Add docker and README

4 files changed, 63 insertions, 2 deletions

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..1d0f46b
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,38 @@
+# Start with R version 4.2.2
+FROM rocker/r-ver:4.2.2
+
+# Install some linux libraries that R packages need
+RUN apt-get update && apt-get install -y \
+  pandoc \
+  libcurl4-openssl-dev \
+  libfontconfig1-dev \
+  libssl-dev \
+  cmake \
+  libxml2-dev \
+  libxt6
+
+# Set renv version 0.15.5
+ENV RENV_VERSION 0.15.5
+
+# Install renv
+RUN Rscript -e "install.packages('http://cran.r-project.org/src/contrib/Archive/renv/renv_${RENV_VERSION}.tar.gz', repos=NULL, type='source')"
+
+# Create a working directory
+WORKDIR /unmarked-paper
+
+# Install all R packages specified in renv.lock
+COPY renv.lock renv.lock
+RUN Rscript -e 'renv::restore()'
+
+# Copy necessary files
+COPY unmarked_Paper_Analysis.Rmd unmarked_Paper_Analysis.Rmd
+COPY acfl_roanoke_river.csv acfl_roanoke_river.csv
+
+# Run analysis
+RUN Rscript -e "rmarkdown::render('unmarked_Paper_Analysis.Rmd')"
+
+# Copy other files
+COPY README.md README.md
+
+# Default to bash terminal when running docker image
+CMD ["bash"]
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..2f9dafe
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,8 @@
+docker:
+	docker image build -t unmarked-paper .
+	$(eval ID = $(shell docker create unmarked-paper))
+	mkdir -p docker-output
+	rm -f docker-output/*
+	docker cp $(ID):/unmarked-paper/unmarked_Paper_Analysis.html docker-output/
+	docker cp $(ID):/unmarked-paper/Figure_4.tiff docker-output/
+	docker rm -v $(ID)
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..3b725ca
--- /dev/null
+++ b/README.md
@@ -0,0 +1,15 @@
+# unmarked-paper
+
+Analysis code for Kellner KF, et al. "The unmarked R package: Twelve years of advances in occurrence and abundance modeling in ecology".
+
+This analysis is fully reproducible using the following steps.
+
+1. Copy the data file `acfl_roanoke_river.csv` into this directory.
+2. Install the `renv` package, e.g. with `install.packages('renv')`.
+3. Run `renv::restore()` in this directory. This downloads and locally installs the exact versions of the R packages specified in the `renv.lock` file (it should not affect your existing R package library).
+4. Compile the Rmarkdown document by running `rmarkdown::render("unmarked_Paper_Analysis.Rmd")`. As part of this process, output will be tested to make sure it matches expected results.
+
+This will yield two files: an HTML file with the analysis results, and a TIFF image (Figure 4 in the paper).
+
+Alternatively you can build the Docker image by running `make docker` in this directory at the command line, assuming you have the appropriate software installed.
+In this case, after the Docker image is built the two resulting output files will be copied into a new `docker-output` directory.
diff --git a/unmarked_Paper_Analysis.Rmd b/unmarked_Paper_Analysis.Rmd
index 8ae3168..ada0ff5 100644
--- a/unmarked_Paper_Analysis.Rmd
+++ b/unmarked_Paper_Analysis.Rmd
@@ -409,7 +409,7 @@ stopifnot(pct_decline_plant == 7.0)
 pct_decline_plant
 ```
 
-## Build Figure 5
+## Build Figure 4
 
 Predicted abundance over time by habitat:
 
@@ -441,7 +441,7 @@ ggplot(data=pr, aes(x=Year+2005, y=Predicted)) +
 Save plot to file:
 
 ```{r}
-tiff("Figure_5.tiff", height=5, width=7, units='in', res=300, compression='lzw')
+tiff("Figure_4.tiff", height=5, width=7, units='in', res=300, compression='lzw')
 ggplot(data=pr, aes(x=Year+2005, y=Predicted)) +
   geom_point(data=pr_point, aes(col=Habitat), alpha=0.2) +
   geom_ribbon(aes(ymin=lower, ymax=upper, fill=Habitat), alpha=0.2) +