R/set_defaults.R
In Maritimes/Mar.bycatch: Facilitates Extraction and Linking of Commercial and Observed Fisheries Data for the Maritimes
Defines functions
set_defaults
Documented in
set_defaults
#' @title set_defaults
#' @description This function provides all of the possible parameters understood by this package.
#' Some can be overwritten by \code{fleet_*} wrappers.
#' @details The desired date range can be specified multiple ways - either using \code{year} (alone),
#' \code{dateStart} (alone) or \code{dateStart} with \code{dateEnd} (explained below).
#' @param year default is \code{NULL}. \code{year} can be used if data should be extracted for an
#' entire calendar year (i.e. Jan 1 --> Dec 31). The format is
#' \code{YYYY}, e.g. \code{year = 2018}. \code{dateStart} takes priority over \code{year} if both
#' are provided.
#' @param dateStart default is \code{NULL}. This identifies the start date of the search window, in
#' the format \code{YYYY-MM-DD} (e.g. \code{dateStart = "2019-02-19"}).
#' If no \code{dateEnd} is provided, the window will be for 1 year (i.e, 365 days). ,
#' @param dateEnd default is \code{NULL} format is \code{YYYY-MM-DD}, e.g. \code{dateEnd = "2019-02-19"}.
#' \code{dateEnd} must be associated with a valid entry of
#' \code{dateStart} to identify a block of time for a data extraction (e.g. Jun18, 2018 -->
#' August 27, 2019).
#' @param lics default is \code{'all'}. Fleet wrappers will populate this with a dataframe specifying
#' the licence types, subtypes, gear and licence species valid
#' for a particular fleet. This information comes from \code{Mar.fleets::LIC_CORE}.
#' @param gearSpecs default is \code{'all'}. Fleet wrappers may populate it with a dataframe
#' specifying the particular specifications for a fleets' gear.
#' For example, certain fleets must use particular mesh sizes or shapes. This information comes from
#' \code{Mar.fleets::LIC_GEAR_SPECS}.
#' @param area default is \code{'all'}. Certain fleets are only licenced to fish in certain areas.
#' This information comes from \code{Mar.fleets::licAreas}.
#' @param marfSpp default is \code{'all'}. The marfis species code, usually sent by the fleet
#' wrapper.
#' @param marfGear default is \code{'all'}, but all wrappers have (overwritable) fleet-specific
#' values. This is a vector of MARFIS gear codes known to have caught this species.
#' @param isdbSpp default is \code{'all'}. The ISDB species code, usually sent by the fleet wrapper
#' @param tripcd_id default is \code{NULL}. If a tripcd_id from ISDB is provided, all matting
#' records will be examined for matches
#' @param returnMARFIS default is \code{TRUE}. Do you want a list object containing marfis trip and
#' set information as part of your results?
#' @param returnISDB default is \code{TRUE}. Do you want a list object containing isdb trip and set
#' information as part of your results? (requires \code{returnMARFIS = T})
#' @param areaFile default is \code{'NAFOSubunits_sf'}. This is used to identify which areas to
#' check the trips and sets against. By default,
#' Mar.data::NAFOSubunits_sf is ued, but any objects in Mar.data could be used.
#' @param areaFileField default is \code{'NAFO_1'}. This is a field within the \code{areas} object
#' which specifies exactly which field of the areas object data
#' should be compared against.
#' @param nafoDet default is \code{2}, but values between \code{1} and \code{4} are acceptable. This
#' specifies the level of detail that will be used in the summarized locations table. Using the
#' default value of 2, trips and sets will be summarized by areas such as "4X", "4V" and "5Z" (i.e 2
#' characters). If set to "1", areas would be more general (e.g. "3", "4", "5"; i.e. 1 character),
#' while a value like 4 would summarize the trips and sets into very specific NAFO subunits (e.g.
