R/dataWareHouseTrawlBio.OLD.R
In John-R-Wallace/R-ToolBox: What the package does (short line)
dataWareHouseTrawlBio.OLD <- function (commonName = "canary rockfish", species = NULL, yearRange = c(1000, 5000), projectShort = c("Ask", "AFSC.Shelf", "AFSC.Slope", "WCGBTS.Combo", "WCGBTS.Shelf",
"WCGBTS.Slope", "WCGBTS.Hypoxia", "WCGBTS.Santa.Barb.Basin", "WCGBTS.Shelf.Rockfish", "WCGBTS.Video"), verbose = FALSE, optionDigitsAtLeast11 = TRUE,
type3HaulsOnly = TRUE, removeWaterHauls = TRUE, noCanadianHauls = TRUE, headOnly = FALSE)
{
if(optionDigitsAtLeast11) {
if(options()$digits < 11) options(digits = 11)
}
if (!any(installed.packages()[, 1] %in% "devtools"))
install.packages('devtools')
if (!any(installed.packages()[, 1] %in% "JRWToolBox"))
devtools::install_github("John-R-Wallace/JRWToolBox")
" # lib() will download a function only if needed and then attach it"
JRWToolBox::lib("jsonlite")
JRWToolBox::lib("chron")
" # By using grep() and changing things around I fixed J. Thorson's rename_columns() function found inside the download_catch_rates() function from his FishData paackage "
" # The updated function no longer requires the order of the names inside of newname and origname to be the same. "
rename_columns = function(DF, origname = colnames(DF), newname) {
" # 'age_years' has both age and years, first forcing a change to 'age' "
colnames(DF)[grep("age_years", colnames(DF))] <- "age"
DF_new = DF
for (i in 1:length(newname)) {
Match = grep(newname[i], origname, ignore.case = TRUE)
if (length(Match) == 1)
colnames(DF_new)[Match] = newname[i]
}
return(DF_new)
}
if(is.null(species)) {
species <- JRWToolBox::sciName(commonName)
if(verbose) cat("\n\nScientific Name =", species, "\n\n"); flush.console()
}
projectNames <- JRWToolBox::scanIn("
longProject shortProject
'Groundfish Triennial Shelf Survey' AFSC.Shelf
NA AFSC.Slope
'Groundfish Slope and Shelf Combination Survey' WCGBTS.Combo
'Groundfish Shelf Survey' WCGBTS.Shelf
'Groundfish Slope Survey' WCGBTS.Slope
'Hypoxia Study' WCGBTS.Hypoxia
'Santa Barbara Basin Study' WCGBTS.Santa.Barb.Basin
'Shelf Rockfish [2004-2015]' WCGBTS.Shelf.Rockfish
'Video Study' WCGBTS.Video
")
if( projectShort[1] %in% c('Ask', 'ask')) {
cat("\n\nSelect a project [enter 0 (zero) to abort]:\n\n"); flush.console()
projectShort <- switch(menu(c("AFSC.Shelf","AFSC.Slope","WCGBTS.Combo","WCGBTS.Shelf","WCGBTS.Slope","WCGBTS.Hypoxia","WCGBTS.Santa.Barb.Basin","WCGBTS.Shelf.Rockfish","WCGBTS.Video")) + 1,
stop("No project selected"), "AFSC.Shelf","AFSC.Slope","WCGBTS.Combo","WCGBTS.Shelf","WCGBTS.Slope","WCGBTS.Hypoxia","WCGBTS.Santa.Barb.Basin","WCGBTS.Shelf.Rockfish","WCGBTS.Video")
cat("\n\nTo avoid this menu, the (quoted) project names shown above may be entered into the project argument.\n")
cat("\nOne project name or a vector of project names may be entered. A warning will be shown if a project has no data for the filters given.\n")
}
SpAll <- NULL
for (P in projectShort) {
cat("\n\nDownloading data from the", P, "survey\n"); flush.console()
project <- projectNames$longProject[projectNames$shortProject %in% P]
if (length(yearRange) == 1)
yearRange <- c(yearRange, yearRange)
Vars <- c("project", "trawl_id", "common_name", "scientific_name", "year", "vessel", "pass", "tow", "datetime_utc_iso", "depth_ftm", "weight_kg", "length_cm", "width_cm", "sex", "age_years", "latitude_dd", "longitude_dd")
" # Available, but not used: project, performance (not output, only used as a filter below) "
" # species and performance=Satisfactory added; went with a year range approach for the years to select "
UrlText <- paste0("https://www.webapps.nwfsc.noaa.gov/data/api/v1/source/trawl.individual_fact/selection.json?filters=project=", paste(strsplit(project, " ")[[1]], collapse = "%20"),",",
"station_invalid=0,", "performance=Satisfactory,",
"field_identified_taxonomy_dim$scientific_name=", paste(strsplit(species, " ")[[1]], collapse = "%20"), ",year>=",
yearRange[1], ",year<=", yearRange[2], "&variables=",
paste0(Vars, collapse = ","))
if (verbose) cat("\n\nURL for the species:\n\n", UrlText, "\n\n")
noColFlag <- FALSE
if(headOnly) {
SP <- try(JRWToolBox::headJSON(UrlText))
if(ncol(SP) == 0) noColFlag <- TRUE
} else
SP <- try(jsonlite::fromJSON(UrlText))
if(!is.data.frame(SP) | is.null(ncol(SP)) | noColFlag) {
warning("\n\tNo age data returned by the Warehouse for the filters given. Make sure the year range is correct for the project selected. (NULL is being returned.)\n\n", immediate. = TRUE)
SP <- NULL
} else {
if(verbose) { print(SP[1:4,]); cat("\n\n") }
" # SP.Before <<- SP "
SP <- rename_columns(SP, newname = c("Project", "Trawl_id", "Year", "Vessel", "Pass", "Common_Name", "Scientific_Name", "Tow", "Date", "Depth_ftm", "Weight_kg", "Length_cm", "Width_cm", "Sex", "Age", "Latitude_dd", "Longitude_dd"))
if(verbose) { print(SP[1:4,]); cat("\n\n") }
" # SP.After <<- SP "
SP <- SP[, c("Project", "Trawl_id", "Year", "Vessel", "Pass", "Tow", "Date", "Depth_ftm", "Common_Name", "Scientific_Name", "Weight_kg", "Length_cm", "Width_cm", "Sex", "Age", "Latitude_dd", "Longitude_dd")]
SP$Project <- P
