Switch stockeff

DESCRIPTION

@@ -23,14 +23,15 @@ Suggests:
     ggforce,
     NEFSCspatial
 VignetteBuilder: knitr
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Imports: 
     data.table,
     sf,
     DBI,
     odbc,
     magrittr,
     ggplot2,
+    gtools,
     dbutils,
     survdat
 Remotes:

R/adjust_inflation.R

@@ -28,18 +28,20 @@ adjust_inflation <- function(comland, refYear, refMonth){
   sql <- comland$sql
   comland <- comland$comland
 
-  temp <- tempfile()
-  download.file("http://download.bls.gov/pub/time.series/wp/wp.data.3.ProcessedFoods", temp)
-  inflate <- data.table::as.data.table(read.delim(temp))
-  unlink(temp)
-
-  inflate[, series_id := gsub(" ", "", inflate[, series_id])]
-  deflate <- inflate[series_id == "WPU0223", ]
-  deflate[, MONTH := as.numeric(substr(period, 2, 3))]
-  data.table::setnames(deflate, c('year', 'value'), c('YEAR', 'PPI'))
-  deflate <- deflate[, list(YEAR, MONTH, PPI)]
-
+  #This isn't working right now - using downloaded file
+  # temp <- tempfile()
+  # download.file("http://download.bls.gov/pub/time.series/wp/wp.data.3.ProcessedFoods", temp)
+  #inflate <- data.table::as.data.table(read.delim(comlandr::wp.data.3.ProcessedFoods))
+  #unlink(temp)
+
+  # inflate[, series_id := gsub(" ", "", inflate[, series_id])]
+  # deflate <- inflate[series_id == "WPU0223", ]
+  # deflate[, MONTH := as.numeric(substr(period, 2, 3))]
+  # data.table::setnames(deflate, c('year', 'value'), c('YEAR', 'PPI'))
+  # deflate <- deflate[, list(YEAR, MONTH, PPI)]
+
   #Set yearly deflator to 0 instead of 13 to match unknown month designation
+  deflate <- comlandr::deflate
   deflate[MONTH == 13, MONTH := 0]
   deflate.base <- deflate[YEAR == refYear & MONTH == refMonth, PPI]
 

R/assign_unknown.R

@@ -46,8 +46,8 @@ assign_unknown <- function (comData, unkVar,
   comdata[QY %in% 3:4, HY := 2]
 
   #Assign size classes
-  comdata[TONCL1 %in% 1:3, SIZE := 1] #Small
-  comdata[TONCL1 > 3,      SIZE := 2] #Large
+  #comdata[TONCL1 %in% 1:3, SIZE := 1] #Small
+  #comdata[TONCL1 > 3,      SIZE := 2] #Large
 
   for(ivar in 1:length(unkVar)){
     if(unkVar[ivar] %in% knStrata){
@@ -88,7 +88,7 @@ assign_unknown <- function (comData, unkVar,
       #combinations of strata codes
       num.combos <- data.table::setDT(list(gtools::combinations(length(strata.code), 
                                                                 inum, strata.code)))
-      combos <- rbindlist(list(combos, num.combos), fill = T)
+      combos <- data.table::rbindlist(list(combos, num.combos), fill = T)
     }
 
 
@@ -108,7 +108,7 @@ assign_unknown <- function (comData, unkVar,
                                                  'SPPLIVMT'))]
 
           #Remove extra columns from known
-          known.simple <- copy(known)
+          known.simple <- data.table::copy(known)
           known.simple <- known.simple[, c(names(known)[which(names(known) %in%
                                                                 ext.col)]) := NULL]
 
@@ -158,7 +158,7 @@ assign_unknown <- function (comData, unkVar,
       ##Still no match - use 3 or 5 year window then drop year
       if(nrow(unknown) > 0){
         #Remove extra columns from known
-        known.all <- copy(known)
+        known.all <- data.table::copy(known)
         known.all <- known.all[, list(YEAR, NESPP3, VAR, SPPLIVMT)]
 
         #3 year window
@@ -260,7 +260,7 @@ assign_unknown <- function (comData, unkVar,
       ##Still no match - match to species
       if(nrow(unknown) > 0){
         #Remove extra columns from known
-        known.all <- copy(known)
+        known.all <- data.table::copy(known)
         known.all <- known.all[, list(NESPP3, VAR, SPPLIVMT)]
 
