Man pages for eeholmes/DM
Dynamic Model

calcHarvestCalculate harvest rate
calcInitValsCalculate initial values for MCMC.
calculateHarvestedCalculate harvested recruits and escapement
calculatePEandSmsyCalculate process error and SMSY.
centerProdCapCenter productivty and log capacity parameters
conditionalcenterProdCapCenter productivty and log capacity parameters conditioned on...
createBUGSdataCreate bugs data for model with or without age data.
createPriorsCreate a priors list.
createRAVfileCreate rav file.
DMShiny app to run DM and VRAP
findOptimumOptimization functions.
getPostDrawsGet the simulations from a jags output list.
infoHelper file for creating text for the reports.
plotAgeCompCreate plots of age composition
plotCapacityCreate plots of capacity posteriors
plotCoefsCreate plots of covariate coefficients
plotPriorsCreate plots of priors for productivity and log capacity.
plotProductivityCreate plots of productivity posteriors
plotResultsCreate plots from DM runs
readDataThis reads in the csv file saved from an A & P file and...
runJAGSCall JAGS to get the posterior draws.
runModelRun the DM model
selectSRHelper function that takes the name of SR function and...
simplePlotCreate posterior credible interval plots from multiple DM...
srfunctionsSR funcitons
SSTfuncDMOriginal dynamic model
summarizeRunsSummarize runs
uncenterProdCapUncenter productivty and log capacity parameters
writeBUGScodewrite the model in BUGS language
writeReportCreates a report with plots.
writeResultsToFileSave DM output.
eeholmes/DM documentation built on Feb. 7, 2018, 12:11 a.m.