Man pages for wStockhausen/tcsamFunctions
Functions related to the BSAI Tanner crab stock assessment (2015+)
| calcMeanGrowth.DonaldsonEtAl1981 | Calculate mean growth as in Donaldson et al., 1981 |
| calcMeanGrowth.tcsam02 | Calculate mean growth as in TCSAM02 |
| calc.prMat.Males | Function to calculate Pr(mature|z) for new shell males |
| calcPrMoltToMaturity | Calculate the probability at crab size z for the molt to... |
| calcSizeTransitionMatrices | Calculate size transition matrices for Tanner crab |
| calcSizeTransitionMatrix | Calculate a size transition matrix |
| calcSizeTransitionMatrix.LinearGrowthIncrement | Calculate a size transition matrix |
| calcSizeTransitionMtrix.tcsam02 | Calculate the size transition matrix as in TCSAM02 |
| calc.WatZ | Convert Tanner crab size to weight using the current (2015)... |
| calc.WatZ.2014 | Convert Tanner crab size to weight based on the 2014... |
| elem_prod | Implementation of ADMB function "elem_prod" |
| getGrowthParams | Retrieve a list of growth parameters |
| getScaleForAbundance | Get multiplicative scale factor from input abundance units to... |
| getScaleForBiomass | Get multiplicative scale factor from input biomass units to... |
| inputList_AggregateCatchData | Create an input list for aggregate catch data |
| inputList_EffortData | Create an input list for effort data |
| inputList_SizeCompsData | Create an input list for size comps data |
| makeBubblePlots | Make bubble plots of a matrix or list of matrices |
| mfexp | Implemetation of ADMB function "mfexp" |
| pdf_dz | Evaluate a gamma pdf for _molt increment_ parameterized by... |
| pdf_gamma | Evaluate a gamma pdf |
| pdf_z | Evaluate a gamma pdf for _post-molt size_ given pre-molt... |
| plot_pdf | Plot a gamma pdf for post-molt size parameterized by mean and... |
| plotSizeTransitionMatrix | Plot a growth transition matrix as an image |
| selFcn.AscNormal3 | Calculate a ascending normal selectivity function with "3"... |
| selFcn.DoubleNormal | Calculate a double normal selectivity function |
| selFcn.DoubleNormal4a | Calculate a double normal selectivity function with "4a"... |
| simGrowth | Simulate individual growth trajectories based on a size... |
| square | Implemetation of ADMB function "square" |
| subForTCSAM | Make substitutions for "undetermined" |
| writeInputFile_FleetData | Write fleet data (fishery or survey) to a TCSAM input file |
| writeTCSAM02_AggregateCatchData | Write aggregate catch data to a connection in TCSAM02 input... |
| writeTCSAM02_CatchData | Write catch data type (retained catch, total catch, discard... |
| writeTCSAM02_EffortData | Write effort data to a connection in TCSAM02 input format |
| writeTCSAM02_SizeCompsData | Write size composition data to a connection in TCSAM02 input... |