SP$Date <- chron::chron(format(as.POSIXlt(SP$Date, format = "%Y-%m-%dT%H:%M:%S"), "%Y-%m-%d"), format = "y-m-d", out.format = "YYYY-m-d")
if(verbose) {
cat("\n\nFirst few rows of returned data:\n\n")
print(SP[1:4,])
cat("\n\n")
if(P == "WCGBTS.Combo" & any(yearRange[1]:yearRange[2] %in% 2012)) cat("\nNote: the Noah's Ark was chartered for both passes in 2012.\n")
print(table(SP$Vessel, SP$Year, useNA = "ifany"))
cat("\n\n")
}
}
if (any(P %in% c('AFSC.Shelf', 'AFSC.Slope'))) {
Vars <- c("project", "trawl_id", "common_name", "scientific_name", "year", "vessel", "pass", "tow", "datetime_utc_iso", "depth_ftm", "length_cm", "width_cm", "sex", "latitude_dd", "longitude_dd")
UrlText <- paste0("https://www.webapps.nwfsc.noaa.gov/data/api/v1/source/trawl.triennial_length_fact/selection.json?filters=project=", paste(strsplit(project, " ")[[1]], collapse = "%20"),",",
"station_invalid=0,", "performance=Satisfactory,", "field_identified_taxonomy_dim$scientific_name=",
paste(strsplit(species, " ")[[1]], collapse = "%20"), ",year>=", yearRange[1], ",year<=", yearRange[2], "&variables=",
paste0(Vars, collapse = ","))
if (verbose) cat("\n\nURL for AFSC.Shelf lengths:\n\n", UrlText, "\n\n")
noColFlag <- FALSE
if(headOnly) {
LEN <- try(JRWToolBox::headJSON(UrlText))
if(ncol(LEN) == 0) noColFlag <- TRUE
} else
LEN <- try(jsonlite::fromJSON(UrlText))
if(!is.data.frame(LEN) | is.null(ncol(LEN) | noColFlag)) {
warning("\nNo length data returned by the Warehouse for the filters given for Triennial lengths. Make sure the year range is correct for the project selected. (NULL is being returned.)\n\n", immediate. = TRUE)
LEN <- NULL
} else {
if(verbose) { print(LEN[1:4,]); cat("\n\n") }
LEN <- rename_columns(LEN, newname = c("Project", "Trawl_id", "Year", "Vessel", "Pass", "Common_Name", "Scientific_Name", "Tow", "Date", "Depth_ftm", "Length_cm", "Width_cm", "Sex", "Latitude_dd", "Longitude_dd"))
if(verbose) { print(LEN[1:4,]); cat("\n\n") }
LEN <- LEN[, c("Project", "Trawl_id", "Year", "Vessel", "Pass", "Tow", "Date", "Depth_ftm", "Common_Name", "Scientific_Name", "Length_cm", "Width_cm", "Sex", "Latitude_dd", "Longitude_dd")]
LEN$Project <- P
LEN$Date <- chron::chron(format(as.POSIXlt(LEN$Date, format = "%Y-%m-%dT%H:%M:%S"), "%Y-%m-%d"), format = "y-m-d", out.format = "YYYY-m-d")
if(verbose) {
cat("\n\nFirst few rows of returned length data:\n\n")
print(LEN[1:4,])
cat("\n\n")
if(P == "WCGBTS.Combo" & any(yearRange[1]:yearRange[2] %in% 2012)) cat("\nNote: the Noah's Ark was chartered for both passes in 2012.\n")
print(table(LEN$Vessel, LEN$Year, useNA = "ifany"))
cat("\n\n")
}
}
if(type3HaulsOnly) {
if(verbose) cat("\n\nOnly keeping Type 3 hauls, i.e. Standard Bottom Sample (pre-programmed station), from the AFSC lengths and ages\n")
notType3Hauls <- JRWToolBox::scanIn("
198606019330 198606019331 198606019332 198606019333 198606019334 198606019335 198006005268 198006005269 198006005270 198006005271 198006005272 198006005273
198006005274 198006005275 198006005276 198006005277 198006005278 198006005279 198006005280 198006005281 198006005282 198006005283 198006005284 198006005285
198006005286 198006005287 198006005288 198006005289 198006005290 198006005291 198006005292 198006005293 198606037214 198606037215 198606037216 198606037217
198606037218 198606037219 198606037220 198606037221 198606037222 197706025046 198606037223 198606037224 198606037225 198606037227 198606037228 198606037229
198606037230 198606037231 198606037232 198606037233 198606037234 198006019292 198006019293 198006019294 198006019295 198006019296 198006019297 198006019298
198006019299 198006019300 198006019301 198006019303 198006019304 198006019305 198006019306 198006019307 198006019308 198006019309 198006019310 198006019311
198006019312 198006019313 198006019314 198006019291 198006019315 198006019316 198006019317 198006019318 199206083364
", header = FALSE, ncol = 1, matrix = FALSE, numeric = TRUE)
if(!is.null(SP)) SP <- JRWToolBox::renum(SP[!SP$Trawl_id %in% notType3Hauls, ])
if(!is.null(LEN)) LEN <- JRWToolBox::renum(LEN[!LEN$Trawl_id %in% notType3Hauls, ])
}
if(removeWaterHauls) {
if(verbose) cat("\n\nRemoving Water Hauls from AFSC lengths and ages\n")
waterHauls <- JRWToolBox::scanIn("
197706004001 197706004005 197706004011 198606019192 198006005113 198006005115 198006005116 198006005118 198006005119 198006005123 198006005124 198006005009
198006005015 198006005016 198006005127 198006005128 198006005129 198006005130 198006005131 198006005133 198006019003 198006019005 198006019006 198006019010
198006019013 198006019021 198006019027 198606019218 198606019222 198606019223 198606019224 198006005145 198006005146 198006005148 198006005149 198006005151
198006005152 198006005154 198006005156 198006005157 198006005158 198006005159 198006005160 198006005161 198006005164 198006019029 198006019031 198006019033
198006019035 198006019040 198006019044 198006019050 198006019059 198006005174 198006005176 198006005177 198006005178 198006005181 198006005182 198006005183
198006005184 198006005185 198006005194 198006005195 198006005199 198006005200 198006019062 198006019064 198006019067 198006019074 198006019075 198006019081