#' "3PSA","4VSB" and "5ZEM")
#' @param keepSurveyTrips default is \code{TRUE}. Within the ISDB database are non-commercial,
#' survey trips. Setting this to \code{FALSE} ensures these trips are dropped.
#' @param keepMissingGear default is \code{TRUE}. Some fleets have particular allowable gear sizes
#' and types (see gearSpecs). Many cases exist where all of the gear details are not filled it.
#' When this parameter is set to \code{TRUE}, these 'unknown' types and sizes are retained, and the
#' values are set to -999. If it is set to \code{FALSE}, any gears with missing values are dropped
#' - and they are not included in the results.
#' @param maxTripDiff_Hr default is \code{48}. Any MARFIS and ISDB trips that vary by more than the
#' # of days specified here will NOT be considered matches (on the basis of common Vessel, licence
#' and date). They may still match on confirmation codes and/or trip names.
#' @param maxSetDiff_Hr default is \code{48}. Any MARFIS and ISDB sets that vary by more than the
#' # of hours specified here will NOT be considered matches.
#' @param maxSetDiff_Km default is \code{100}. Any MARFIS and ISDB sets with positions more than the
#' # of kilometers specified here will NOT be considered matches.
#' @param dropUnmatchedISDB default is \code{TRUE}.
#' @param manualMatch default is \code{FALSE}. This parameter is only used when calling functions
#' from \code{manual_matcher()}. It ensures that the functions work properly with its reduced
#' input format.
#' @param socks default is \code{FALSE}. Normally, un-QC'd wrappers generate a prompt forcing the
#' user to acknowledge that they are aware that the script needs further testing. Setting this to
#' TRUE will prevent the prompt from showing up. Why 'socks'? You had to be there.
#' @param useLocal default is \code{FALSE}. This specifies whether to run the script against local
#' data or against Oracle (requires network or VPN).
#' Depending on your value for \code{useLocal}, different values become necessary.
#' \itemize{
#' \item{useLocal=TRUE} This implies that you have local data you want to use.
#' \itemize{
#' \item param \code{data.dir} required. This is the path to your local data
#' }
#' \item{useLocal=FALSE} This implies that you have will query Oracle for the necessary data.
#' Include all of the following:
#' \itemize{
#' \item param \code{oracle.username} required
#' \item param \code{oracle.password} required
#' \item param \code{oracle.dsn} required
#' \item param \code{usepkg} required
#' }
#' }
#' @param data.dir default is \code{'file.path(getwd(), "data")'}. Necessary for useLocal == T.
#' This is the path to a folder where your *.rdata files are stored.
#' @param oracle.username default is \code{'_none_'}. This is your username for accessing oracle
#' objects.
#' @param oracle.password default is \code{'_none_'}. This is your password for accessing oracle
#' objects.
#' @param oracle.dsn default is \code{'_none_'}. This is your dsn/ODBC identifier for accessing
#' oracle objects. Normally, the value should be "PTRAN"
#' @param usepkg default is \code{'roracle'}. This indicates whether the connection to Oracle should
#' use \code{'rodbc'} or \code{'roracle'} to connect. rodbc can
#' be slightly easier to setup, but roracle will extract data faster.
#' @param debug default is \code{FALSE}. If TRUE, this parameter causes the package to run in
#' debug mode, providing much extraneous information.
#' @param debugLics default is \code{NULL}. If a vector of LICENCE_IDs is provided, the script will
#' provide information about when the script drops them from
#' consideration.
#' @param debugVRs default is \code{NULL}. If a vector of VR numbers is provided, the script will
#' provide information about when the script drops them from
#' consideration.
#' @param debugMARFTripIDs default is \code{NULL}. If a vector of MARFIS trip IDs is provided, the
#' script will provide information about when the script drops them from
#' consideration.
#' @param debugISDBTripIDs default is \code{NULL}. If a vector of ISDB trip IDs is provided, the
#' script will provide information about when the script drops them from
#' consideration.
