Makevars \
   && echo ""                                                       >> $HOME/.R/Makevars \
+  && echo "CC17=clang++"                                           >> $HOME/.R/Makevars \
+  && echo "CXX17=clang++"                                          >> $HOME/.R/Makevars \
+  && echo "CXX17FLAGS=-Os"                                         >> $HOME/.R/Makevars \
+  && echo "CXX17FLAGS+= -Wno-unused-variable -Wno-unused-function" >> $HOME/.R/Makevars \
+  && echo "CXX17FLAGS+= -Wno-unknown-pragmas -Wno-macro-redefined" >> $HOME/.R/Makevars \
+  && echo ""                                                       >> $HOME/.R/Makevars \
   && install2.r --error \
     anytime \
     bayesplot \
@@ -50,6 +68,7 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
     fs \
     furrr \
     loo \
+    markdown \
     modeltime \
     posterior \
     projpred \
@@ -70,8 +89,6 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
     timetk
 
 
-COPY build/logging.conf /etc/rstudio/
-
 WORKDIR /tmp
 
 COPY build/docker_install_sys_rpkgs.R /tmp
@@ -107,5 +124,14 @@ RUN Rscript /tmp/docker_install_user_rpkgs.R
 USER root
 
 RUN chown -R rstudio:rstudio /home/rstudio \
-  && chmod ugo+rx /home/rstudio
+  && chmod ugo+rx /home/rstudio \
+  && chown -R rstudio:rstudio /home/rstudio/.cmdstan
+
+
+ARG BUILD_DATE
+
+LABEL org.opencontainers.image.source="https://github.com/kaybenleroll/btydbayes_investigation" \
+      org.opencontainers.image.authors="Mick Cooney <[email protected]>" \
+      org.label-schema.build-date=$BUILD_DATE
+
 

Makefile

@@ -9,6 +9,7 @@ DOCKER_USER=rstudio
 DOCKER_PASS=CHANGEME
 DOCKER_UID=$(shell id -u)
 DOCKER_GID=$(shell id -g)
+DOCKER_BUILD_ARGS=
 
 RSTUDIO_PORT=8787
 
@@ -30,8 +31,7 @@ all-html: $(HTML_FILES)
 
 .qmd.html:
 	echo "TIMESTAMP:" `date` "- Rendering script $<"  >> output.log 2>&1
-	quarto render $< --to html                        >> output.log 2>&1
-#	Rscript -e 'quarto::quarto_render("$<")'          >> output.log 2>&1
+	quarto render $< --to html >> output.log 2>&1
 	echo "TIMESTAMP:" `date` "- Finished $*.html"         >> output.log 2>&1
 
 
@@ -44,14 +44,25 @@ full_deps.dot:
 depgraph: full_deps.png
 
 
+exploring_shortsynth_data.html: generate_transaction_datasets.html
+exploring_longsynth_data.html: generate_transaction_datasets.html
 exploring_online_retail_transactions.html: retrieve_retail_data.html
+exploring_cdnow_dataset.html: retrieve_retail_data.html
+
+initial_pnbd_models.html: exploring_shortsynth_data.html
+construct_longsynth_fixed_pnbd_models.html: exploring_longsynth_data.html
 construct_onlineretail_fixed_pnbd_models.html: exploring_online_retail_transactions.html
+construct_cdnow_fixed_pnbd_models.html: exploring_cdnow_dataset.html
 
-initial_pnbd_models.html: generate_transaction_datasets.html
+construct_shortsynth_onehier_pnbd_models.html: initial_pnbd_models.html
+construct_longsynth_onehier_pnbd_models.html: construct_longsynth_fixed_pnbd_models.html
+construct_onlineretail_onehier_pnbd_models.html: construct_onlineretail_fixed_pnbd_models.html
+construct_cdnow_onehier_pnbd_models.html: construct_cdnow_fixed_pnbd_models.html
 
-construct_longsynth_fixed_pnbd_models.html: initial_pnbd_models.html
-construct_onlineretail_fixed_pnbd_models.html: exploring_online_retail_transactions.html \
-  initial_pnbd_models.html
+construct_shortsynth_twohier_pnbd_models.html: construct_shortsynth_onehier_pnbd_models.html
+construct_longsynth_twohier_pnbd_models.html: construct_longsynth_onehier_pnbd_models.html
+construct_onlineretail_twohier_pnbd_models.html: construct_onlineretail_onehier_pnbd_models.html
+construct_cdnow_twohier_pnbd_models.html: construct_cdnow_onehier_pnbd_models.html
 
 
 mrproper: clean-cache clean-data clean-html clean-precompute clean-models
@@ -79,7 +90,15 @@ clean-models:
 
