Estimating uncertainty in right whale location following visual or acoustic detection.
This project accompanies the following manuscript:
Johnson HD, Baumgartner MF, Taggart CT. 2020. Estimating North Atlantic right whale (Eubalaena glacialis) location uncertainty following visual or acoustic detection to inform dynamic management. Conservation Science and Practice. e267. https://doi.org/10.1111/csp2.267
The article is available here.
master.R - master script (with simulation parameters) that executes entire analysis
src/ - all source code for analysis, including functions (functions.R) and scripts to produce various figures (f_*.R)
runs/ - data from each model run
cache/ - cached data used across runs or figures
figures/ - figures used in the manuscript
The entire simulation and figures should be reproducible by running the master.R script. On doing so you may be prompted to download and install the libraries required in src/functions.R. Note that the default number of simulated right whales is 1e5 (nrws = 1e5), and this will likely take hours to run depending on your computer specs. I suggest using something smaller, like 1e2, to start.
Below is the output from sessionInfo() on the machine I used for the analysis:
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] raster_3.0-7 sp_1.3-2 gridExtra_2.3 forcats_0.4.0 stringr_1.4.0
[6] dplyr_0.8.3 purrr_0.3.3 readr_1.3.1 tidyr_1.0.0 tibble_2.1.3
[11] ggplot2_3.2.1 tidyverse_1.3.0 oce_1.1-1 gsw_1.0-5 testthat_2.3.1
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 haven_2.2.0 lattice_0.20-38 colorspace_1.4-1 vctrs_0.2.1
[6] generics_0.0.2 rlang_0.4.2 pillar_1.4.3 glue_1.3.1 withr_2.1.2
[11] DBI_1.1.0 dbplyr_1.4.2 modelr_0.1.5 readxl_1.3.1 lifecycle_0.1.0
[16] munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 rvest_0.3.5 codetools_0.2-16
[21] fansi_0.4.0 broom_0.5.3 Rcpp_1.0.3 scales_1.1.0 backports_1.1.5
[26] jsonlite_1.6 fs_1.3.1 hms_0.5.2 stringi_1.4.3 grid_3.6.2
[31] cli_2.0.0 tools_3.6.2 magrittr_1.5 lazyeval_0.2.2 crayon_1.3.4
[36] pkgconfig_2.0.3 zeallot_0.1.0 xml2_1.2.2 reprex_0.3.0 lubridate_1.7.4
[41] assertthat_0.2.1 httr_1.4.1 rstudioapi_0.10 R6_2.4.1 nlme_3.1-142
[46] compiler_3.6.2