#' @param debugISDBTripNames default is \code{NULL}. If a vector of ISDB trip names is provided,
#' the script will provide information about when the script drops them from
#' consideration. Trip "names" are typically in a format like "J18-1234" or "A18-1234A".
#' @param ... other arguments passed to methods
#' @family coreFuncs
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
set_defaults <- function(lics = 'all',
gearSpecs = 'all',
area = 'all',
marfGear = 'all',
marfSpp = 'all',
isdbSpp = 'all',
tripcd_id = NULL,
returnMARFIS = T,
returnISDB = T,
areaFile = 'NAFOSubunits_sf',
areaFileField = 'NAFO_1',
nafoDet = 2,
dateStart = NULL,
dateEnd = NULL,
year = NULL,
keepSurveyTrips = TRUE,
keepMissingGear = TRUE,
maxTripDiff_Hr = 48,
maxSetDiff_Hr = 48,
maxSetDiff_Km = 100,
dropUnmatchedISDB = TRUE,
manualMatch = FALSE,
socks =FALSE,
data.dir = file.path(getwd(), 'data'),
oracle.username = '_none_',
oracle.password = '_none_',
oracle.dsn = 'PTRAN',
usepkg = 'roracle',
useLocal = FALSE,
debugLics = NULL,
debugVRs = NULL,
debugMARFTripIDs = NULL,
debugISDBTripIDs = NULL,
debugISDBTripNames = NULL,
debug=FALSE,
...){
defaults <- as.list(environment())
sentArgs <- list(...)
#ensure hardcoded args take priority over user args
submittedArgs <- Mar.utils::combine_lists(primary = sentArgs$argsFn, ancilliary = sentArgs$argsUser, quietly = T)
#ensure submitted args take priority over default args
argg <- Mar.utils::combine_lists(primary = submittedArgs, ancilliary = defaults, quietly = T)
if (argg$debug) t27 <- Mar.utils::where_now(returnTime = T)
# have all of our arguments - further process some of them ------------------------------------------------------------------------------------------------
# convert year (if present to dateStart and dateEnd)
dateArgs <- Mar.utils::vali_dates(dateStart = argg$dateStart, dateEnd = argg$dateEnd, year = argg$year, quietly = T)
argg$dateStart <- dateArgs$dateStart
argg$dateEnd <- dateArgs$dateEnd
argg$year <- NULL
#set the field to use for non-NAFO
if (argg$areaFile != 'NAFOSubunits_sf' && argg$areaFileField == 'NAFO_1'){
if (argg$areaFile == 'Strata_Mar_sf') argg$areaFileField = 'StrataID'
if (argg$areaFile == 'Strata_Mar_4VSW_sf') argg$areaFileField = 'StrataID'
if (argg$areaFile == 'LFAs_sf') argg$areaFileField = 'LFA'
if (argg$areaFile == 'Grids_Lobster_sf') argg$areaFileField = 'GRID'
if (argg$areaFile == 'Areas_Snowcrab_sf') argg$areaFileField = 'AREA1'
if (argg$areaFile == 'Areas_Snowcrab_Slope_sf') argg$areaFileField = 'AREA2'
if (argg$areaFile == 'Areas_Shrimp_sf') argg$areaFileField = 'BOX_NAME'
if (argg$areaFile == 'Areas_Surfclam_sf') argg$areaFileField = 'AREA'
if (argg$areaFile == 'Areas_Halibut_sf') argg$areaFileField = 'Strata'
if (argg$areaFile == 'Areas_Scallop_sf') argg$areaFileField = 'StrataID'
if (argg$areaFile == 'SPAs_Scallop_sf') argg$areaFileField = 'layer'
}
# notify user on unknown sent parameters
jakes <- setdiff(names(argg),names(defaults))
if ("quietly" %in% jakes) message("The 'quietly' parameter is no longer valid")
jakes = jakes[!(jakes %in% 'quietly')]
if (length(jakes)>0){
warning(paste0("This package does not understand the following parameter(s): ",paste0(jakes,collapse = ",")))
}
paramDf <- argg
paramDf <- replace(paramDf, sapply(paramDf, is.data.frame), "see <results>$params$fleet$...")
