age_representativeness_plot | Compare length histogram of aged samples to all lengthed... |
ask_password | Get password from the user if 'interactive()' |
capValues | Decrease all values greater than a maximum specified value. |
changecol_pacfin | Change Column Names of PacFIN Data To Match Survey |
checkGrade | Check Sample Numbers for Grade |
checkLenAge | Calculate von Bertalanffy Growth Parameters |
cleanColumns | Change Column Names to Vdrfd |
cleanColumns.bds | Clean columns of PacFIN biological data |
cleanColumns.catch | Clean columns of PacFIN catch data |
cleanPacFIN | Clean raw PacFIN data |
codify_age_method | Code ageing methods to standardized character strings |
combineCalCOM | Combine CalCOM and PacFIN data |
comps_bins | Bin a vector of data into groups |
comps_wide | Convert long data frame with composition data to wide data... |
convertlength_skate | Convert Disc and Interspiracular Width to Length |
doSexRatio | Assign gender for unsexed fish |
EF1_Denominator | Calculate the denominator for the level-1 expansion factor. |
EF1_Numerator | Calculate the numerator for the first level expansion factor |
find.matching.rows | Function find.matching.rows |
formatCatch | Format catches from long to wide |
getAge | Get age information for each fish |
getAgeMethod | Get the ageing method used for the age that is agreed to be... |
getArea | Get the general area that the information was taken from |
get_codelist | Get a list of available options, e.g., code_list, from PacFIN |
getComps | Aggregate length, age, or age-at-length composition data by... |
getDB | Get a connection to a database and return a query |
getExpansion_1 | First-Stage Expansion for Composition Data |
getExpansion_2 | Second-stage expansion of composition samples up to catch... |
getGearGroup | Create column for gear called 'geargroup' according to PacFIN... |
getLength | Get length for PacFIN commercial samples |
getSeason | Add a column to 'Pdata' for season. |
getState | Create a state column based on input column specified in... |
getUserName | Get your username for the 'database' of interest |
getweight | Calculate weight from length and the weight-length... |
getWLpars | Calculate weight-length relationship parameters |
grep_final_age | Find the column with the best age information |
PacFIN.Utilities | PacFIN.Utilities: Functions for working up PacFIN data |
PacFIN.Utilities-deprecated | Deprecated function in package 'PacFIN.Utilities' |
pipe | Pipe operator |
plotCleaned | Plot cleaned fishery age- or length-composition data. |
plotRawData | Diagnostic plots and summaries for a raw PacFIN dataset... |
plotStrat | Plot Length Distributions with Aged and All Fish |
plotWL | Plot of the weight-length relationship by sex |
PullBDS.PacFIN | Pull biological data |
PullCatch.PacFIN | Pull catch data from PacFIN |
PullNominal.PacFIN | Pull the species information table and return nominal code(s) |
sql | Write SQL text |
stopifnotcolumn | Stop if column name is not present in the data |
summaryAgeMethod | The number of samples per combination of ageing methods |
tableSample | Table of Sample Size By Fleet and Year |
writeComps | Write out composition data formatted for Stock Synthesis. |
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