198006019084 198606019269 198606019271 198606019278 198606019279 198006005203 198006005205 198006005207 198006005208 198006005209 198006005210 198006005216
198006005232 198006019093 198006019097 198006019098 198006019112 198006019113 198006019115 198006019116 198006019124 198006019127 198606019292 198606019296
198606019305 198606019311 198606019312 198606019315 198606019318 198006005248 198006005257 198006019135 198006019141 198006019151 198006019155 198006019158
198006019161 198606019320 198006005267 198006005017 198006005018 198006005020 198006005021 198006005025 198006005026 198006005029 198006005031 198006005036
197706004023 197706004031 197706004204 197706004206 198006005038 198006005042 198006005043 197706004037 197706004043 198006005047 198006005048 198006005050
198006005051 198006005052 198006005053 198006005055 198006005060 198006005063 198006005064 197706004047 197706004050 198006005069 198006005070 197706004067
197706004072 197706004076 198006005072 198006005073 198006005076 198006005085 198006005107 198006005109 198006005110 197706004083 197706004088 197706004265
197706004280 197706004091 197706004094 197706004096 197706004097 197706004113 197706004115 198906019225 198906019252 197706004121 198606019137 198906019262
197706004171 197706004173 197706004174 198606019166 197706022001 197706022020 198906019183 197706022224 197706022231 198306040287 198306040301 198306039109
198306040316 198306039132 198306039159 198306039202 198906073009 198906073010 198906073014 198906073017 198306039224 198306039231 198306039235 198306039239
198306039243 198306039244 198306039246 198306039250 198006019169 198006019171 198006019173 198006019175 198006019178 198006019179 198006019183 198006019185
198006019187 198006019188 198006019189 198906019015 197706022028 197706022037 197706022043 197706022045 197706022053 198906019018 198906019032 198906019036
197706025005 197706025009 197706025010 197706025015 197706025017 197706025018 197706025021 197706025022 197706025026 197706025027 197706025028 197706025029
197706025032 197706025034 198606037137 198606037139 198006019199 198006019201 198006019202 198006019211 198006019220 198006019221 198006019222 198006019223
198006019225 197706022063 197706022067 197706022084 198606037150 199206037158 198006019229 198006019233 198006019234 198006019239 198006019250 198006019254
197706025035 197706025043 197706025049 197706025050 197706025051 197706025052 197706025053 197706025054 197706025056 197706025057 197706025058 197706025059
197706025060 197706025064 198906019070 198306039050 198306039058 197706022089 197706022098 198606037188 198006019258 198006019259 198906019094 198906019097
198906019098 198906019100 198906019102 197706025068 197706025070 197706025071 197706025072 197706025073 197706025074 197706025082 197706025084 197706025085
198006019269 198006019272 198006019273 198006019279 198006019281 198306039079 198306039082 198306039088 197706022135 197706022140 198006019287 198906019113
198906019116 198906019120 198906019132 197706022153 197706022154 197706022156 197706022168 198906019151 198906019155 198906019161 198306040262 198306040273
197706022184 197706022185 197706022193 198306040167 198306040174 198306040188 198306040190 198306040194 198306040203 199206083002 198306040221 199206083190
199206083018 199206083022 199206083023 199206083030 198906073080 198306040006 198306040011 198306040031 199206083310 199206083311 198906073097 198906073110
198906073111 198906073117 198306040065 199206083043 199206083045 199206083050 199206083056 199206083058 199206083065 199206083087 198906073124 198906073143
198306040072 198306040083 198306040097 198906073172 198306040105 199206083109 199206083110 199206083140 198906073210 198306040134 198306040143 198306040145
199506016009 199506016036 197706620041 199506037069 199506016129 199506016137 199506016143 199506016144 199506016031 199506037187
", header = FALSE, ncol = 1, matrix = FALSE, numeric = TRUE)
if(!is.null(SP)) SP <- JRWToolBox::renum(SP[!SP$Trawl_id %in% waterHauls, ])
if(!is.null(LEN)) LEN <- JRWToolBox::renum(LEN[!LEN$Trawl_id %in% waterHauls, ])
}
if(noCanadianHauls) {
if(verbose) cat("\n\nRemoving Canadian hauls from the AFSC lengths and ages\n")
CanadianTows <- JRWToolBox::scanIn("
198006005238 198006005239 198006005240 198006005241 198006005242 198006005243 198006005244 198006005246 198006005247 198006005248 198006005249 198006005250
198006005251 198006005252 198006005253 198006005254 198006005255 198006005256 198006005257 198006005258 198006005260 198006005261 198006005263 198006005264
198006005265 198006005266 198006005267 198906019240 198906019241 198906019242 198906019243 198906019245 198906019246 198906019247 198906019248 198906019250
198906019251 198906019252 198906019253 198906019256 198906019257 198906019258 198906019259 198906019260 198906019261 198906019262 198906019263 198906019264
198906019265 198906019266 198906019267 198906019268 198906019269 198906019270 198906019271 198906019272 198906019273 198906019274 198906019275 198906019276