paramDf[lengths(paramDf)>1]<- paste0(paramDf[lengths(paramDf)>1])
paramDf <- replace(paramDf, sapply(paramDf, is.null), "<NULL>")
paramDf <- data.frame(PARAMETER=names(paramDf), VALUE = unlist(paramDf), row.names = NULL)
paramDf[paramDf$PARAMETER=="dateStart","VALUE"] <- format(as.Date(argg$dateStart, origin = "1970-01-01"), "%Y-%m-%d")
paramDf[paramDf$PARAMETER=="dateEnd","VALUE"] <- format(as.Date(argg$dateEnd, origin = "1970-01-01"), "%Y-%m-%d")
paramDf$SOURCE <- NA
paramDf[is.na(paramDf$SOURCE),"SOURCE"] <- "default value (overwritable by user)"
paramDf[paramDf$PARAMETER %in% names(sentArgs$argsUser),"SOURCE"] <- "user-supplied"
paramDf[paramDf$PARAMETER %in% names(sentArgs$argsFn),"SOURCE"] <- "hardcoded for this fleet"
# browser()
# softCoded <- c()
if("year" %in% names(sentArgs$argsUser)){
paramDf[paramDf$PARAMETER == "dateStart","SOURCE"] <- "derived from user-supplied 'year'"
paramDf[paramDf$PARAMETER == "dateEnd","SOURCE"] <- "derived from user-supplied 'year'"
}
toMatch <- c("TRUE", "FALSE","c\\(.*","^[0-9]*$")
paramDf[!grepl(paste(toMatch, collapse = '|'),paramDf$VALUE),"VALUE"]<- paste0('"',paramDf[!grepl(paste(toMatch, collapse = '|'),paramDf$VALUE),"VALUE"],'"')
paramDf <- paramDf[with(paramDf,order(-rank(SOURCE), PARAMETER)),c( "SOURCE", "PARAMETER","VALUE")]
paramDf$VALUE<- ifelse(nchar(paramDf$VALUE)>150,"<Too long to display>",paramDf$VALUE)
paramDf[paramDf$PARAMETER == "oracle.password","VALUE"]<- "*****"
paramDf <- rbind(paramDf, c("metadata","Date Run", format(Sys.Date(), "%Y-%m-%d")))
if(all(is.na(utils::packageDescription("Mar.fleets")))){
paramDf <- rbind(paramDf, c("metadata","Mar.fleets not installed"))
}else{
paramDf <- rbind(paramDf, c("metadata","Mar.fleets version", utils::packageDescription("Mar.fleets")$Version))
}
# paramDf <- rbind(paramDf, c("metadata","Mar.fleets version", utils::packageDescription("Mar.fleets")$Version))
if(exists("dbEnv")){
dbEnv$debugLics <- argg$debugLics
dbEnv$debugVRs <- argg$debugVRs
dbEnv$debugMARFTripIDs <- argg$debugMARFTripIDs
dbEnv$debugISDBTripIDs <- argg$debugISDBTripIDs
if (!is.null(argg$debugISDBTripNames)) {
dbEnv$debugISDBTripNamesLookup <- clean_ISDB_Trip(df=data.frame(ISDB_TRIP = argg$debugISDBTripNames), field = "ISDB_TRIP", out_name = "ISDB_TRIP_CLN")
dbEnv$debugISDBTripNames <- dbEnv$debugISDBTripNamesLookup$ISDB_TRIP_CLN
}
}
res <- list()
res[["params"]]<- paramDf
res[["args"]]<- argg
if (argg$debug){
t27_ <- proc.time() - t27
message("\tExiting set_defaults() (",round(t27_[1],0),"s elapsed)")
}
return(res)
}
Maritimes/Mar.bycatch documentation built on Feb. 6, 2024, 3:27 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions set_defaults
Documented in set_defaults
#' @title set_defaults
#' @description This function provides all of the possible parameters understood by this package.
