Before installing datalimited2, you will need to install JAGS (for BSM) and a C++ compiler (i.e., Xcode for Macs, RTools for Windows; for installing packages using the "devtools" package).
The "datalimited2" R package can then be installed from GitHub with:
# Run if you don't already have devtools installed
install.packages("devtools")
# Run once devtools is successfully installed
devtools::install_github("cfree14/datalimited2")
library(datalimited2)The package implements the following catch-only stock assessment models:
- cMSY from Froese et al. 2017; see
?cmsy2 - Bayesian surplus production model (BSM) from Froese et al. 2017; see
?bsm - Boosted regression tree approach (zBRT) from Zhou et al. 2017a; see
?zbrt - Optimized catch-only model (OCOM) from Zhou et al. 2017b; see
?ocom - Refined ORCS approach (rORCS) from Free et al. 2017; see
?rorcs - Multispecies cMSY (MS-cMSY) from Free et al. in prep; see
?ms_cmsy
The results of all but the rORCS model can be visualized using the ?plot_dlm function.
The performance of catch-only methods (i.e., their ability to accurately estimate B/BMSY or accurately classify categorical status) can be compared using the ?performance function.
Many of these catch-only methods require estimates of resilience to set priors and resilience estimates can be retrieved from FishBase/SeaLifeBase busing the ?resilience function.
To cite the package, cite the authors of the original assessment method (shown below) and the following:
Free CM (2018) datalimited2: More stock assessment methods for data-limited fisheries. R package version 0.1.0. https://github.com/cfree14/datalimited2
Free CM, Rudd MB, Kleisner KM, Thorson JT, Longo C, Minto C, Jensen OP (in prep) Multispecies catch-only models for assessing data-limited fisheries.
Free CM, Jensen OP, Wiedenmann J, Deroba JJ (2017) The refined ORCS approach: a catch-based method for estimating stock status and catch limits for data-poor fish stocks. Fisheries Research 193: 60-70.
Froese R, Demirel N, Coro G, Kleisner KM, Winker H (2017) Estimating fisheries reference points from catch and resilience. Fish & Fisheries 18(3): 506-526.
Zhou S, Punt AE, Ye Y, Ellis N, Dichmont CM, Haddon M, Smith DC, Smith ADM (2017a) Estimating stock depletion level from patterns of catch history. Fish & Fisheries 18(4): 742-751.
Zhou S, Punt AE, Smith ADM, Ye Y, Haddon M, Dichmont CM, Smith DC (2017b) An optimised catch-only assessment method for data poor fisheries. ICES Journal of Marine Science: doi:10.1093/icesjms/fsx226.