198906019277 198906019278 198906019279 198906019280 198906019281 198906019282 198906019283 198906019284 198906019285 198906019286 198906019287 198906019288
198906019289 198906019290 198906019291 198906019292 198906019293 198906019294 198906019295 198906019296 198906019297 198906019298 198906019299 198906019300
198906019301 198906019302 198906019303 198306040279 198306040280 198306040281 198306040282 198306040283 198306040284 198306040285 198306040286 198306040287
198306040288 198306040289 198306040290 198306040291 198306040292 198306040293 198306039234 198306039235 198306039236 198306039237 198306039238 198306039239
198306039240 198306039241 198306039242 198306039243 198306039244 198306039246 198306039248 198306039249 198306039250 198306039251 198606037204 199206037166
199206037168 199206037169 199206037170 199206037171 199206037183 199206037184 199206037185 199206037186 199206037187 199206037188 199206037189 199206037190
199206037191 199206037192 199206037193 199206037195 199206037196 199206037197 199206037198 199206037199 199206037200 199206037201 199206037202 199206037203
199206037204 199206037205 198006019257 198006019258 198006019259 198006019260 198006019261 198006019262 198006019263 198006019264 198006019265 198006019267
198006019268 198006019269 198006019270 198006019271 198006019272 198006019273 198006019274 198006019275 198006019276 198006019277 198006019278 198006019279
198006019280 198006019281 198006019282 198006019283 198006019284 198006019285 198006019286 198006019287 198006019288 198006019289 198306040263 198306040265
198306040266 198306040267 198306040268 198306040270 198306040271 198306040273 198306040274 198306040275 198306040276 198306040277 198306040278 198906073245
198906073246 198906073247 198906073248 198906073249 198906073250 198906073251 198306039252 198306039253 198306039254 198306039261 198306039262 198306039263
199206083327 199206083328 199206083329 199206083330 199206083331 199206083332 199206083333 199206083334 199206083335 199206083336 199206083337 199206083338
199206083339 199206083340 199206083341 199206083342 199206083343 199206083344 199206083346 199206083347 199206083348 199206083349 199206083350 199206083351
199206083352 199206083353 199206083354 199206083355 199206083356 199206083357 199206083358 199206083359 199206083361 199206083363 199806023291 199806023292
199806023293 199806023268 199806023270 199806023271 199806023272 199806023273 199806023274 199806023275 199806023281 199806023282 199806023283 199806023284
199806023285 199806023287 199806023288 199806023289 199506037309 199506037310 199506037311 199506037312 199506037313 199506037295 199506037296 199506037297
199506037299 199506037300 199506037301 199506037302 199506037303 199506037304 199506037305 199506037306 199506037307 199506037308 199506037281 199506037282
199506037283 199506037284 199506037285 199506037286 199506037287 199506037288 199806023253 199806023254 199806023255 199806023256 199806023258 199806023259
199506037289 199506037290 199506037291 199506037292 199506037293 199506037294 199506037267 199506037268 199506037269 199506037270 199506037271 199506037272
199506037273 199506037274 199506037275 199506037276 199506037277 199506037278 199506037279 199506037280 199506037254 199506037255 199506037256 199506037257
199506037258 199506037259 199806023260 199806023261 199806023262 199506037260 199506037261 199506037262 199506037263 199506037264 199506037265 199506037266
199506037239 199506037240 199506037241 199506037242 199506037243 199506037244 199506037247 199506037248 199506037249 199506037250 199506037251 199506037252
199806023276 199806023277 199806023278 199806023279 199806023280 199806023290 199806016234 199806016235 199806016236 199806016237 199806016243 199806016244
199806016245 199806016246 199806016247 199806016248 199806016249 199806016232 199806016233 199806016250 199806016251 199806016252 199806016253 199806016254
199806016256 199806016257 199806016238 199806016239 199806016240 199806016241 199806016242 199806023263 199806023264 200106149229 200106149249 200106149210
200106149256 200106149257 200106149258 200106149259 200106149260 200106149261 200106149263 200106149264 200106149265 200106149266 200106149267 200106149268
200106149269 200106149226 200106149227 200106149228 200106149230 200106149231 200106149235 200106149236 200106149239 200106149240 200106149241 200106149242
200106149246 200106149250 200106149251 200106149253 200106149255 200106149254 200106149232 200106149247 200106149262 200106149234 200106149252 200106149248
200106149211
", header = FALSE, ncol = 1, matrix = FALSE, numeric = TRUE)
if(!is.null(SP)) SP <- JRWToolBox::renum(SP[!SP$Trawl_id %in% CanadianTows, ])
if(!is.null(LEN)) LEN <- JRWToolBox::renum(LEN[!LEN$Trawl_id %in% CanadianTows, ])
}
}
SpAll <- rbind(SpAll, SP)
}
if (any(projectShort %in% c('AFSC.Shelf', 'AFSC.Slope'))) {
cat("\n\nThe object returned is a list with data frames named 'Lengths' (AFSC) and 'Ages' (all projects) since at least one of projects was from the AFSC.\n\n")
SpAll <- list(Lengths = LEN, Ages = SpAll)
}
cat("\n")
SpAll
}
John-R-Wallace/R-ToolBox documentation built on April 22, 2024, 8:29 p.m.
