| adjustAlaska | (SPFI) Sum SEAK CWT data |
| buildCMZfishery | (ISBM/CYER) Build a mapping table to define a fishery group's... |
| build_jurisdiction | Create new jurisdiction data frame. |
| buildmodel.list | (Calibration Performance) Automatic Creation Of argument List |
| build_stocks.key | Create a new stocks.key data frame from *.STF files. |
| calc_AAPC | (SPFI) Data imputation by the Accrued APC (AAPC) method. |
| calc_APC | (SPFI) Data imputation by the Average Proportion Correction... |
| calcCYER | (ISBM/CYER) Calculate CYER and its index. |
| calcCYERindex | Calculate the Catch year exploitation rate index (CYER... |
| calc_Difference | (SPFI) Calculate difference between distribution parameters... |
| calc_d.tsa | (SPFI) Calculate the distribution parameters grouped by... |
| calc_fp | (FP) Calculate fisheries policy (FP) scaler. |
| calc_GLMC | (SPFI) Data imputation by the GLMC method. |
| calc_hcwt.ty | (SPFI) Calculate the CWT harvest rate parameters grouped by... |
| calc_H.ty | (SPFI) Calculate the AEQ stratum harvest rate parameters... |
| calc_H.ty2 | (SPFI) Calculate the AEQ stratum harvest rate parameters... |
| calc_H.ty3 | (SPFI) Calculate the AEQ stratum harvest rate parameters... |
| calc_H.y | (SPFI) Calculate the AEQ fishery harvest rate parameters... |
| calc_H.y2 | (SPFI) Calculate the harvest rate parameters grouped by year. |
| calcIndexError | Calculate errors of ISBM and CYER |
| calcMPEfreq | (Calibration Performance) Frequency counts by MPE bin ranges. |
| calc_N.ty | (SPFI) Calculate the abundance by fishery stratum and year. |
| calc_N.y | (SPFI) Calculate the total yearly abundance across fishery... |
| calcPMs | (Calibration Performance) Group Performance Measures |
| calcRanks | (Calibration Performance) Rank Calculation |
| calc_SPFI | (SPFI) Wrapper function to calculate the stratified... |
| calc_S.ty | (SPFI) Calculate the stata specific harvest rate indices by... |
| calc_S.y | (SPFI) Calculate the SPFI grouped by year. |
| calc_tsa.sum | (SPFI) Sum CWT catch by fishery, stock, and age. |
| calc_T.ty | (SPFI) Calculate the Pacific Salmon Treaty catch, grouped by... |
| calc_ty.sum | (SPFI) Sum CWT catch by fishery, and year. |
| checkMissingfiles | (HRJ) Check for matching B & C file names in the vector of... |
| cleanCMZ | Clean *cmz.csv files for easy importing. |
| combinePTdata | (ISBM/CYER) Combine the data from multiple .pt files. |
| ctctools | ctctools: Analytical tools for the Chinook Technical... |
| ctctools-deprecated | Deprecated functions in ctctools |
| fishery.def | Data defining each fishery. |
| importCatch.jon | Import catch csv file made by Jonathan Carey. |
| importFCSCCC | (Calibration Performance) Import FCS and CCC files |
| importTableOfDifferences | (Calibration Performance) Import and combine tables of... |
| jurisdiction | Jurisdiction data for each stock |
| mergeFCSCCC | (Calibration Performance) Merge FCS And CCC Data |
| minimizeDistribution | Minimization to estimate distribution parameter |
| plotFCSCCC | (Calibration Performance) Model Comparison Plots |
| plotFCSvsCCC | plotFCSvsCCC |
| plotFPAseries | Plot series found in *.fpa files. |
| plot_fpseries | (FP) Plot time series of FP values. |
| plotPM | (Calibration Performance) Lattice plot to compare PMs across... |
| read_BSE | Read BSE file |
| readCatchData | (SPFI) Read the CTC catch data files (*.cat). |
| readCCC | (Calibration Performance) Import checkCCC Files |
| readDataArchive | Read text files that are stored in a PBS archive format. |
| readFCS | (Calibration Performance) Import FCS Files |
| read_FPA | Read FPA files. |
| readHRJAccessDatabase | (HRJ) Read in data from the HRJ (MS Access) data base. |
| readHRJtext | (HRJ) Read in and combine multiple HRJ text files. |
| read_mdl | Read in mdl files of cwt recovery data. |
| read_modelstocklist.csv | Read model stock list file. |
| readMortalityDist | (ISBM/CYER) Import motality distribution CMZ (*.csv) files. |
| readPT | (ISBM/CYER) Import one or more ISBM index (*.pt) files. |
| readPTfromstep11csv | (ISBM/CYER) Import one or more ISBM index files, in step11... |
| read_stkfile | Read in stk file of base period exploitation rates. |
| readStockData | (SPFI) Read CTC stock file (stocfile.stf). |
| readTHECCC | Read the model output CCC raw file ("THE" CCC file) |
| reshapeHRJtolong | (HRJ) Reshape wide formatted HRJ file to long format. |
| reshapeHRJtowide | (HRJ) Reshape HRJ data frame from long to wide format for... |
| stocks.key | Data defining each stock. |
| sumPMs | (Calibration Performance) Performance Measure Summation |
| tabulateMetrics | (Calibration Performance) Tabulate Ranking |
| updateStockByName | (HRJ) Add stock number to HRJ data frame based on its three... |
| writeCalibrationTable1 | (Calibration Performance) Write Table1 To csv |
| writeCalibrationTable3 | (Calibration Performance) Write Table3 |
| writeCalibrationTable4 | (Calibration Performance) Write Table4 |
| writeCalibrationTable5 | (Calibration Performance) |
| write_fpa | Write FPA text file |
| writeHRJAccessDatabase | (HRJ) Write HRJ "B" & "C" tables to MS Access database. |
| writeHRJcsv | (HRJ) Write HRJ "B" & "C" tables to csv (text) files. |
| writeModelListBuilder | (Calibration Performance) Build, save, and open an R script... |
| writeScriptCalibrationTester | (Calibration Performance) Build, save, and open an R script... |
| writeScriptFP | (FP) Build, save, and open an R script to help execute FP... |
| writeScriptHRJ | (SPFI) Build, save, and open an R script to help manage HRJ... |
| writeScriptISBM | (ISBM/CYER) Build, save, and open an R script to help compare... |
| writeScriptSPFI | (SPFI) Build, save, and open an R script to help execute... |
| writeSPFItable6.6 | (SPFI) Write csv file of summarized SPFI results. |
| writeSTFfile | Write .stf text file. |
| writeTableOfDifferences | (Calibration Performance) |
