From 4683a3f12fc769f8b9ccb028c8dff594ddcf3cea Mon Sep 17 00:00:00 2001 From: kellijohnson-NOAA Date: Tue, 25 Apr 2023 14:35:58 -0700 Subject: [PATCH] document() --- NAMESPACE | 1 - man/EF1_Denominator.Rd | 16 ++++++---------- man/EF1_Numerator.Rd | 16 ++++++---------- man/PacFIN.Utilities-deprecated.Rd | 8 ++++++++ man/PullBDS.PacFIN.Rd | 14 +++++--------- man/PullCatch.PacFIN.Rd | 16 ++++++---------- man/age_representativeness_plot.Rd | 2 +- man/changecol_pacfin.Rd | 9 ++++++--- man/checkLenAge.Rd | 18 +++++++----------- man/cleanPacFIN.Rd | 16 ++++++---------- man/doSexRatio.Rd | 2 +- man/find.matching.rows.Rd | 9 ++++++++- man/getAge.Rd | 16 ++++++---------- man/getArea.Rd | 16 ++++++---------- man/getComps.Rd | 16 ++++++---------- man/getExpansion_1.Rd | 16 ++++++---------- man/getExpansion_2.Rd | 23 +++++++++-------------- man/getGearGroup.Rd | 19 +++++++++---------- man/getLength.Rd | 14 +++++--------- man/getSeason.Rd | 16 ++++++---------- man/getState.Rd | 16 ++++++---------- man/getWLpars.Rd | 16 ++++++---------- man/summaryAgeMethod.Rd | 18 +++++++----------- man/tableSample.Rd | 2 +- man/writeComps.Rd | 16 ++++++---------- 25 files changed, 139 insertions(+), 192 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index f914b83..42e79f7 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -11,7 +11,6 @@ export(capValues) export(changecol_pacfin) export(checkINPFC) export(checkLenAge) -export(cleanAges) export(cleanColumns) export(cleanPacFIN) export(combineCalCOM) diff --git a/man/EF1_Denominator.Rd b/man/EF1_Denominator.Rd index 537eeef..15b126f 100644 --- a/man/EF1_Denominator.Rd +++ b/man/EF1_Denominator.Rd @@ -12,7 +12,7 @@ EF1_Denominator( mb = 3.5, ua = 2e-06, ub = 3.5, - verbose = FALSE, + verbose = TRUE, plot = FALSE, col.weight = "weightkg" ) @@ -36,15 +36,11 @@ which originated in 2014. Data are pulled using sql calls, see \item{ub}{Unsexed weight length exponent.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} \item{plot}{A logical that specifies if plots should be created or not. The default is \code{FALSE}.} diff --git a/man/EF1_Numerator.Rd b/man/EF1_Numerator.Rd index 7d854f5..61adb3a 100644 --- a/man/EF1_Numerator.Rd +++ b/man/EF1_Numerator.Rd @@ -4,7 +4,7 @@ \alias{EF1_Numerator} \title{Calculate the numerator for the first level expansion factor} \usage{ -EF1_Numerator(Pdata, verbose = FALSE, plot = FALSE) +EF1_Numerator(Pdata, verbose = TRUE, plot = FALSE) } \arguments{ \item{Pdata}{A data frame of biological samples @@ -13,15 +13,11 @@ Pacific Fishieries Information Network (PacFIN) data warehouse, which originated in 2014. Data are pulled using sql calls, see \code{\link{PullBDS.PacFIN}()}.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} \item{plot}{Argument takes either a logical or character value specifying the file name if you want to write the plots to a disk rather than printing them diff --git a/man/PacFIN.Utilities-deprecated.Rd b/man/PacFIN.Utilities-deprecated.Rd index 4642002..7b615f2 100644 --- a/man/PacFIN.Utilities-deprecated.Rd +++ b/man/PacFIN.Utilities-deprecated.Rd @@ -4,11 +4,14 @@ \alias{PacFIN.Utilities-deprecated} \alias{checkINPFC} \alias{ls_INPFC} +\alias{cleanAges} \title{Deprecated function in package \pkg{PacFIN.Utilities}} \usage{ checkINPFC(...) ls_INPFC(...) + +cleanAges(...) } \description{ The functions listed below are deprecated and @@ -26,4 +29,9 @@ Functions related to INPFC areas have been deprecated in favor of PSMFC areas. Functions related to INPFC areas have been deprecated in favor of PSMFC areas. } +\section{cleanAges}{ + +\code{cleanAges} was moved to \code{\link[=cleanPacFIN]{cleanPacFIN()}} +} + \keyword{internal} diff --git a/man/PullBDS.PacFIN.Rd b/man/PullBDS.PacFIN.Rd index a4560a6..da4dcfd 100644 --- a/man/PullBDS.PacFIN.Rd +++ b/man/PullBDS.PacFIN.Rd @@ -45,15 +45,11 @@ saved in it.