diff --git a/.gitignore b/.gitignore
index c2c8b2614a5136064c19c2924a67dbc3292baa0d..b5404c2b8ec307c56aefd7c53b9dd0027f5ecf7c 100755
--- a/.gitignore
+++ b/.gitignore
@@ -46,3 +46,4 @@ rsAbsence.pdf
# some folders
misc/
+submission/
diff --git a/Dockerfile b/Dockerfile
index 2fd937f910a186846341667a9ff8213f0c3d08e4..5fda983d1c615820982ab83d407615f4157459a0 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,5 @@
## set R version (https://hub.docker.com/r/rocker/verse/tags)
-FROM rocker/verse:4.2.3
+FROM rocker/verse:4.3
## name of the manuscript (as in Makefile and paper/Makefile)
ENV FILE=rsabsence
diff --git a/Makefile b/Makefile
index 3f8d79738a67f326be1b71899929fc6721538be5..2b01c0680eed98bbc519fc96a030c2bdf7a61037 100755
--- a/Makefile
+++ b/Makefile
@@ -13,19 +13,10 @@ dbuild: Dockerfile
docker build \
-t $(FILE) .
-## run docker image that produces pdf from within docker
+## run docker image that produces *tex* from within docker
+## and compiles to *pdf* outside docker
docker: dbuild
docker run \
- --rm \
- --env pdfdocker="true" \
- --env FILE=$(FILE) \
- --volume $(CURDIR):/output \
- $(FILE)
- mv $(FILE).pdf ./
-
-## run docker image that produces tex from within docker
-docker2: dbuild
- docker run \
--rm \
--env FILE=$(FILE) \
-v $(CURDIR):/output \
@@ -37,3 +28,13 @@ docker2: dbuild
rmdir figure/
cd paper && make pdf2 clean
mv paper/$(FILE).pdf ./
+
+## run docker image that produces *pdf* from within docker
+docker2: dbuild
+ docker run \
+ --rm \
+ --env pdfdocker="true" \
+ --env FILE=$(FILE) \
+ --volume $(CURDIR):/output \
+ $(FILE)
+ mv $(FILE).pdf ./
diff --git a/README.md b/README.md
index 7632c2e1d446f6bfe2bae24d12f7b8e2ea800757..bf271fe7cdfc82574a411ca91c2be4c30f9256d9 100755
--- a/README.md
+++ b/README.md
@@ -11,35 +11,41 @@ Our results can be reproduced in two ways
### 1. Reproducing the results locally
-Make sure that LaTeX (e.g., texlive-full on Ubuntu), R, and the R packages
-indicated in the `./CRANpackages.txt` file are installed
+
+Make sure that R, and the R packages indicated in the `./CRANpackages.txt` file
+are installed
```sh
## install packages from CRAN by running from a shell
R -e 'install.packages(read.delim("CRANpackages.txt", header = FALSE)[,1])'
```
-Then run
+To only rerun the R code without recompiling the manuscript use the file
+`./paper/rsabsence.R`. To recompile the manuscript, make also sure that Make,
+LaTeX and all necessary LaTeX packages (e.g., the texlive-full distribution on
+Ubuntu) are installed. Then run
```
make local
```
-this should produce `./rsabsence.pdf`
+this should produce `./rsabsence.pdf`.
+
Although the analyses depend on only few dependencies, this approach may lead to
different results (or not even compile successfully) in the future if R or the
-packages change. The R and R package versions which were used when the thesis
-was successfully compiled the last time are visible in the following output
+packages change. The R and R package versions which were used when the paper was
+successfully compiled before submission are visible in the following output
```r
sessionInfo()
-#> R version 4.2.3 (2023-03-15)
+#> R version 4.3.0 (2023-04-21)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.6 LTS
+#>
#> Matrix products: default
-#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
+#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#>
#> locale:
@@ -50,40 +56,42 @@ sessionInfo()
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C
#>
+#> time zone: Europe/Zurich
+#> tzcode source: system (glibc)
+#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
-#> [1] reporttools_1.1.3 xtable_1.8-4 dplyr_1.1.1 gridExtra_2.3
+#> [1] reporttools_1.1.3 xtable_1.8-4 dplyr_1.1.2 gridExtra_2.3
#> [5] ggplot2_3.4.2 knitr_1.42
#>
#> loaded via a namespace (and not attached):
-#> [1] fansi_1.0.4 withr_2.5.0 utf8_1.2.3 grid_4.2.3
-#> [5] R6_2.5.1 lifecycle_1.0.3 gtable_0.3.3 magrittr_2.0.3
-#> [9] scales_1.2.1 pillar_1.9.0 rlang_1.1.0 cli_3.6.1
-#> [13] generics_0.1.3 vctrs_0.6.1 tools_4.2.3 glue_1.6.2
-#> [17] munsell_0.5.0 xfun_0.38 compiler_4.2.3 pkgconfig_2.0.3
-#> [21] colorspace_2.1-0 tidyselect_1.2.0 tibble_3.2.1
+#> [1] vctrs_0.6.2 cli_3.6.1 rlang_1.1.0 xfun_0.39
+#> [5] generics_0.1.3 labeling_0.4.2 glue_1.6.2 colorspace_2.1-0
+#> [9] scales_1.2.1 fansi_1.0.4 grid_4.3.0 munsell_0.5.0
+#> [13] tibble_3.2.1 lifecycle_1.0.3 compiler_4.3.0 pkgconfig_2.0.3
+#> [17] farver_2.1.1 viridisLite_0.4.1 R6_2.5.1 tidyselect_1.2.0
+#> [21] utf8_1.2.3 pillar_1.9.0 magrittr_2.0.3 tools_4.3.0
+#> [25] withr_2.5.0 gtable_0.3.3
cat(paste(Sys.time(), Sys.timezone(), "\n"))
-#> 2023-04-06 13:56:17 Europe/Zurich
+#> 2023-05-08 09:19:12.440643 Europe/Zurich
```
### 2. Reproducing the results within a Docker container
-Make sure that Docker with root rights is installed. Then run
+Make sure that Make, LaTeX with all necessary packages (e.g., the texlive-full
+distribution on Ubuntu), and Docker with root rights are installed. Then run
```
make docker
```
-This may take some time as TinyTeX needs to install several LaTeX packages (run
-`make docker2` to compile only R code within the container but run LaTeX
-locally). The Docker approach reruns the analyses in a Docker container which
-encapsulates the computational environment (R and R package versions) that was
-used in the original analysis. The only way this approach could become
-non-reproducible is when the
-[rocker/verse](https://hub.docker.com/r/rocker/verse/tags) base image becomes
-unavailable and/or the Posit Public Package Manager (RStudio Package Manager,
-RSPM) snapshot of CRAN becomes unavailable.
+The Docker approach reruns the analyses in a Docker container which encapsulates
+the computational environment (R and R package versions) that was used in the
+original analysis. The only way this approach could become non-reproducible is
+when the [rocker/verse](https://hub.docker.com/r/rocker/verse/tags) base image
+becomes unavailable and/or the Posit Public Package Manager (RStudio Package
+Manager, RSPM) snapshot of CRAN becomes unavailable.
diff --git a/rsabsence.pdf b/rsabsence.pdf
index 7e2e8680c4a3b98936af4777beb42470e9824070..9f8dd90f70396a8140799ac48760b49a3dbf3b8b 100644
Binary files a/rsabsence.pdf and b/rsabsence.pdf differ