readData: This reads in the csv file saved from an A & P file and...
In eeholmes/DM: Dynamic Model

Description Usage Arguments Value

The DM tab of the A & P excel file has all the necessary inputs to run DM. This reads that .csv file and makes a list needed for the DM functions. creates input which has the other user specified values for the rav file.

1	readData(a.and.p.file, input, folder = "./", silent = FALSE)

a.and.p.file

a csv file saved from the DM tab of an A & P excel file

input

a list with the other values needed for a DM run. The following are the defaults used, but can be passed in to specify something different.

population: name of the population. Defaults to using value in A and P file.
naturalMort: vector of natural mortality for age 1:6. Defaults to c(0.5,0.4,0.3,0.2,0.1,0)
firstYear: First year of spawner data to use. Defaults to using value in cell C4 on DynamicsInput tab in A and P file.
lastYear: Last year of spawner data to use. Defaults to using value in cell C5 on DynamicsInput tab in A and P file.
MSYfirstYear: Defaults to using firstYear.
MSYlastYear: Defaults to using lastYear.
analysisType: "DM" or "SS". Defaults to DM.
SRfunction: ("ricker")/"bevertonHolt"/"hockeyStick": spawner-recruit function
includeMarineSurvival: "yes"/("no"): include marine survival covariate
includeFlow: "yes"/("no"): include flow covariate
initialPopSize: Initial population size for age 2 to 5. Defaults to using values in cells N6:Q6 on DynamicsInput tab in A and P file.
prod: Used for initial conditions of optimizers and MCMC algorithm. Default is NA which means the ML estimates are used as the initial conditions.
cap: Used for initial conditions of optimizers and MCMC algorithm. Default is NA which means the ML estimates are used as the initial conditions.
msCoef: Used for initial conditions of optimizers and MCMC algorithm. Default is NA which means the ML estimates are used as the initial conditions.
flowCoef: Used for initial conditions of optimizers and MCMC algorithm. Default is NA which means the ML estimates are used as the initial conditions.
centerMS: Set mean of the MS covariate to zero in the SR function. Default is TRUE.
centerFlow: Set mean of the flow covariate to zero in the SR function. Default is TRUE.
escapementObsSD: NULL
age2correction: Correction for seeing fewer age 2 fish when sampling for age composition. The value to pass in is an estimate of detection probability for age 2 fish / detection probability for ages 3-5 fish. Default is 1.0: no correction.