Man pages for nwfsc-assess/PacFIN.Utilities
Generate fishery composition data from PacFIN data for the NWFSC
| 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 |
| 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 |
| get_pacfin_expansions | Expand bds data up to the tow and catch level |
| 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 |
| pacfintools | pacfintools: Functions for working up PacFIN data |
| pacfintools-deprecated | Deprecated function in package 'pacfintools' |
| 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 |