} The default is the current working directory. The path can be relative or absolute.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} } \value{ An RData object is saved to the disk and the pulled data diff --git a/man/PullCatch.PacFIN.Rd b/man/PullCatch.PacFIN.Rd index 1a73cf3..082b0f1 100644 --- a/man/PullCatch.PacFIN.Rd +++ b/man/PullCatch.PacFIN.Rd @@ -11,7 +11,7 @@ PullCatch.PacFIN( password = ask_password(), savedir = getwd(), addnominal = TRUE, - verbose = FALSE + verbose = TRUE ) } \arguments{ @@ -64,15 +64,11 @@ you only want nominal catch for one or if you only wanted nominal catch. Nominal species code will be searched for using \code{\link[=PullNominal.PacFIN]{PullNominal.PacFIN()}} if the input value for \code{addnominal} is \code{TRUE}.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} } \value{ A \code{.RData} file is saved with the object inside the file stored as diff --git a/man/age_representativeness_plot.Rd b/man/age_representativeness_plot.Rd index a172d3c..332de1b 100644 --- a/man/age_representativeness_plot.Rd +++ b/man/age_representativeness_plot.Rd @@ -54,5 +54,5 @@ as \code{sum(sqrt(pi1*pi2))} where pi1 and pi2 are the proportion of data in bin i for each of the two distributions. } \author{ -Ian Taylor, Kathryn L. Doering, Brian Langseth, Kelli Johnson +Ian G. Taylor, Kathryn L. Doering, Brian Langseth, Kelli F. Johnson } diff --git a/man/changecol_pacfin.Rd b/man/changecol_pacfin.Rd index eca968a..9579681 100644 --- a/man/changecol_pacfin.Rd +++ b/man/changecol_pacfin.Rd @@ -4,13 +4,16 @@ \alias{changecol_pacfin} \title{Change Column Names of PacFIN Data To Match Survey} \usage{ -changecol_pacfin(data, verbose = FALSE) +changecol_pacfin(data, verbose = TRUE) } \arguments{ \item{data}{A data frame with names matching those from PacFIN.} -\item{verbose}{A logical value specifying if you want messages printed to -the screen or not. The default is \code{FALSE}, which does not print them.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} } \value{ A data frame with names similar to those exported by the survey-data diff --git a/man/checkLenAge.Rd b/man/checkLenAge.Rd index af061e0..9585177 100644 --- a/man/checkLenAge.Rd +++ b/man/checkLenAge.Rd @@ -15,7 +15,7 @@ checkLenAge( sdFactor = 4, Optim = TRUE, precision = 1, - verbose = FALSE, + verbose = TRUE, dir = NULL ) } @@ -65,15 +65,11 @@ for predictions.} of digits the results will have after passing them through \code{\link{round}(x, digits = precision)}.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} \item{dir}{A file path to a directory where you want information saved to a file, or multiple files. If \code{NULL}, which is the default, then @@ -89,5 +85,5 @@ Outliers are determined using standard deviations (i.e., \code{sdFactor} input parameter). } \author{ -Chantel Wetzel, Vlada Gertseva, James Thorson +Chantel R. Wetzel, Vlada Gertseva, James Thorson } diff --git a/man/cleanPacFIN.Rd b/man/cleanPacFIN.Rd index 0598968..cf3691e 100644 --- a/man/cleanPacFIN.Rd +++ b/man/cleanPacFIN.Rd @@ -16,7 +16,7 @@ cleanPacFIN( keep_states = c("WA", "OR", "CA"), CLEAN = TRUE, spp = NULL, - verbose = FALSE, + verbose = TRUE, savedir ) } @@ -106,15 +106,11 @@ ensure that the methods are species specific. Leave \code{NULL} if generic methods work for your species. Currently, sablefish is the only species with species-specific code.