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dataWareHouseTrawlBio.OLD <- function (commonName = "canary rockfish", species = NULL, yearRange = c(1000, 5000), projectShort = c("Ask", "AFSC.Shelf", "AFSC.Slope", "WCGBTS.Combo", "WCGBTS.Shelf",
"WCGBTS.Slope", "WCGBTS.Hypoxia", "WCGBTS.Santa.Barb.Basin", "WCGBTS.Shelf.Rockfish", "WCGBTS.Video"), verbose = FALSE, optionDigitsAtLeast11 = TRUE,
type3HaulsOnly = TRUE, removeWaterHauls = TRUE, noCanadianHauls = TRUE, headOnly = FALSE)
{
if(optionDigitsAtLeast11) {
if(options()$digits < 11) options(digits = 11)
}
if (!any(installed.packages()[, 1] %in% "devtools"))
install.packages('devtools')
if (!any(installed.packages()[, 1] %in% "JRWToolBox"))
devtools::install_github("John-R-Wallace/JRWToolBox")
" # lib() will download a function only if needed and then attach it"
JRWToolBox::lib("jsonlite")
JRWToolBox::lib("chron")
" # By using grep() and changing things around I fixed J. Thorson's rename_columns() function found inside the download_catch_rates() function from his FishData paackage "
" # The updated function no longer requires the order of the names inside of newname and origname to be the same. "
rename_columns = function(DF, origname = colnames(DF), newname) {
" # 'age_years' has both age and years, first forcing a change to 'age' "
colnames(DF)[grep("age_years", colnames(DF))] <- "age"
DF_new = DF
for (i in 1:length(newname)) {
Match = grep(newname[i], origname, ignore.case = TRUE)
if (length(Match) == 1)
colnames(DF_new)[Match] = newname[i]
}
return(DF_new)
}
if(is.null(species)) {
species <- JRWToolBox::sciName(commonName)
if(verbose) cat("\n\nScientific Name =", species, "\n\n"); flush.console()
}
projectNames <- JRWToolBox::scanIn("
longProject shortProject
'Groundfish Triennial Shelf Survey' AFSC.Shelf
NA AFSC.Slope
'Groundfish Slope and Shelf Combination Survey' WCGBTS.Combo
'Groundfish Shelf Survey' WCGBTS.Shelf
'Groundfish Slope Survey' WCGBTS.Slope
'Hypoxia Study' WCGBTS.Hypoxia
'Santa Barbara Basin Study' WCGBTS.Santa.Barb.Basin
'Shelf Rockfish [2004-2015]' WCGBTS.Shelf.Rockfish
'Video Study' WCGBTS.Video
")
if( projectShort[1] %in% c('Ask', 'ask')) {
cat("\n\nSelect a project [enter 0 (zero) to abort]:\n\n"); flush.console()
projectShort <- switch(menu(c("AFSC.Shelf","AFSC.Slope","WCGBTS.Combo","WCGBTS.Shelf","WCGBTS.Slope","WCGBTS.Hypoxia","WCGBTS.Santa.Barb.Basin","WCGBTS.Shelf.Rockfish","WCGBTS.Video")) + 1,
stop("No project selected"), "AFSC.Shelf","AFSC.Slope","WCGBTS.Combo","WCGBTS.Shelf","WCGBTS.Slope","WCGBTS.Hypoxia","WCGBTS.Santa.Barb.Basin","WCGBTS.Shelf.Rockfish","WCGBTS.Video")
cat("\n\nTo avoid this menu, the (quoted) project names shown above may be entered into the project argument.\n")
cat("\nOne project name or a vector of project names may be entered. A warning will be shown if a project has no data for the filters given.\n")
}
SpAll <- NULL
for (P in projectShort) {
cat("\n\nDownloading data from the", P, "survey\n"); flush.console()
project <- projectNames$longProject[projectNames$shortProject %in% P]
if (length(yearRange) == 1)
yearRange <- c(yearRange, yearRange)
Vars <- c("project", "trawl_id", "common_name", "scientific_name", "year", "vessel", "pass", "tow", "datetime_utc_iso", "depth_ftm", "weight_kg", "length_cm", "width_cm", "sex", "age_years", "latitude_dd", "longitude_dd")
" # Available, but not used: project, performance (not output, only used as a filter below) "
" # species and performance=Satisfactory added; went with a year range approach for the years to select "
UrlText <- paste0("https://www.webapps.nwfsc.noaa.gov/data/api/v1/source/trawl.individual_fact/selection.json?filters=project=", paste(strsplit(project, " ")[[1]], collapse = "%20"),",",
"station_invalid=0,", "performance=Satisfactory,",
"field_identified_taxonomy_dim$scientific_name=", paste(strsplit(species, " ")[[1]], collapse = "%20"), ",year>=",
yearRange[1], ",year<=", yearRange[2], "&variables=",
paste0(Vars, collapse = ","))
if (verbose) cat("\n\nURL for the species:\n\n", UrlText, "\n\n")
noColFlag <- FALSE
if(headOnly) {
SP <- try(JRWToolBox::headJSON(UrlText))
if(ncol(SP) == 0) noColFlag <- TRUE
} else
SP <- try(jsonlite::fromJSON(UrlText))
if(!is.data.frame(SP) | is.null(ncol(SP)) | noColFlag) {
warning("\n\tNo age data returned by the Warehouse for the filters given. Make sure the year range is correct for the project selected. (NULL is being returned.)\n\n", immediate. = TRUE)
SP <- NULL
} else {
if(verbose) { print(SP[1:4,]); cat("\n\n") }
" # SP.Before <<- SP "
SP <- rename_columns(SP, newname = c("Project", "Trawl_id", "Year", "Vessel", "Pass", "Common_Name", "Scientific_Name", "Tow", "Date", "Depth_ftm", "Weight_kg", "Length_cm", "Width_cm", "Sex", "Age", "Latitude_dd", "Longitude_dd"))
if(verbose) { print(SP[1:4,]); cat("\n\n") }
" # SP.After <<- SP "
SP <- SP[, c("Project", "Trawl_id", "Year", "Vessel", "Pass", "Tow", "Date", "Depth_ftm", "Common_Name", "Scientific_Name", "Weight_kg", "Length_cm", "Width_cm", "Sex", "Age", "Latitude_dd", "Longitude_dd")]
SP$Project <- P