#' Some can be overwritten by \code{fleet_*} wrappers.
#' @details The desired date range can be specified multiple ways - either using \code{year} (alone),
#' \code{dateStart} (alone) or \code{dateStart} with \code{dateEnd} (explained below).
#' @param year default is \code{NULL}. \code{year} can be used if data should be extracted for an
#' entire calendar year (i.e. Jan 1 --> Dec 31). The format is
#' \code{YYYY}, e.g. \code{year = 2018}. \code{dateStart} takes priority over \code{year} if both
#' are provided.
#' @param dateStart default is \code{NULL}. This identifies the start date of the search window, in
#' the format \code{YYYY-MM-DD} (e.g. \code{dateStart = "2019-02-19"}).
#' If no \code{dateEnd} is provided, the window will be for 1 year (i.e, 365 days). ,
#' @param dateEnd default is \code{NULL} format is \code{YYYY-MM-DD}, e.g. \code{dateEnd = "2019-02-19"}.
#' \code{dateEnd} must be associated with a valid entry of
#' \code{dateStart} to identify a block of time for a data extraction (e.g. Jun18, 2018 -->
#' August 27, 2019).
#' @param lics default is \code{'all'}. Fleet wrappers will populate this with a dataframe specifying
#' the licence types, subtypes, gear and licence species valid
#' for a particular fleet. This information comes from \code{Mar.fleets::LIC_CORE}.
#' @param gearSpecs default is \code{'all'}. Fleet wrappers may populate it with a dataframe
#' specifying the particular specifications for a fleets' gear.
#' For example, certain fleets must use particular mesh sizes or shapes. This information comes from
#' \code{Mar.fleets::LIC_GEAR_SPECS}.
#' @param area default is \code{'all'}. Certain fleets are only licenced to fish in certain areas.
#' This information comes from \code{Mar.fleets::licAreas}.
#' @param marfSpp default is \code{'all'}. The marfis species code, usually sent by the fleet
#' wrapper.
#' @param marfGear default is \code{'all'}, but all wrappers have (overwritable) fleet-specific
#' values. This is a vector of MARFIS gear codes known to have caught this species.
#' @param isdbSpp default is \code{'all'}. The ISDB species code, usually sent by the fleet wrapper
#' @param tripcd_id default is \code{NULL}. If a tripcd_id from ISDB is provided, all matting
#' records will be examined for matches
#' @param returnMARFIS default is \code{TRUE}. Do you want a list object containing marfis trip and
#' set information as part of your results?
#' @param returnISDB default is \code{TRUE}. Do you want a list object containing isdb trip and set
#' information as part of your results? (requires \code{returnMARFIS = T})
#' @param areaFile default is \code{'NAFOSubunits_sf'}. This is used to identify which areas to
#' check the trips and sets against. By default,
#' Mar.data::NAFOSubunits_sf is ued, but any objects in Mar.data could be used.
#' @param areaFileField default is \code{'NAFO_1'}. This is a field within the \code{areas} object
#' which specifies exactly which field of the areas object data
#' should be compared against.
#' @param nafoDet default is \code{2}, but values between \code{1} and \code{4} are acceptable. This
#' specifies the level of detail that will be used in the summarized locations table. Using the
#' default value of 2, trips and sets will be summarized by areas such as "4X", "4V" and "5Z" (i.e 2
#' characters). If set to "1", areas would be more general (e.g. "3", "4", "5"; i.e. 1 character),
#' while a value like 4 would summarize the trips and sets into very specific NAFO subunits (e.g.
#' "3PSA","4VSB" and "5ZEM")
#' @param keepSurveyTrips default is \code{TRUE}. Within the ISDB database are non-commercial,
#' survey trips. Setting this to \code{FALSE} ensures these trips are dropped.