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} \item{savedir}{A file path to the directory where the results will be saved. The default is the current working directory. diff --git a/man/doSexRatio.Rd b/man/doSexRatio.Rd index 5a715fb..09235c8 100644 --- a/man/doSexRatio.Rd +++ b/man/doSexRatio.Rd @@ -59,5 +59,5 @@ observations from adjacent bins will be used \link{getComps}, \link{writeComps} } \author{ -Andi Stephens, Kelli F. Johnson, and Chantel Wetzel +Andi Stephens, Kelli F. Johnson, and Chantel R. Wetzel } diff --git a/man/find.matching.rows.Rd b/man/find.matching.rows.Rd index ed0032d..48062e8 100644 --- a/man/find.matching.rows.Rd +++ b/man/find.matching.rows.Rd @@ -4,7 +4,14 @@ \alias{find.matching.rows} \title{Function find.matching.rows} \usage{ -find.matching.rows(file, table, findex = 1, tindex = 1, tcol = 2, round. = T) +find.matching.rows( + file, + table, + findex = 1, + tindex = 1, + tcol = 2, + round. = TRUE +) } \arguments{ \item{file}{Rows to be matched from \code{table}} diff --git a/man/getAge.Rd b/man/getAge.Rd index 9aef618..f8053c4 100644 --- a/man/getAge.Rd +++ b/man/getAge.Rd @@ -4,7 +4,7 @@ \alias{getAge} \title{Get age information for each fish} \usage{ -getAge(Pdata, verbose = FALSE, keep, col.bestage = "FISH_AGE_YEARS_FINAL") +getAge(Pdata, verbose = TRUE, keep, col.bestage = "FISH_AGE_YEARS_FINAL") } \arguments{ \item{Pdata}{A data frame of biological samples @@ -13,15 +13,11 @@ Pacific Fishieries Information Network (PacFIN) data warehouse, which originated in 2014. Data are pulled using sql calls, see \code{\link{PullBDS.PacFIN}()}.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} \item{keep}{A vector of values that represent what you want to keep. Values of \code{NA}, \code{""}, and numeric values are acceptable. diff --git a/man/getArea.Rd b/man/getArea.Rd index 38b4221..28e34ab 100644 --- a/man/getArea.Rd +++ b/man/getArea.Rd @@ -4,7 +4,7 @@ \alias{getArea} \title{Get the general area that the information was taken from} \usage{ -getArea(Pdata, verbose = FALSE) +getArea(Pdata, verbose = TRUE) } \arguments{ \item{Pdata}{A data frame of biological samples @@ -13,15 +13,11 @@ Pacific Fishieries Information Network (PacFIN) data warehouse, which originated in 2014. Data are pulled using sql calls, see \code{\link{PullBDS.PacFIN}()}.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} } \value{ A vector of characters with the same length as \code{NROW(Pdata)}. Rows of data diff --git a/man/getComps.Rd b/man/getComps.Rd index 45b4417..d0ab835 100644 --- a/man/getComps.Rd +++ b/man/getComps.Rd @@ -10,7 +10,7 @@ getComps( strat = NULL, Comps = c("AAL", "LEN", "AGE"), defaults = c("fleet", "fishyr", "season"), - verbose = FALSE, + verbose = TRUE, ... ) } @@ -40,15 +40,11 @@ Note that the entry needs to be in all upper-case letters.} which will typically be left at their default value of \code{c('fleet', 'fishyr', 'season')}.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} \item{...}{Pass additional arguments to \code{getcomps_long}, such as \code{dropmissing = FALSE} where the default behavior is diff --git a/man/getExpansion_1.Rd b/man/getExpansion_1.Rd index 390a3f1..3cd42fd 100644 --- a/man/getExpansion_1.Rd +++ b/man/getExpansion_1.Rd @@ -14,7 +14,7 @@ getExpansion_1( mb = NA, ua = NA, ub = NA, - verbose = FALSE, + verbose = TRUE, plot = FALSE ) } @@ -44,15 +44,11 @@ Set \code{maxExp = Inf} to see largest values.} \item{ub}{Unsexed weight length exponent.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} \item{plot}{Argument takes either a logical or character value specifying the file name if you want to write the plots to a disk rather than printing them diff --git a/man/getExpansion_2.Rd b/man/getExpansion_2.Rd index 38a3d26..b9c36fc 100644 --- a/man/getExpansion_2.Rd +++ b/man/getExpansion_2.Rd @@ -22,7 +22,7 @@ Pacific Fishieries Information Network (PacFIN) data warehouse, which originated in 2014. Data are pulled using sql calls, see \code{\link{PullBDS.PacFIN}()}.