This package is hidden from search results because it is not hosted in the universe of the upstream ownernwfsc-math-bio. See also theR-universe documentation.

Package: DM 1.7.5

Elizabeth Holmes - NOAA Federal

DM: Dynamic Model

This package uses comma-delimited data exported from the A&P Excel files to estimate the SR parameters for a user-specified SR function.

Authors:Eli Holmes, Martin Liermann, Howard Coleman, NOAA, Seattle, USA

DM_1.7.5.tar.gz
DM_1.7.5.zip(r-4.5)DM_1.7.5.zip(r-4.4)DM_1.7.5.zip(r-4.3)
DM_1.7.5.tgz(r-4.5-any)DM_1.7.5.tgz(r-4.4-any)DM_1.7.5.tgz(r-4.3-any)
DM_1.7.5.tar.gz(r-4.5-noble)DM_1.7.5.tar.gz(r-4.4-noble)
DM_1.7.5.tgz(r-4.4-emscripten)DM_1.7.5.tgz(r-4.3-emscripten)
DM.pdf |DM.html✨
DM/json (API)
NEWS

# Install 'DM' in R:

install.packages('DM', repos = c('https://nmfs-opensci.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nwfsc-math-bio/dm/issues

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC
c++– GNU Standard C++ Library v3

On CRAN:

bayesian protected-species salmon jags cpp

3.31 score 410 scripts 12 exports 66 dependencies

Last updated 7 years agofrom:b8feb2e17a. Checks:1 ERROR, 7 WARNING. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	FAIL	Jan 27 2025
R-4.5-win	WARNING	Jan 27 2025
R-4.5-mac	WARNING	Jan 27 2025
R-4.5-linux	WARNING	Jan 27 2025
R-4.4-win	WARNING	Jan 27 2025
R-4.4-mac	WARNING	Jan 27 2025
R-4.3-win	WARNING	Jan 27 2025
R-4.3-mac	WARNING	Jan 27 2025

Exports:centerProdCap createPriors createRAVfile findOptimum getPostDraws plotPriors plotResults readData runModel uncenterProdCap writeReport writeResultsToFile

Dependencies:abind base64enc boot bslib cachem cli coda codetools commonmark crayon DEoptimR digest doParallel doSNOW evaluate fastmap fontawesome foreach fs GenSA glue Gmedian highr htmltools httpuv iterators jquerylib jsonlite KernSmooth knitr later lattice lifecycle magrittr Matrix memoise mime openxlsx promises R2jags R2WinBUGS R6 rappdirs Rcpp RcppArmadillo RcppEigen rjags rlang rmarkdown robustbase RSpectra sass shiny shinyAce snow sourcetools stringi stringr tinytex vctrs VRAP withr xfun xtable yaml zip

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate harvest rate	calcHarvest
Calculate initial values for MCMC.	calcInitVals
Calculate harvested recruits and escapement	calculateHarvested
Calculate process error and SMSY.	calculatePEandSmsy
Center productivty and log capacity parameters	centerProdCap
Center productivty and log capacity parameters conditioned on values in input	conditionalcenterProdCap
Create bugs data for model with or without age data.	createBUGSdata
Create a priors list.	createPriors
Create rav file.	createRAVfile
Shiny app to run DM and VRAP	DM DMVRAP
Optimization functions.	findOptimum
Get the simulations from a jags output list.	getPostDraws
Helper file for creating text for the reports.	info
Create plots of age composition	plotAgeComp
Create plots of capacity posteriors	plotCapacity
Create plots of covariate coefficients	plotCoefs
Create plots of priors for productivity and log capacity.	plotPriors
Create plots of productivity posteriors	plotProductivity
Create plots from DM runs	plotResults
This reads in the csv file saved from an A & P file and creates dat and input	readData
Call JAGS to get the posterior draws.	runJAGS
Run the DM model	runModel
Helper function that takes the name of SR function and returns the recruits	selectSR
Create posterior credible interval plots from multiple DM runs	simplePlot
SR funcitons	bevertonHolt hockeyStick ricker srfunctions
Original dynamic model	SSTfuncDM
Summarize runs	summarizeRuns
Uncenter productivty and log capacity parameters	uncenterProdCap
write the model in BUGS language	writeBUGScode
Creates a report with plots.	writeReport
Save DM output.	writeResultsToFile