Dockerize the quarto environment

.gitignore

@@ -1,6 +1,9 @@
 # Ignore for publishing
 /.quarto/
 /_site/
+# Ignore the rendered files but keep the directory
+/docs/*
+!docs/.keep
 
 .Rhistory
 .Rprofile

08-Appendix.qmd

@@ -514,7 +514,7 @@ s1e_heart_plot
 
 I also explored whether participants reported different levels of need-threat between Time 3 and Time 5. Results are plotted in @fig-s1e-nts-across-time-plot.
 
-```{r s1e-exploratory-NTS-mixed, cache=TRUE}
+```{r s1e-exploratory-NTS-mixed}
 # Exploratory Mixed Model with Time --------------------------------------------
 # run model
 NTS_vars <- c("nts_belonging_mean", "nts_esteem_mean",
@@ -691,7 +691,7 @@ s2_mnsdcor %>% as_tibble() %>%
 ```
 
 #### Bivariate Scatter Plot Matrix
-```{r s2-matplot, fig.cap = "Matrix Plot for Study 2 Variables", fig.height=15, fig.width=15, message=FALSE, warning=FALSE, cache=TRUE}
+```{r s2-matplot, fig.cap = "Matrix Plot for Study 2 Variables", fig.height=15, fig.width=15, message=FALSE, warning=FALSE}
 #| label: fig-s2-matplot
 # Study 2 - Matrix Plot
 s2_df %>%
@@ -908,8 +908,7 @@ s3_mnsdcor %>% as_tibble() %>%
   kable_styling_cortable()
 ```
 
-```{r appendix-s3-ggpairs, fig.cap='Study 3 - Bivariate Scatter Plot Matrix',fig.height=15, fig.width=15, out.width='100%', message=FALSE, warning=FALSE, cache=TRUE}
-#| label: fig-appendix-s3-ggpairs 
+```{r appendix-s3-ggpairs, fig.cap='Study 3 - Bivariate Scatter Plot Matrix',fig.height=15, fig.width=15, out.width='100%', message=FALSE, warning=FALSE}
 # GG Pairs for Study 3
 s3_df %>%
   dplyr::select(parasocial, social_world, T1_Heart_1, T1_Valence_1, T1_Arousal_1, T1_Dominance_1,

Dockerfile

@@ -1,87 +1,42 @@
-FROM rocker/rstudio:4
-
-# Install Ubuntu distributions of R Packages
-RUN apt-get update
-RUN apt-get install -y zlib1g-dev
-RUN 
-RUN install2.r -e here 
-RUN install2.r -e haven
-
-# xml2
-RUN apt-get install -y libxml2-dev
-RUN install2.r -e xml2 
-
-# svg lite
-RUN apt-get -y install libfontconfig1-dev
-RUN install2.r -e svglite 
-
-RUN install2.r -e patchwork 
-RUN install2.r -e table1 
-RUN install2.r -e papaja 
-RUN install2.r -e kableExtra
-RUN install2.r -e tidyr 
-RUN install2.r -e tibble 
-
-RUN install2.r -e bookdown
-
-
-RUN install2.r -e remotes
-# ggtext
-RUN apt-get -y install libcurl4-openssl-dev
-RUN install2.r -e ggtext
-RUN install2.r -e labelled
-
-# Install R packages on GitHub
-RUN Rscript -e "remotes::install_github('achetverikov/APAstats')"
+FROM rocker/rstudio:4.4.2
 
+# Install renv
+RUN R -e "install.packages('renv', repos = c(CRAN = 'https://cloud.r-project.org'))"
 
-RUN install2.r -e readr 
-RUN install2.r -e stringr
-RUN install2.r -e purrr
-RUN install2.r -e tinytex
+# Get the renv files from the current project 
+RUN mkdir -p /project
+WORKDIR /project
+COPY renv.lock renv.lock
 
+# Specify library paths for installation
+RUN mkdir -p renv
+COPY renv/activate.R renv/activate.R
+COPY renv/settings.json renv/settings.json
 
-RUN apt-get -y install libcairo2-dev libharfbuzz-dev libfribidi-dev
-RUN apt-get -y install libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
-RUN install2.r -e flextable
-RUN install2.r -e metathis
-RUN install2.r -e Hmisc
-RUN install2.r -e GGally
-RUN install2.r -e corrr
-
-RUN apt-get -y install cmake
-RUN install2.r -e lme4
-
-RUN install2.r -e lmerTest
-RUN install2.r -e forestplot
-RUN install2.r -e broom.mixed
-RUN install2.r -e ggpubr
-RUN install2.r -e pacman
-
-RUN install2.r -e tidyverse
-RUN install2.r -e rio
-
-RUN install2.r -e english
-RUN install2.r -e sjlabelled
-RUN install2.r -e sjPlot
-RUN install2.r -e ggh4x
-RUN install2.r -e knitcitations
-
-
-RUN install2.r -e wordcloud
-RUN install2.r -e emmeans
-RUN install2.r -e tidytext
-RUN install2.r -e ggmosaic
-RUN install2.r -e broom
-RUN install2.r -e codebook
-RUN install2.r -e effectsize
+# Install system dependencies
+RUN apt-get update
+## xml2
+RUN apt-get install -y libxml2-dev
+## png
+RUN apt-get install -y libpng-dev
+## curl
+RUN apt-get install -y libcurl4-openssl-dev
+## cmake (for nloptr)
+RUN apt-get install -y cmake 
+## gert
+RUN apt-get install -y libgit2-dev 
+## systemfonts
+RUN apt-get install -y libfontconfig1-dev
+## Other dependencies
+RUN apt-get install -y libcairo2-dev libharfbuzz-dev libfribidi-dev
+RUN apt-get install -y libfreetype6-dev libtiff5-dev libjpeg-dev
+
+# Restore the packages via renv
+RUN R -e "renv::restore()"
+
+# Install knitr and rmarkdown packages
+RUN R -e "install.packages('knitr', repos = c(CRAN = 'https://cloud.r-project.org'))"
+RUN R -e "install.packages('rmarkdown', repos = c(CRAN = 'https://cloud.r-project.org'))"
 