#' @param keepMissingGear default is \code{TRUE}. Some fleets have particular allowable gear sizes
#' and types (see gearSpecs). Many cases exist where all of the gear details are not filled it.
#' When this parameter is set to \code{TRUE}, these 'unknown' types and sizes are retained, and the
#' values are set to -999. If it is set to \code{FALSE}, any gears with missing values are dropped
#' - and they are not included in the results.
#' @param maxTripDiff_Hr default is \code{48}. Any MARFIS and ISDB trips that vary by more than the
#' # of days specified here will NOT be considered matches (on the basis of common Vessel, licence
#' and date). They may still match on confirmation codes and/or trip names.
#' @param maxSetDiff_Hr default is \code{48}. Any MARFIS and ISDB sets that vary by more than the
#' # of hours specified here will NOT be considered matches.
#' @param maxSetDiff_Km default is \code{100}. Any MARFIS and ISDB sets with positions more than the
#' # of kilometers specified here will NOT be considered matches.
#' @param dropUnmatchedISDB default is \code{TRUE}.
#' @param manualMatch default is \code{FALSE}. This parameter is only used when calling functions
#' from \code{manual_matcher()}. It ensures that the functions work properly with its reduced
#' input format.
#' @param socks default is \code{FALSE}. Normally, un-QC'd wrappers generate a prompt forcing the
#' user to acknowledge that they are aware that the script needs further testing. Setting this to
#' TRUE will prevent the prompt from showing up. Why 'socks'? You had to be there.
#' @param useLocal default is \code{FALSE}. This specifies whether to run the script against local
#' data or against Oracle (requires network or VPN).
#' Depending on your value for \code{useLocal}, different values become necessary.
#' \itemize{
#' \item{useLocal=TRUE} This implies that you have local data you want to use.
#' \itemize{
#' \item param \code{data.dir} required. This is the path to your local data
#' }
#' \item{useLocal=FALSE} This implies that you have will query Oracle for the necessary data.
#' Include all of the following:
#' \itemize{
#' \item param \code{oracle.username} required
#' \item param \code{oracle.password} required
#' \item param \code{oracle.dsn} required
#' \item param \code{usepkg} required
#' }
#' }
#' @param data.dir default is \code{'file.path(getwd(), "data")'}. Necessary for useLocal == T.
#' This is the path to a folder where your *.rdata files are stored.
#' @param oracle.username default is \code{'_none_'}. This is your username for accessing oracle
#' objects.
#' @param oracle.password default is \code{'_none_'}. This is your password for accessing oracle
#' objects.
#' @param oracle.dsn default is \code{'_none_'}. This is your dsn/ODBC identifier for accessing
#' oracle objects. Normally, the value should be "PTRAN"
#' @param usepkg default is \code{'roracle'}. This indicates whether the connection to Oracle should
#' use \code{'rodbc'} or \code{'roracle'} to connect. rodbc can
#' be slightly easier to setup, but roracle will extract data faster.
#' @param debug default is \code{FALSE}. If TRUE, this parameter causes the package to run in
#' debug mode, providing much extraneous information.
#' @param debugLics default is \code{NULL}. If a vector of LICENCE_IDs is provided, the script will
#' provide information about when the script drops them from
#' consideration.
#' @param debugVRs default is \code{NULL}. If a vector of VR numbers is provided, the script will
#' provide information about when the script drops them from
#' consideration.
#' @param debugMARFTripIDs default is \code{NULL}. If a vector of MARFIS trip IDs is provided, the
#' script will provide information about when the script drops them from
#' consideration.
#' @param debugISDBTripIDs default is \code{NULL}. If a vector of ISDB trip IDs is provided, the
#' script will provide information about when the script drops them from
#' consideration.
