This is a place to:
-
Share R code used by the OFP-SAM team, mainly functions that do not have a home in a package (yet).
-
Organize and communicate R code development and maintenance by the OFP-SAM team.
The OFP-SAM team maintains, to a varying degree, the following R packages related to Multifan-CL:
| Package | Maintainer | Created | Last modified | Dependencies | Purpose |
|---|---|---|---|---|---|
| diags4MFCL | Nicholas | 2020 Apr | 2022 Nov | FLR4MFCL, frqit, data.table, ggplot2, ggthemes, magrittr, RColorBrewer | Present MFCL results and diagnostics |
| condor | Arni | 2023 Feb | 2023 Jun | ssh | Interact with Condor from R via SSH |
| frqit | Matt | 2020 May | 2021 Jun | FLR4MFCL | Read and manipulate MFCL frq files |
| FLR4MFCL | Rob | 2015 Mar | 2023 Jun | FLCore | Tame MULTIFAN-CL |
| miWantemLuk | Rob | 2021 Feb | 2023 Jun | FLR4MFCL, chorddiag, hrbrthemes, networkD3, patchwork, r2d3, tidyverse, viridis | Graphing and data visualisation |
| R4MFCL | Arni | 2011 May | 2023 Feb | data.table, dplyr, ggmap, ggplot2, gridExtra, magrittr, mapdata, maps, reshape2, rlang, RODBC, RSQLite, scales, stringr, tidyr, viridis, xtable | Automate the running and analysis of MFCL stock assessments |
This table was last updated on 30 Jun 2023.
Finlay has developed two kinds of Shiny apps to browse OFP-SAM stock assessments:
- Stepwise app to plot individual or several models
- Grid app to plot all grid models
Arni applied the Stepwise app to the YFT 2020 review, based on the SKJ 2022 Stepwise app. Jemery and Arni then adapted the Stepwise app to the BET and YFT 2023 assessments.
The following repositories contain OFP-SAM Shiny apps for stock assessments:
| Purpose | Repository | Online |
|---|---|---|
| Development | https://github.com/PacificCommunity/ofp-sam-shinyMFCL | - |
| BET 2020 sensitivities | https://github.com/PacificCommunity/ofp-sam-shinyMFCL/tree/main/examples/bet_2020_sensitivities | - |
| BET 2023 stepwise | https://github.com/PacificCommunity/ofp-sam-bet-2023-shiny | - |
| SKJ 2022 sensitivities | https://github.com/PacificCommunity/ofp-sam-shinyMFCL/tree/main/examples/skj_2022_reg5_sens | - |
| SKJ 2022 stepwise | https://github.com/PacificCommunity/ofp-sam-shinyMFCL/tree/main/examples/skj_2022_stepwise | - |
| YFT 2020 review | https://github.com/PacificCommunity/ofp-sam-shinyMFCL/tree/main/examples/yft_2020_review | - |
| YFT 2023 stepwise | https://github.com/PacificCommunity/ofp-sam-yft-2023-shiny | - |