sdmgamindex

This repository was previously forked from casperwberg/surveyIndex and previously named emilymarkowitz-noaa/surveyIndex.

R package for calculating survey indices by age from DATRAS exchange data.

This code is always in development. Find code used for various reports in the code releases.

Code has been modified and adapted by:

Emily Markowitz (Emily.Markowitz AT noaa.gov; @EmilyMarkowitz-NOAA)

Margaret Siple (Margaret.Siple AT noaa.gov; @MargaretSiple-noaa)

Alaska Fisheries Science Center

National Marine Fisheries Service

National Oceanic and Atmospheric Administration

Seattle, WA 98195

Code was originally developed by:

Casper W. Berg (https://orbit.dtu.dk/en/persons/casper-willestofte-berg; @casperwberg)

National Institute of Aquatic Resources,

Technical University of Denmark

Based on the work published in: Berg et al. (2014)

Repository: remotes::install_github("casperwberg/surveyIndex/surveyIndex")

Installation

To install you need the DATRAS package

library(remotes)
remotes::install_github("DTUAqua/DATRAS/DATRAS")
# remotes::install_github("casperwberg/sdmgamindex/sdmgamindex")
remotes::install_github("noaa-afsc/sdmgamindex")

Usage

See examples in the pkgdown site and in the ?get_surveyidx() documentation.

Metadata

This package was last produced using:

## R version 4.3.1 (2023-06-16 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                           LC_TIME=English_United States.utf8    
## 
## time zone: America/Los_Angeles
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] knitr_1.45    badger_0.2.3  pkgdown_2.0.7 usethis_2.2.3 here_1.0.1   
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.4        httr2_1.0.0         xfun_0.42           ggplot2_3.5.0       htmlwidgets_1.6.4   devtools_2.4.5      remotes_2.4.2.1     gh_1.4.0            yulab.utils_0.1.4   vctrs_0.6.5         tools_4.3.1         generics_0.1.3      curl_5.2.1         
## [14] tibble_3.2.1        fansi_1.0.6         pkgconfig_2.0.3     RColorBrewer_1.1-3  lifecycle_1.0.4     compiler_4.3.1      stringr_1.5.1       credentials_2.0.1   dlstats_0.1.7       munsell_0.5.0       janitor_2.2.0       snakecase_0.11.1    httpuv_1.6.14      
## [27] sys_3.4.2           htmltools_0.5.7     yaml_2.3.8          crayon_1.5.2        later_1.3.2         pillar_1.9.0        urlchecker_1.0.1    ellipsis_0.3.2      RODBC_1.3-23        openssl_2.1.1       cachem_1.0.8        sessioninfo_1.2.2   mime_0.12          
## [40] tidyselect_1.2.0    digest_0.6.34       stringi_1.8.3       dplyr_1.1.4         purrr_1.0.2         rprojroot_2.0.4     fastmap_1.1.1       grid_4.3.1          colorspace_2.1-0    cli_3.6.2           magrittr_2.0.3      pkgbuild_1.4.3      utf8_1.2.4         
## [53] rappdirs_0.3.3      scales_1.3.0        promises_1.2.1      lubridate_1.9.3     timechange_0.3.0    rmarkdown_2.25      gitcreds_0.1.2      rvcheck_0.2.1       askpass_1.2.0       memoise_2.0.1       shiny_1.8.0         evaluate_0.23       miniUI_0.1.1.1     
## [66] profvis_0.3.8       rlang_1.1.3         gert_2.0.1          Rcpp_1.0.12         xtable_1.8-4        glue_1.7.0          BiocManager_1.30.22 pkgload_1.3.4       rstudioapi_0.15.0   jsonlite_1.8.8      R6_2.5.1            fs_1.6.3

NOAA README

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

NOAA License

Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.

U.S. Department of Commerce | National Oceanographic and Atmospheric Administration | NOAA Fisheries

Berg, C. W., Nielsen, A., and Kristensen, K. (2014). Evaluation of alternative age-based methods for estimating relative abundance from survey data in relation to assessment models. Fish. Res., 151, 91–99. https://doi.org/10.1016/j.fishres.2013.10.005