} -\item{Catch}{A dataframe of catch data, in pounds or in metric tonnes.} +\item{Catch}{A data frame of catch data, in pounds or in metric tonnes.} \item{Units}{The units of the \code{Catch} data frame, see \code{measurements::conv_unit_options[["mass"]]} @@ -58,15 +58,11 @@ were needed between functions. You can use as many levels of stratification as you want except year because it is already included in the call to \link[stats:aggregate]{stats::aggregate}.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} \item{savedir}{A file path to the directory where the results will be saved. The default is the current working directory. @@ -76,10 +72,9 @@ The path can be relative or absolute.} The input PacFIN dataset, with column \code{Expansion_Factor_2} appended. } \description{ -The second-stage expansion calculates the -per-year and stratification (e.g., gear group) total catch -divided by the sampled catch and appends it to the input data as -\code{Expansion_Factor_2}. +The second-stage expansion calculates the per-year and stratification (e.g., +gear group) total catch divided by the sampled catch and appends it to the +input data as \code{Expansion_Factor_2}. } \details{ Find the catch for each year and grouping in \code{Catch} and divide by the diff --git a/man/getGearGroup.Rd b/man/getGearGroup.Rd index f5aed95..a8cce07 100644 --- a/man/getGearGroup.Rd +++ b/man/getGearGroup.Rd @@ -18,15 +18,11 @@ ensure that the methods are species specific. Leave \code{NULL} if generic methods work for your species. Currently, sablefish is the only species with species-specific code.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} } \value{ A modified data frame where an additional column labeled @@ -40,7 +36,10 @@ is used to create a column in \code{Pdata} called \code{geargroup}, where \code{Pdata$GRID} is recoded to \code{geargroup} according to the gear table. } \examples{ -ex <- getGearGroup(data.frame(GRID = c("PRT", "BMT", "FPT")), verbose = FALSE) +ex <- getGearGroup( + data.frame(GRID = c("PRT", "BMT", "FPT")), + verbose = FALSE +) table(ex) testthat::expect_equal(ex[ex[, "geargroup"] == "POT", "GRID"], "FPT") diff --git a/man/getLength.Rd b/man/getLength.Rd index b2e75b7..8b7ef77 100644 --- a/man/getLength.Rd +++ b/man/getLength.Rd @@ -13,15 +13,11 @@ Pacific Fishieries Information Network (PacFIN) data warehouse, which originated in 2014. Data are pulled using sql calls, see \code{\link{PullBDS.PacFIN}()}.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} \item{keep}{A vector of values that represent what you want to keep. Values of \code{NA}, \code{""}, and numeric values are acceptable. diff --git a/man/getSeason.Rd b/man/getSeason.Rd index 94b8be5..d42bb40 100644 --- a/man/getSeason.Rd +++ b/man/getSeason.Rd @@ -10,7 +10,7 @@ getSeason( yearUp = NULL, yearDown = NULL, plotResults = FALSE, - verbose = FALSE + verbose = TRUE ) } \arguments{ @@ -41,15 +41,11 @@ if winter months belong to the previous year then use \code{yearUp = 1:2}.} \item{plotResults}{A logical value specifying if plots should or should not be created and shown in the console.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} } \value{ An additional column \code{season} is added to \code{Pdata}. diff --git a/man/getState.Rd b/man/getState.Rd index dfd7ccd..c7f8973 100644 --- a/man/getState.Rd +++ b/man/getState.Rd @@ -4,7 +4,7 @@ \alias{getState} \title{Create a state column based on input column specified in \code{source}} \usage{ -getState(Pdata, source = c("AGENCY_CODE", "SOURCE_AGID"), verbose = FALSE) +getState(Pdata, source = c("AGENCY_CODE", "SOURCE_AGID"), verbose = TRUE) } \arguments{ \item{Pdata}{A data frame of biological samples @@ -17,15 +17,11 @@ which originated in 2014. Data are pulled using sql calls, see \code{Pdata}. See the function call for options, where only the first value will be used.