SP$Date <- chron::chron(format(as.POSIXlt(SP$Date, format = "%Y-%m-%dT%H:%M:%S"), "%Y-%m-%d"), format = "y-m-d", out.format = "YYYY-m-d")
if(verbose) {
cat("\n\nFirst few rows of returned data:\n\n")
print(SP[1:4,])
cat("\n\n")
if(P == "WCGBTS.Combo" & any(yearRange[1]:yearRange[2] %in% 2012)) cat("\nNote: the Noah's Ark was chartered for both passes in 2012.\n")
print(table(SP$Vessel, SP$Year, useNA = "ifany"))
cat("\n\n")
}
}
if (any(P %in% c('AFSC.Shelf', 'AFSC.Slope'))) {
Vars <- c("project", "trawl_id", "common_name", "scientific_name", "year", "vessel", "pass", "tow", "datetime_utc_iso", "depth_ftm", "length_cm", "width_cm", "sex", "latitude_dd", "longitude_dd")
UrlText <- paste0("https://www.webapps.nwfsc.noaa.gov/data/api/v1/source/trawl.triennial_length_fact/selection.json?filters=project=", paste(strsplit(project, " ")[[1]], collapse = "%20"),",",
"station_invalid=0,", "performance=Satisfactory,", "field_identified_taxonomy_dim$scientific_name=",
paste(strsplit(species, " ")[[1]], collapse = "%20"), ",year>=", yearRange[1], ",year<=", yearRange[2], "&variables=",
paste0(Vars, collapse = ","))
if (verbose) cat("\n\nURL for AFSC.Shelf lengths:\n\n", UrlText, "\n\n")
noColFlag <- FALSE
if(headOnly) {
LEN <- try(JRWToolBox::headJSON(UrlText))
if(ncol(LEN) == 0) noColFlag <- TRUE
} else
LEN <- try(jsonlite::fromJSON(UrlText))
if(!is.data.frame(LEN) | is.null(ncol(LEN) | noColFlag)) {
warning("\nNo length data returned by the Warehouse for the filters given for Triennial lengths. Make sure the year range is correct for the project selected. (NULL is being returned.)\n\n", immediate. = TRUE)
LEN <- NULL
} else {
if(verbose) { print(LEN[1:4,]); cat("\n\n") }
LEN <- rename_columns(LEN, newname = c("Project", "Trawl_id", "Year", "Vessel", "Pass", "Common_Name", "Scientific_Name", "Tow", "Date", "Depth_ftm", "Length_cm", "Width_cm", "Sex", "Latitude_dd", "Longitude_dd"))
if(verbose) { print(LEN[1:4,]); cat("\n\n") }
LEN <- LEN[, c("Project", "Trawl_id", "Year", "Vessel", "Pass", "Tow", "Date", "Depth_ftm", "Common_Name", "Scientific_Name", "Length_cm", "Width_cm", "Sex", "Latitude_dd", "Longitude_dd")]
LEN$Project <- P
LEN$Date <- chron::chron(format(as.POSIXlt(LEN$Date, format = "%Y-%m-%dT%H:%M:%S"), "%Y-%m-%d"), format = "y-m-d", out.format = "YYYY-m-d")
if(verbose) {
cat("\n\nFirst few rows of returned length data:\n\n")
print(LEN[1:4,])
cat("\n\n")
if(P == "WCGBTS.Combo" & any(yearRange[1]:yearRange[2] %in% 2012)) cat("\nNote: the Noah's Ark was chartered for both passes in 2012.\n")
print(table(LEN$Vessel, LEN$Year, useNA = "ifany"))
cat("\n\n")
}
}
if(type3HaulsOnly) {
if(verbose) cat("\n\nOnly keeping Type 3 hauls, i.e. Standard Bottom Sample (pre-programmed station), from the AFSC lengths and ages\n")
notType3Hauls <- JRWToolBox::scanIn("
198606019330 198606019331 198606019332 198606019333 198606019334 198606019335 198006005268 198006005269 198006005270 198006005271 198006005272 198006005273
198006005274 198006005275 198006005276 198006005277 198006005278 198006005279 198006005280 198006005281 198006005282 198006005283 198006005284 198006005285
198006005286 198006005287 198006005288 198006005289 198006005290 198006005291 198006005292 198006005293 198606037214 198606037215 198606037216 198606037217
198606037218 198606037219 198606037220 198606037221 198606037222 197706025046 198606037223 198606037224 198606037225 198606037227 198606037228 198606037229
198606037230 198606037231 198606037232 198606037233 198606037234 198006019292 198006019293 198006019294 198006019295 198006019296 198006019297 198006019298
198006019299 198006019300 198006019301 198006019303 198006019304 198006019305 198006019306 198006019307 198006019308 198006019309 198006019310 198006019311
198006019312 198006019313 198006019314 198006019291 198006019315 198006019316 198006019317 198006019318 199206083364
", header = FALSE, ncol = 1, matrix = FALSE, numeric = TRUE)
if(!is.null(SP)) SP <- JRWToolBox::renum(SP[!SP$Trawl_id %in% notType3Hauls, ])
if(!is.null(LEN)) LEN <- JRWToolBox::renum(LEN[!LEN$Trawl_id %in% notType3Hauls, ])
}
if(removeWaterHauls) {
if(verbose) cat("\n\nRemoving Water Hauls from AFSC lengths and ages\n")
waterHauls <- JRWToolBox::scanIn("
197706004001 197706004005 197706004011 198606019192 198006005113 198006005115 198006005116 198006005118 198006005119 198006005123 198006005124 198006005009
198006005015 198006005016 198006005127 198006005128 198006005129 198006005130 198006005131 198006005133 198006019003 198006019005 198006019006 198006019010
198006019013 198006019021 198006019027 198606019218 198606019222 198606019223 198606019224 198006005145 198006005146 198006005148 198006005149 198006005151
198006005152 198006005154 198006005156 198006005157 198006005158 198006005159 198006005160 198006005161 198006005164 198006019029 198006019031 198006019033
198006019035 198006019040 198006019044 198006019050 198006019059 198006005174 198006005176 198006005177 198006005178 198006005181 198006005182 198006005183
198006005184 198006005185 198006005194 198006005195 198006005199 198006005200 198006019062 198006019064 198006019067 198006019074 198006019075 198006019081