 ### Docker targets
 docker-build-image: Dockerfile
-	docker build -t ${IMAGE_TAG} -f Dockerfile .
+	docker build -t ${IMAGE_TAG} \
+	  ${DOCKER_BUILD_ARGS} \
+	  --build-arg BUILD_DATE=$(shell date -u +'%Y-%m-%dT%H:%M:%SZ') \
+	  -f Dockerfile . 2>&1 | tee -a docker_build.log
+
+docker-show-context:
+	docker build -f build/context.dockerfile -t context-image .
+	docker run --rm -it context-image find /tmp/build
+	docker rmi test:latest
 
 docker-run:
 	docker run --rm -d \
@@ -92,6 +111,10 @@ docker-run:
 	  --name ${CONTAINER_NAME} \
 	  ${IMAGE_TAG}
 
+docker-fix-permissions:
+	docker exec ${CONTAINER_NAME} bash -c "chown -R ${DOCKER_USER}:${DOCKER_USER} /home/${DOCKER_USER}"
+
+
 docker-bash:
 	docker exec -it -u ${DOCKER_USER} ${CONTAINER_NAME} bash
 

btydbayes_investigation.Rproj

@@ -16,3 +16,5 @@ AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 
 BuildType: Makefile
+
+MarkdownReferences: Document

build/Renviron.site

@@ -0,0 +1,15 @@
+R_LIBS=${R_LIBS-'/usr/local/lib/R/site-library:/usr/local/lib/R/library'}
+CRAN=https://packagemanager.posit.co/cran/2023-10-06
+CWD=/home/rstudio
+DEFAULT_USER=rstudio
+GROUPID=1000
+HOSTNAME=2a08c571a82c
+LANG=en_US.UTF-8
+PANDOC_VERSION=default
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+QUARTO_VERSION=default
+R_HOME=/usr/local/lib/R
+R_VERSION=4.3.1
+S6_VERSION=v2.1.0.2
+USER=rstudio
+USERID=1000

build/Rprofile.site

@@ -0,0 +1,3 @@
+options(repos = c(CRAN = 'https://packagemanager.posit.co/cran/2023-10-06'), download.file.method = 'libcurl')
+# https://docs.rstudio.com/rspm/admin/serving-binaries/#binaries-r-configuration-linux
+options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])))

build/context.dockerfile

@@ -0,0 +1,5 @@
+FROM busybox
+
+RUN mkdir /tmp/build/
+# Add context to /tmp/build/
+COPY . /tmp/build/

build/docker_install_user_rpkgs.R

@@ -1,6 +1,6 @@
 remotes::install_github(
   "stan-dev/cmdstanr",
-  ref     = "v0.5.3",
+  ref     = "v0.6.1",
   upgrade = "never"
 )
 
@@ -15,16 +15,24 @@ remotes::install_github(
 library(cmdstanr)
 
 cmdstan_flags <- list(
+  "CC"         = "clang",
   "CXX"        = "clang++",
   "CXXFLAGS"   = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined",
+  "CC11"       = "clang",
+  "CXX11"      = "clang++",
+  "CXX11FLAGS" = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined",
+  "CC14"       = "clang",
   "CXX14"      = "clang++",
-  "CXX14FLAGS" = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined"
+  "CXX14FLAGS" = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined",
+  "CC17"       = "clang",
+  "CXX17"      = "clang++",
+  "CXX17FLAGS" = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined"
 )
 
 install_cmdstan(
   cores       = parallel::detectCores(),
   cpp_options = cmdstan_flags,
   quiet       = FALSE,
   overwrite   = FALSE,
-  version     = "2.32.1"
+  version     = "2.33.0"
 )

calculate_var_sizes.R

@@ -0,0 +1,23 @@
+
+calculate_object_size <- function(x) {
+  message(glue("Calculating size for object {x}"))
+
+  size <- x |>
+    get() |>
+    obj_size()
+
+  return(size)
+}
+
+
+var_sizes_tbl <- ls() |>
+  enframe(name = NULL, value = "object_name") |>
+  mutate(
+    object_size = map_dbl(
+      object_name, calculate_object_size,
+      .progress = FALSE
+      ),
+    object_size_mb = object_size / (1024 * 1024)
+    )
+
+var_sizes_tbl |> glimpse()