README.md

In McCannLab/spatial_fingerprints: Research compendium

:book: Spatial Fingerprinting - research compendium

Installation

install.packages("remotes")
remotes::install_github("McCannLab/spatial_fingerprints")

Data

Raw data are included in data/data.rda and will be available on Dryad upon manuscript acceptance. See R.get_data_ready.R to see how to access the data within the package. Note that data can easy be written in .csv format using the following:

write.csv(get_data_ready(), file = "data_f_cs.csv",
row.names = FALSE)
# transformed data (PCA)
write.csv(get_data_ready(pca = TRUE), file = "inst/extdata/data_f_pca.csv",
row.names = FALSE)

Reproducibility

Note that this project involved relatively long simulation (roughly .5core year) that were run on Compute Canada'servers. The code to run these simulations are included in this repository:

• for the simulations performed with R, see R/scr_simulations.R;
• for the simulations performed with Julia, see inst/julia/scripts.jl and inst/julia/README.md.

The results of those simulations were save in output/ but not included in this repository due to size constrains (~10Go total).

Once the package is installed, the following can be run:

library(spatialfingerprints)
pipeline()

Note that all steps to reproduce figure that require data that are not included in this repository have been commented out.

McCannLab/spatial_fingerprints documentation built on March 13, 2021, 12:02 a.m.