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} } \value{ The input data frame is returned with an additional column, diff --git a/man/getWLpars.Rd b/man/getWLpars.Rd index 66d615c..cbfd9ef 100644 --- a/man/getWLpars.Rd +++ b/man/getWLpars.Rd @@ -8,7 +8,7 @@ getWLpars( data, col.length = "lengthcm", col.weight = "weightkg", - verbose = FALSE + verbose = TRUE ) } \arguments{ @@ -30,15 +30,11 @@ weight-length parameters are calculated using centimeters and kilograms. The reported values are easily scaled to give you results in grams if you wish to have more standard parameter estimates.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} } \value{ A data frame of weight-length parameters by sex. diff --git a/man/summaryAgeMethod.Rd b/man/summaryAgeMethod.Rd index ce3d0bc..b826578 100644 --- a/man/summaryAgeMethod.Rd +++ b/man/summaryAgeMethod.Rd @@ -4,7 +4,7 @@ \alias{summaryAgeMethod} \title{Summary of available age methods} \usage{ -summaryAgeMethod(Pdata, verbose = FALSE) +summaryAgeMethod(Pdata, verbose = TRUE) } \arguments{ \item{Pdata}{A data frame of biological samples @@ -13,15 +13,11 @@ Pacific Fishieries Information Network (PacFIN) data warehouse, which originated in 2014. Data are pulled using sql calls, see \code{\link{PullBDS.PacFIN}()}.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} } \value{ A data frame of counts for each age method. @@ -29,5 +25,5 @@ If \code{verbose}, then text explaining the summary is also printed to the screen prior to returning the table. } \description{ -Use \link[dplyr:count]{dplyr::count} to summarize the available age types. +Use \code{\link[dplyr:count]{dplyr::count()}} to summarize the available age types. } diff --git a/man/tableSample.Rd b/man/tableSample.Rd index bc3e8c8..9f88dfd 100644 --- a/man/tableSample.Rd +++ b/man/tableSample.Rd @@ -51,5 +51,5 @@ Create a table of samples by fleet and year to be included in an assessment document. } \author{ -Chantel Wetzel +Chantel R. Wetzel } diff --git a/man/writeComps.Rd b/man/writeComps.Rd index e4d2f35..3de3bc8 100644 --- a/man/writeComps.Rd +++ b/man/writeComps.Rd @@ -71,15 +71,11 @@ value to (value is passed to \code{round()}). NULL will skip rounding.} \item{overwrite}{A logical value specifying whether to overwrite an existing file if the file associated with the input \code{fname} already exists.} -\item{verbose}{A logical value specifying if output should be written -to the screen or not. Good for testing and exploring your data but -can be turned off when output indicates errors. -The printing doesn't affect any of the returned objects, instead, -printing makes it easier to see if the data has errors and what was -done to rectify them in the given function. -Sorry, but the default is to always print to the screen, -i.e., \code{verbose = TRUE}, so you do not miss out on anything. -This is standard practice for packages in the pfmc-assessments organization.} +\item{verbose}{A logical specifying if output should be written to the +screen or not. Good for testing and exploring your data but can be turned +off when output indicates information that you already know. The printing +of output to the screen does not affect any of the returned objects. The +default is to always print to the screen, i.e., \code{verbose = TRUE}.} } \value{ Appends data to the file given in \code{fname}. @@ -134,5 +130,5 @@ were used in stratifying the data. \code{\link{getComps}}, \code{\link{doSexRatio}} } \author{ -Andi Stephens, Chantel Wetzel, Kelli Johnson, Ian Taylor +Andi Stephens, Chantel R. Wetzel, Kelli F. Johnson, Ian G. Taylor }