#' @param debugISDBTripNames default is \code{NULL}. If a vector of ISDB trip names is provided,
#' the script will provide information about when the script drops them from
#' consideration. Trip "names" are typically in a format like "J18-1234" or "A18-1234A".
#' @param ... other arguments passed to methods
#' @family coreFuncs
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
set_defaults <- function(lics = 'all',
gearSpecs = 'all',
area = 'all',
marfGear = 'all',
marfSpp = 'all',
isdbSpp = 'all',
tripcd_id = NULL,
returnMARFIS = T,
returnISDB = T,
areaFile = 'NAFOSubunits_sf',
areaFileField = 'NAFO_1',
nafoDet = 2,
dateStart = NULL,
dateEnd = NULL,
year = NULL,
keepSurveyTrips = TRUE,
keepMissingGear = TRUE,
maxTripDiff_Hr = 48,
maxSetDiff_Hr = 48,
maxSetDiff_Km = 100,
dropUnmatchedISDB = TRUE,
manualMatch = FALSE,
socks =FALSE,
data.dir = file.path(getwd(), 'data'),
oracle.username = '_none_',
oracle.password = '_none_',
oracle.dsn = 'PTRAN',
usepkg = 'roracle',
useLocal = FALSE,
debugLics = NULL,
debugVRs = NULL,
debugMARFTripIDs = NULL,
debugISDBTripIDs = NULL,
debugISDBTripNames = NULL,
debug=FALSE,
...){
defaults <- as.list(environment())
sentArgs <- list(...)
#ensure hardcoded args take priority over user args
submittedArgs <- Mar.utils::combine_lists(primary = sentArgs$argsFn, ancilliary = sentArgs$argsUser, quietly = T)
#ensure submitted args take priority over default args
argg <- Mar.utils::combine_lists(primary = submittedArgs, ancilliary = defaults, quietly = T)
if (argg$debug) t27 <- Mar.utils::where_now(returnTime = T)
# have all of our arguments - further process some of them ------------------------------------------------------------------------------------------------
# convert year (if present to dateStart and dateEnd)
dateArgs <- Mar.utils::vali_dates(dateStart = argg$dateStart, dateEnd = argg$dateEnd, year = argg$year, quietly = T)
argg$dateStart <- dateArgs$dateStart
argg$dateEnd <- dateArgs$dateEnd
argg$year <- NULL
#set the field to use for non-NAFO
if (argg$areaFile != 'NAFOSubunits_sf' && argg$areaFileField == 'NAFO_1'){
if (argg$areaFile == 'Strata_Mar_sf') argg$areaFileField = 'StrataID'
if (argg$areaFile == 'Strata_Mar_4VSW_sf') argg$areaFileField = 'StrataID'
if (argg$areaFile == 'LFAs_sf') argg$areaFileField = 'LFA'
if (argg$areaFile == 'Grids_Lobster_sf') argg$areaFileField = 'GRID'
if (argg$areaFile == 'Areas_Snowcrab_sf') argg$areaFileField = 'AREA1'
if (argg$areaFile == 'Areas_Snowcrab_Slope_sf') argg$areaFileField = 'AREA2'
if (argg$areaFile == 'Areas_Shrimp_sf') argg$areaFileField = 'BOX_NAME'
if (argg$areaFile == 'Areas_Surfclam_sf') argg$areaFileField = 'AREA'
if (argg$areaFile == 'Areas_Halibut_sf') argg$areaFileField = 'Strata'
if (argg$areaFile == 'Areas_Scallop_sf') argg$areaFileField = 'StrataID'
if (argg$areaFile == 'SPAs_Scallop_sf') argg$areaFileField = 'layer'
}
# notify user on unknown sent parameters
jakes <- setdiff(names(argg),names(defaults))
if ("quietly" %in% jakes) message("The 'quietly' parameter is no longer valid")
jakes = jakes[!(jakes %in% 'quietly')]
if (length(jakes)>0){
warning(paste0("This package does not understand the following parameter(s): ",paste0(jakes,collapse = ",")))
}
paramDf <- argg
paramDf <- replace(paramDf, sapply(paramDf, is.data.frame), "see <results>$params$fleet$...")