 # Install tinytex as the rstudio user
-USER rstudio
-RUN Rscript -e "tinytex::install_tinytex(force = TRUE)"
-ENV PATH="${PATH}:/home/rstudio/bin"
-
-# Start the RStudio server as root
-USER root
-ENV USER=rstudio
-CMD ["/usr/lib/rstudio-server/bin/rserver","--server-daemonize=0","--auth-none=1"]
+RUN Rscript -e "tinytex::install_tinytex(force = TRUE)"

docker-compose.yml

@@ -5,6 +5,17 @@ services:
       - 8787:8787
     volumes:
       - ./:/home/rstudio/dissertation/
-    environment:
-      - PASSWORD=changeme # default username is rstudio
-
+    working_dir: /home/rstudio/dissertation
+    command: quarto render # Render the book
+    ## To launch RStudio server use the command & environment below
+    ## -------------------------
+    # user: root # For launching RStudio server
+    # command:
+    #   [
+    #     "/usr/lib/rstudio-server/bin/rserver",
+    #     "--server-daemonize=0",
+    #     "--auth-none=1",
+    #   ]
+    # environment:
+    #   - PASSWORD=changeme # default username is rstudio
+    #   - USER=root # For launching RStudio server

packages.bib

@@ -1,9 +1,9 @@
 @Manual{R-apastats,
   title = {apastats: APA-style results},
   author = {Andrey Chetverikov},
-  year = {2025},
   note = {R package version 0.5, commit acbf761e3f66643c96e9b6ad65fdcd4af01382ed},
   url = {https://github.com/achetverikov/APAstats},
+  year = {2025},
 }
 
 @Manual{R-base,
@@ -174,14 +174,6 @@ @Manual{R-lme4
   url = {https://github.com/lme4/lme4/},
 }
 
-@Manual{R-lubridate,
-  title = {lubridate: Make Dealing with Dates a Little Easier},
-  author = {Vitalie Spinu and Garrett Grolemund and Hadley Wickham},
-  year = {2024},
-  note = {R package version 1.9.4},
-  url = {https://lubridate.tidyverse.org},
-}
-
 @Manual{R-Matrix,
   title = {Matrix: Sparse and Dense Matrix Classes and Methods},
   author = {Douglas Bates and Martin Maechler and Mikael Jagan},
@@ -253,14 +245,6 @@ @Manual{R-tidytext
   url = {https://juliasilge.github.io/tidytext/},
 }
 
-@Manual{R-tidyverse,
-  title = {tidyverse: Easily Install and Load the Tidyverse},
-  author = {Hadley Wickham},
-  year = {2023},
-  note = {R package version 2.0.0},
-  url = {https://tidyverse.tidyverse.org},
-}
-
 @Manual{R-wordcloud,
   title = {wordcloud: Word Clouds},
   author = {Ian Fellows},
@@ -333,17 +317,6 @@ @Article{lme42015
   doi = {10.18637/jss.v067.i01},
 }
 
-@Article{lubridate2011,
-  title = {Dates and Times Made Easy with {lubridate}},
-  author = {Garrett Grolemund and Hadley Wickham},
-  journal = {Journal of Statistical Software},
-  year = {2011},
-  volume = {40},
-  number = {3},
-  pages = {1--25},
-  url = {https://www.jstatsoft.org/v40/i03/},
-}
-
 @Article{tidytext2016,
   title = {tidytext: Text Mining and Analysis Using Tidy Data Principles in R},
   author = {Julia Silge and David Robinson},
@@ -356,14 +329,3 @@ @Article{tidytext2016
   journal = {JOSS},
 }
 
-@Article{tidyverse2019,
-  title = {Welcome to the {tidyverse}},
-  author = {Hadley Wickham and Mara Averick and Jennifer Bryan and Winston Chang and Lucy D'Agostino McGowan and Romain François and Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
-  year = {2019},
-  journal = {Journal of Open Source Software},
-  volume = {4},
-  number = {43},
-  pages = {1686},
-  doi = {10.21105/joss.01686},
-}
-