baydem

The R package baydem (for bayESIAN demOGRAPHY) provides tools for reconstructing past and present demography.

Quickstart

Use of the two options below to install baydem and its dependencies, then read the vignette for the standard pipeline:

TODO: add vignettte link

Installation

There are two options for installing and using the package:

(1) Install on an existing computer with necessary dependencies

(2) Build a Docker image using the Dockerfile

Option 1: Install on an existing computer with necessary dependencies

Details will vary based on the machine and operating system since certain R packages on which baydem depends require the installation of tools outside R. The following should be sufficient:

(a) Install devtools with its dependencies https://www.rdocumentation.org/packages/devtools

(b) Install rstan with its dependencies http://mc-stan.org/rstan/

(c) Install baydem

Having completed the preceding steps, install baydem with the following commands in R:

library(devtools)
install_github("eehh-stanford/baydem")

Option 2: Build a Docker image using the Dockerfile

First, clone the database and build the Docker image (rather than cloning the entire directory, one can also just download Dockerfile and setup.R from the github repository and place them in the working directory).

To force all docker material to be (re)downloaded prior to creating the Docker image – a step you should be certain you want to take – use: “docker system prune -a”

git clone https://github.com/eehh-stanford/baydem
cd baydem
docker build -t michaelholtonprice/baydem .

Start a container. Use the -v tag to mirror a directory for passing files between the host machine and the Docker container. The directory to the left of the semicolon is for the host machine and the directory to the right of the semicolon is for the Docker container. The path for the host machine will need to be modified for your situation.

docker run --name baydem -itv //c/mirrored_baydem_data:/data michaelholtonprice/baydem

The Docker container already has baydem installed, and it is likely the latest version. However, the latest version can be (re)installed by cloning the github repository inside the Docker container and using devtools::install_local. Following this, the test scripts can be run to check the installation (they will take perhaps 30 minutes to complete):

git clone https://github.com/eehh-stanford/baydem
cd baydem
R
library(devtools)
install_local(".",force=T,dep=F)
test()