Man pages for PSC-CoTC/AnnualReport
Writes the Annual Report using a pre and post season FRAM DB.
| BuildFisheryTable | Make a table of fishery mortality |
| checkFramCommentCol | Check if the FRAM database as the new Comments fields for... |
| combine_GS_fishery_mortality | Combines the GS MUs for the fishery.mortality DF (pre or post... |
| combine_GS_stock_summary | Combines the GS MUs for the stock.summary DF (pre or post... |
| CompilePscData | Compile a FRAM model run into PSC fishery and stock groupings |
| createImportFiles | Create Import Files |
| CreateTable1 | Generate the Table 1 of the PSC Annual report for the... |
| CreateTable2 | Generate the Table 2 of the PSC Annual report for the... |
| CreateTable3 | Create Table 3 within the Annual report based on PSC... |
| exportFisheryERs | xlsx of fishery ers |
| FisheryMortSqlFilename | Constants for dealing with a FRAM Database |
| FormatDouble | Formats a value to an double in text form with the specified... |
| formatHtml | Retreives HTML text, binds parameters to the text |
| FormatInt | Formats a value to an integer in text form. This is typically... |
| FormatNameIdText | Formats parallel vectors of names and IDs a single text... |
| formatPkgTextFile | Get the path to a file within an R package |
| formatSql | Retreives Sql Statement text from a file, binds parameters to... |
| FormatTruncTextSet | Formats a vector of strings to a single text block. If more... |
| FramGetSingleRecruitScalar | Recruit Scalar FRAM SQL scripts ————- |
| GetColumnSums | Sum columns |
| getFramBackwardEscapement | A helper function retrieving the escapement values used by... |
| getFramBaseFisheries | Get the dataframe of valid fisheries and time steps from the... |
| getFramBaseStocks | Get the data frame of valid stocks from the base period of a... |
| getFramData | Generic function that retrieves data from database using sql... |
| getFramFisheries | A helper function loading the list of FRAM fisheries in the... |
| getFramFisheryMortality | A helper function loading the total mortalities for all... |
| getFramFisheryScalars | Get the dataframe of fishery scalars used to parameterize... |
| getFramRunInfo | Retrieve the details about a specific FRAM run, by run name |
| getFramRunTable | Retrieve all FRAM runs in a specific data base and species |
| getFramStockRecruitScalars | Get the data frame of stock recruit scalars for particular... |
| getFramStocks | A helper function loading the list of FRAM stocks |
| getFramTotalEscapement | A helper function loading the stock specific escapement from... |
| getFramTotalFisheryMortality | A helper function loading the total mortalities for all... |
| getPersonFramFisheries | Retrieve a data frame with the relationships between CoTC... |
| getPersonFramStocks | Retrieve a data frame with the relationships between CoTC... |
| getPreseasonERs | Writes of preseaon FRAM data |
| GetPscEscapement | Sum up the escapement from a fram run to PSC Stocks |
| GetPscMortality | Sum up the fishery mortalities from a fram run to PSC Stocks |
| GetPstStockCountryCap | Calculate Country Specific PSC Stock ER Cap based on stock... |
| GetPstStockStatusCap | Identifies the stock status of PSC Stocks based on the... |
| GetTammData | Reads the various values of the TAMM spreadsheet and packages... |
| GetTammEscapement | Reads the specific Escapement values from a TAMM model... |
| GetTammFisheryMortality | Reads the specific Stock/Fishery mortality values from a TAMM... |
| GetTammValues | A helper function loading the total mortalities from the TAMM... |
| GetTimeStampText | Provides a standardized text based time stamp for inclusion... |
| importFramTemplates | Import an updated .csv postseason template into a FRAM... |
| kFramBackwardEscSqlFilename | Backward FRAM SQL scripts ————- |
| kFramGetSingleNonRetention | Non-Retention FRAM SQL scripts ————- |
| LoadConfigFiles | Loads a R source file that is used for configuration |
| loadPscData | A function that loads the PSC stock and fishery reference... |
| LoadSourceFile | Loads an R file. This function makes sure a given source... |
| pairEscapementFlags | Matches escapment flags for marked and unmarked stocks, to... |
| parseImportFile | Parses the import file format and returns the results into a... |
| postSeasonTable3Summary | Creates a .xlsx workbook of the "Table3" from the annual... |
| ReadCsv | Read a CSV file from a predefined data directory Optionally,... |
| ReadMemoryCsv | A helper function for reading CSV formated text from a R... |
| RunSqlFile | A helper function that loads an SQL script, updates the... |
| SummaryRegionTotals | Make a table of fishery mortality |
| TitleCase | Convert text into title case Got this regex from:... |
| updateFisheryScalars | Update the fishery scalars and non retention values for an... |
| updateTargetEscapement | Update the stock recruit scalars and the backward FRAM target... |
| ValidateRunInfo | Checks run data retrieved from the FRAM database. |
| ValidateValueDomain | A helper function for validating data within a pre-defined... |
| validEscapementFlags | Validates the escapement flags against the escapement values... |
| validFisheries | Validates the fishery definitions for parametrization of the... |
| validMarkInfo | Validates the mark rate information for mark-selective... |
| validPostSeasonCatch | Validates the catch data for parametrization of a FRAM... |
| validTargetEscapement | Validates the target escapement definitions for... |
| writeAnnualReport | Writes .pdf document of the annual report |
| WriteCsv | A helper function for writing CSV files. This is a simple... |
| writeImportFile | Functions for writing .csv files for CoTC scientists to... |
| WriteMemoryCsv | A helper function for writing CSV file format text into R... |
| WriteProtectedCsv | A helper function for writing CSV files and setting them to... |
| WritePSCFramTables | writes .csv of PSC tables |
