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-4.7)DM_1.7.5.zip(r-4.6)DM_1.7.5.zip(r-4.5)
DM_1.7.5.tgz(r-4.6-any)DM_1.7.5.tgz(r-4.5-any)
DM_1.7.5.tar.gz(r-4.7-any)DM_1.7.5.tar.gz(r-4.6-any)
DM_1.7.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DM/json (API)

# 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:

Conda:

bayesianprotected-speciessalmonjagscpp

3.39 score 487 scripts 12 exports 66 dependencies

Last updated from:b8feb2e17a. Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING149
source / vignettesERROR258
linux-release-x86_64WARNING171
macos-release-arm64WARNING117
macos-oldrel-arm64WARNING124
windows-develWARNING95
windows-releaseWARNING118
windows-oldrelWARNING95
wasm-releaseOK123

Exports:centerProdCapcreatePriorscreateRAVfilefindOptimumgetPostDrawsplotPriorsplotResultsreadDatarunModeluncenterProdCapwriteReportwriteResultsToFile

Dependencies:abindbase64encbootbslibcachemclicodacodetoolscommonmarkDEoptimRdigestdoParalleldoSNOWevaluatefastmapfontawesomeforeachfsGenSAglueGmedianhighrhtmltoolshttpuviteratorsjquerylibjsonliteKernSmoothknitrlaterlatticelifecyclemagrittrMatrixmemoisemimeopenxlsxotelpromisesR2jagsR2WinBUGSR6rappdirsRcppRcppArmadilloRcppEigenrjagsrlangrmarkdownrobustbaseRSpectrasassshinyshinyAcesnowsourcetoolsstringistringrtinytexvctrsVRAPwithrxfunxtableyamlzip

Readme and manuals

Help Manual

Help pageTopics
Calculate harvest ratecalcHarvest
Calculate initial values for MCMC.calcInitVals
Calculate harvested recruits and escapementcalculateHarvested
Calculate process error and SMSY.calculatePEandSmsy
Center productivty and log capacity parameterscenterProdCap
Center productivty and log capacity parameters conditioned on values in inputconditionalcenterProdCap
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 VRAPDM 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 compositionplotAgeComp
Create plots of capacity posteriorsplotCapacity
Create plots of covariate coefficientsplotCoefs
Create plots of priors for productivity and log capacity.plotPriors
Create plots of productivity posteriorsplotProductivity
Create plots from DM runsplotResults
This reads in the csv file saved from an A & P file and creates dat and inputreadData
Call JAGS to get the posterior draws.runJAGS
Run the DM modelrunModel
Helper function that takes the name of SR function and returns the recruitsselectSR
Create posterior credible interval plots from multiple DM runssimplePlot
SR funcitonsbevertonHolt hockeyStick ricker srfunctions
Original dynamic modelSSTfuncDM
Summarize runssummarizeRuns
Uncenter productivty and log capacity parametersuncenterProdCap
write the model in BUGS languagewriteBUGScode
Creates a report with plots.writeReport
Save DM output.writeResultsToFile