198006019084 198606019269 198606019271 198606019278 198606019279 198006005203 198006005205 198006005207 198006005208 198006005209 198006005210 198006005216
198006005232 198006019093 198006019097 198006019098 198006019112 198006019113 198006019115 198006019116 198006019124 198006019127 198606019292 198606019296
198606019305 198606019311 198606019312 198606019315 198606019318 198006005248 198006005257 198006019135 198006019141 198006019151 198006019155 198006019158
198006019161 198606019320 198006005267 198006005017 198006005018 198006005020 198006005021 198006005025 198006005026 198006005029 198006005031 198006005036
197706004023 197706004031 197706004204 197706004206 198006005038 198006005042 198006005043 197706004037 197706004043 198006005047 198006005048 198006005050
198006005051 198006005052 198006005053 198006005055 198006005060 198006005063 198006005064 197706004047 197706004050 198006005069 198006005070 197706004067
197706004072 197706004076 198006005072 198006005073 198006005076 198006005085 198006005107 198006005109 198006005110 197706004083 197706004088 197706004265
197706004280 197706004091 197706004094 197706004096 197706004097 197706004113 197706004115 198906019225 198906019252 197706004121 198606019137 198906019262
197706004171 197706004173 197706004174 198606019166 197706022001 197706022020 198906019183 197706022224 197706022231 198306040287 198306040301 198306039109
198306040316 198306039132 198306039159 198306039202 198906073009 198906073010 198906073014 198906073017 198306039224 198306039231 198306039235 198306039239
198306039243 198306039244 198306039246 198306039250 198006019169 198006019171 198006019173 198006019175 198006019178 198006019179 198006019183 198006019185
198006019187 198006019188 198006019189 198906019015 197706022028 197706022037 197706022043 197706022045 197706022053 198906019018 198906019032 198906019036
197706025005 197706025009 197706025010 197706025015 197706025017 197706025018 197706025021 197706025022 197706025026 197706025027 197706025028 197706025029
197706025032 197706025034 198606037137 198606037139 198006019199 198006019201 198006019202 198006019211 198006019220 198006019221 198006019222 198006019223
198006019225 197706022063 197706022067 197706022084 198606037150 199206037158 198006019229 198006019233 198006019234 198006019239 198006019250 198006019254
197706025035 197706025043 197706025049 197706025050 197706025051 197706025052 197706025053 197706025054 197706025056 197706025057 197706025058 197706025059
197706025060 197706025064 198906019070 198306039050 198306039058 197706022089 197706022098 198606037188 198006019258 198006019259 198906019094 198906019097
198906019098 198906019100 198906019102 197706025068 197706025070 197706025071 197706025072 197706025073 197706025074 197706025082 197706025084 197706025085
198006019269 198006019272 198006019273 198006019279 198006019281 198306039079 198306039082 198306039088 197706022135 197706022140 198006019287 198906019113
198906019116 198906019120 198906019132 197706022153 197706022154 197706022156 197706022168 198906019151 198906019155 198906019161 198306040262 198306040273
197706022184 197706022185 197706022193 198306040167 198306040174 198306040188 198306040190 198306040194 198306040203 199206083002 198306040221 199206083190
199206083018 199206083022 199206083023 199206083030 198906073080 198306040006 198306040011 198306040031 199206083310 199206083311 198906073097 198906073110
198906073111 198906073117 198306040065 199206083043 199206083045 199206083050 199206083056 199206083058 199206083065 199206083087 198906073124 198906073143
198306040072 198306040083 198306040097 198906073172 198306040105 199206083109 199206083110 199206083140 198906073210 198306040134 198306040143 198306040145
199506016009 199506016036 197706620041 199506037069 199506016129 199506016137 199506016143 199506016144 199506016031 199506037187
", header = FALSE, ncol = 1, matrix = FALSE, numeric = TRUE)
if(!is.null(SP)) SP <- JRWToolBox::renum(SP[!SP$Trawl_id %in% waterHauls, ])
if(!is.null(LEN)) LEN <- JRWToolBox::renum(LEN[!LEN$Trawl_id %in% waterHauls, ])
}
if(noCanadianHauls) {
if(verbose) cat("\n\nRemoving Canadian hauls from the AFSC lengths and ages\n")
CanadianTows <- JRWToolBox::scanIn("
198006005238 198006005239 198006005240 198006005241 198006005242 198006005243 198006005244 198006005246 198006005247 198006005248 198006005249 198006005250
198006005251 198006005252 198006005253 198006005254 198006005255 198006005256 198006005257 198006005258 198006005260 198006005261 198006005263 198006005264
198006005265 198006005266 198006005267 198906019240 198906019241 198906019242 198906019243 198906019245 198906019246 198906019247 198906019248 198906019250
198906019251 198906019252 198906019253 198906019256 198906019257 198906019258 198906019259 198906019260 198906019261 198906019262 198906019263 198906019264
198906019265 198906019266 198906019267 198906019268 198906019269 198906019270 198906019271 198906019272 198906019273 198906019274 198906019275 198906019276