paramDf[lengths(paramDf)>1]<- paste0(paramDf[lengths(paramDf)>1])
paramDf <- replace(paramDf, sapply(paramDf, is.null), "<NULL>")
paramDf <- data.frame(PARAMETER=names(paramDf), VALUE = unlist(paramDf), row.names = NULL)
paramDf[paramDf$PARAMETER=="dateStart","VALUE"] <- format(as.Date(argg$dateStart, origin = "1970-01-01"), "%Y-%m-%d")
paramDf[paramDf$PARAMETER=="dateEnd","VALUE"] <- format(as.Date(argg$dateEnd, origin = "1970-01-01"), "%Y-%m-%d")
paramDf$SOURCE <- NA
paramDf[is.na(paramDf$SOURCE),"SOURCE"] <- "default value (overwritable by user)"
paramDf[paramDf$PARAMETER %in% names(sentArgs$argsUser),"SOURCE"] <- "user-supplied"
paramDf[paramDf$PARAMETER %in% names(sentArgs$argsFn),"SOURCE"] <- "hardcoded for this fleet"
# browser()
# softCoded <- c()
if("year" %in% names(sentArgs$argsUser)){
paramDf[paramDf$PARAMETER == "dateStart","SOURCE"] <- "derived from user-supplied 'year'"
paramDf[paramDf$PARAMETER == "dateEnd","SOURCE"] <- "derived from user-supplied 'year'"
}
toMatch <- c("TRUE", "FALSE","c\\(.*","^[0-9]*$")
paramDf[!grepl(paste(toMatch, collapse = '|'),paramDf$VALUE),"VALUE"]<- paste0('"',paramDf[!grepl(paste(toMatch, collapse = '|'),paramDf$VALUE),"VALUE"],'"')
paramDf <- paramDf[with(paramDf,order(-rank(SOURCE), PARAMETER)),c( "SOURCE", "PARAMETER","VALUE")]
paramDf$VALUE<- ifelse(nchar(paramDf$VALUE)>150,"<Too long to display>",paramDf$VALUE)
paramDf[paramDf$PARAMETER == "oracle.password","VALUE"]<- "*****"
paramDf <- rbind(paramDf, c("metadata","Date Run", format(Sys.Date(), "%Y-%m-%d")))
if(all(is.na(utils::packageDescription("Mar.fleets")))){
paramDf <- rbind(paramDf, c("metadata","Mar.fleets not installed"))
}else{
paramDf <- rbind(paramDf, c("metadata","Mar.fleets version", utils::packageDescription("Mar.fleets")$Version))
}
# paramDf <- rbind(paramDf, c("metadata","Mar.fleets version", utils::packageDescription("Mar.fleets")$Version))
if(exists("dbEnv")){
dbEnv$debugLics <- argg$debugLics
dbEnv$debugVRs <- argg$debugVRs
dbEnv$debugMARFTripIDs <- argg$debugMARFTripIDs
dbEnv$debugISDBTripIDs <- argg$debugISDBTripIDs
if (!is.null(argg$debugISDBTripNames)) {
dbEnv$debugISDBTripNamesLookup <- clean_ISDB_Trip(df=data.frame(ISDB_TRIP = argg$debugISDBTripNames), field = "ISDB_TRIP", out_name = "ISDB_TRIP_CLN")
dbEnv$debugISDBTripNames <- dbEnv$debugISDBTripNamesLookup$ISDB_TRIP_CLN
}
}
res <- list()
res[["params"]]<- paramDf
res[["args"]]<- argg
if (argg$debug){
t27_ <- proc.time() - t27
message("\tExiting set_defaults() (",round(t27_[1],0),"s elapsed)")
}
return(res)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.