198906019277 198906019278 198906019279 198906019280 198906019281 198906019282 198906019283 198906019284 198906019285 198906019286 198906019287 198906019288
198906019289 198906019290 198906019291 198906019292 198906019293 198906019294 198906019295 198906019296 198906019297 198906019298 198906019299 198906019300
198906019301 198906019302 198906019303 198306040279 198306040280 198306040281 198306040282 198306040283 198306040284 198306040285 198306040286 198306040287
198306040288 198306040289 198306040290 198306040291 198306040292 198306040293 198306039234 198306039235 198306039236 198306039237 198306039238 198306039239
198306039240 198306039241 198306039242 198306039243 198306039244 198306039246 198306039248 198306039249 198306039250 198306039251 198606037204 199206037166
199206037168 199206037169 199206037170 199206037171 199206037183 199206037184 199206037185 199206037186 199206037187 199206037188 199206037189 199206037190
199206037191 199206037192 199206037193 199206037195 199206037196 199206037197 199206037198 199206037199 199206037200 199206037201 199206037202 199206037203
199206037204 199206037205 198006019257 198006019258 198006019259 198006019260 198006019261 198006019262 198006019263 198006019264 198006019265 198006019267
198006019268 198006019269 198006019270 198006019271 198006019272 198006019273 198006019274 198006019275 198006019276 198006019277 198006019278 198006019279
198006019280 198006019281 198006019282 198006019283 198006019284 198006019285 198006019286 198006019287 198006019288 198006019289 198306040263 198306040265
198306040266 198306040267 198306040268 198306040270 198306040271 198306040273 198306040274 198306040275 198306040276 198306040277 198306040278 198906073245
198906073246 198906073247 198906073248 198906073249 198906073250 198906073251 198306039252 198306039253 198306039254 198306039261 198306039262 198306039263
199206083327 199206083328 199206083329 199206083330 199206083331 199206083332 199206083333 199206083334 199206083335 199206083336 199206083337 199206083338
199206083339 199206083340 199206083341 199206083342 199206083343 199206083344 199206083346 199206083347 199206083348 199206083349 199206083350 199206083351
199206083352 199206083353 199206083354 199206083355 199206083356 199206083357 199206083358 199206083359 199206083361 199206083363 199806023291 199806023292
199806023293 199806023268 199806023270 199806023271 199806023272 199806023273 199806023274 199806023275 199806023281 199806023282 199806023283 199806023284
199806023285 199806023287 199806023288 199806023289 199506037309 199506037310 199506037311 199506037312 199506037313 199506037295 199506037296 199506037297
199506037299 199506037300 199506037301 199506037302 199506037303 199506037304 199506037305 199506037306 199506037307 199506037308 199506037281 199506037282
199506037283 199506037284 199506037285 199506037286 199506037287 199506037288 199806023253 199806023254 199806023255 199806023256 199806023258 199806023259
199506037289 199506037290 199506037291 199506037292 199506037293 199506037294 199506037267 199506037268 199506037269 199506037270 199506037271 199506037272
199506037273 199506037274 199506037275 199506037276 199506037277 199506037278 199506037279 199506037280 199506037254 199506037255 199506037256 199506037257
199506037258 199506037259 199806023260 199806023261 199806023262 199506037260 199506037261 199506037262 199506037263 199506037264 199506037265 199506037266
199506037239 199506037240 199506037241 199506037242 199506037243 199506037244 199506037247 199506037248 199506037249 199506037250 199506037251 199506037252
199806023276 199806023277 199806023278 199806023279 199806023280 199806023290 199806016234 199806016235 199806016236 199806016237 199806016243 199806016244
199806016245 199806016246 199806016247 199806016248 199806016249 199806016232 199806016233 199806016250 199806016251 199806016252 199806016253 199806016254
199806016256 199806016257 199806016238 199806016239 199806016240 199806016241 199806016242 199806023263 199806023264 200106149229 200106149249 200106149210
200106149256 200106149257 200106149258 200106149259 200106149260 200106149261 200106149263 200106149264 200106149265 200106149266 200106149267 200106149268
200106149269 200106149226 200106149227 200106149228 200106149230 200106149231 200106149235 200106149236 200106149239 200106149240 200106149241 200106149242
200106149246 200106149250 200106149251 200106149253 200106149255 200106149254 200106149232 200106149247 200106149262 200106149234 200106149252 200106149248
200106149211
", header = FALSE, ncol = 1, matrix = FALSE, numeric = TRUE)
if(!is.null(SP)) SP <- JRWToolBox::renum(SP[!SP$Trawl_id %in% CanadianTows, ])
if(!is.null(LEN)) LEN <- JRWToolBox::renum(LEN[!LEN$Trawl_id %in% CanadianTows, ])
}
}
SpAll <- rbind(SpAll, SP)
}
if (any(projectShort %in% c('AFSC.Shelf', 'AFSC.Slope'))) {
cat("\n\nThe object returned is a list with data frames named 'Lengths' (AFSC) and 'Ages' (all projects) since at least one of projects was from the AFSC.\n\n")
SpAll <- list(Lengths = LEN, Ages = SpAll)
}
cat("\n")
SpAll
}
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