         #Sum landings per stratification

R/disaggregate_skates_hakes.R

@@ -122,21 +122,21 @@ disaggregate_skates_hakes <- function(comland, channel, filterByYear, filterByAr
         #put skates in comland format to merge back
         #Little
         little <- comland.skates[, list(YEAR, AREA, MONTH, NEGEAR,
-                                        TONCL1, NESPP3, UTILCD, MESHCAT, MKTCAT, 
+                                        TONCL2, NESPP3, UTILCD, MESHCAT, MARKET_CODE, 
                                         little, little.value, US)]
         little[, NESPP3 := 366]
         data.table::setnames(little, c('little', 'little.value'), c('SPPLIVMT', 'SPPVALUE'))
         little <- little[SPPLIVMT > 0, ]
         #Winter
         winter <- comland.skates[, list(YEAR, AREA, MONTH, NEGEAR,
-                                        TONCL1, NESPP3, UTILCD, MESHCAT, MKTCAT, 
+                                        TONCL2, NESPP3, UTILCD, MESHCAT, MARKET_CODE, 
                                         winter, winter.value, US)]
         winter[, NESPP3 := 367]
         data.table::setnames(winter, c('winter', 'winter.value'), c('SPPLIVMT', 'SPPVALUE'))
         winter <- winter[SPPLIVMT > 0, ]
         #Other skates
         other <- comland.skates[, list(YEAR, AREA, MONTH, NEGEAR,
-                                       TONCL1, NESPP3, UTILCD, MESHCAT, MKTCAT, 
+                                       TONCL2, NESPP3, UTILCD, MESHCAT, MARKET_CODE, 
                                        other.skate, other.skate.value, US)]
         other[, NESPP3 := 365]
         data.table::setnames(other, c('other.skate', 'other.skate.value'), c('SPPLIVMT', 'SPPVALUE'))
@@ -239,21 +239,21 @@ disaggregate_skates_hakes <- function(comland, channel, filterByYear, filterByAr
         #Silver (509), offshore (508), whiting (507)
         #put hakes in comland format to merge back
         silver <- comland.hakes[, list(YEAR, AREA, MONTH, NEGEAR,
-                                       TONCL1, NESPP3, UTILCD, MESHCAT, MKTCAT, 
+                                       TONCL2, NESPP3, UTILCD, MESHCAT, MARKET_CODE, 
                                        silver, silver.value, US)]
         silver[, NESPP3 := 509]
         data.table::setnames(silver, c('silver', 'silver.value'), c('SPPLIVMT', 'SPPVALUE'))
         silver <- silver[SPPLIVMT > 0, ]
 
         offshore <- comland.hakes[, list(YEAR, AREA, MONTH, NEGEAR,
-                                         TONCL1, NESPP3, UTILCD, MESHCAT, MKTCAT, 
+                                         TONCL2, NESPP3, UTILCD, MESHCAT, MARKET_CODE, 
                                          offshore, offshore.value, US)]
         offshore[, NESPP3 := 508]
         data.table::setnames(offshore, c('offshore', 'offshore.value'), c('SPPLIVMT', 'SPPVALUE'))
         offshore <- offshore[SPPLIVMT > 0, ]
 
         other <- comland.hakes[, list(YEAR, AREA, MONTH, NEGEAR,
-                                      TONCL1, NESPP3, UTILCD, MESHCAT, MKTCAT, 
+                                      TONCL2, NESPP3, UTILCD, MESHCAT, MARKET_CODE, 
                                       other.hakes, other.hakes.value, US)]
         other[, NESPP3 := 507]
         data.table::setnames(other, c('other.hakes', 'other.hakes.value'), c('SPPLIVMT', 'SPPVALUE'))

R/get_comland_data.R

@@ -4,22 +4,40 @@
 #'
 #'@param channel an Object inherited from \link[DBI]{DBIConnection-class}. This object is used to connect
 #' to communicate with the database engine. (see \code{\link[dbutils]{connect_to_database}})
-#'@param endyear Numeric Scalar. Final year of query.
-#'@param landed Character String. Use landed weight ("y" - meatwt) for scallops and clams instead of live weight ("n" - livewt).
-#'@param out.dir path to directory where final output will be saved
+#'@param filterByYear numeric vector
+#'@param filterByArea numeric vector
+#'@param useLanded boolean
+#'@param removeParts boolean
+#'@param useHerringMaine boolean
+#'@param useForeign boolean
+#'@param refYear numeric
+#'@param refMonth numeric
+#'@param disaggSkatesHakes boolean
+#'@param aggArea boolean
+#'@param userAreas data frame
+#'@param areaDescription character string
+#'@param propDescription character string
+#'@param applyPropLand boolean
+#'@param applyPropValue boolean
+#'@param aggGear boolean
+#'@param userGears data frame
+#'@param fleetDescription character string
+#'@param unkVar character vector
+#'@param knStrata character vector
 #'
-#'
-#'@return Data frame (data.table) (n x 10)
+#'@return Data frame (data.table) (n x 12)
 #'Each row of the data.table represents a species record for a given tow/trip
 #'
 #'\item{YEAR}{Year of trip/tow}
 #'\item{MONTH}{Month of trip/tow}
 #'\item{NEGEAR}{Fishing gear used on trip/tow}
-#'\item{TONCL1}{Tonnage class of the fishing vessel}
+#'\item{TONCL2}{Tonnage class of the fishing vessel (2 digit value)}
 #'\item{NESPP3}{Species code (3 charachters)}
-#'\item{NESPP4}{Species code and market code (4 characters)}
-#'\item{AREA}{Statistical area in which species was reportly caught}
+#'\item{MARKET_CODE}{market code (2 characters)}
+#'\item{MESHCAT}{Code to describe the mesh size for a trawl vessel}
+#'\item{AREA/EPU}{Statistical area/ Ecological Production Unit in which species was reportly caught}
 #'\item{UTILCD}{Utilization code}
+#'\item{US}{Landing from the USA vessels or foreign vessels}
 #'\item{SPPLIVLB}{live weight (landed = "n") or landed weight (landed="y") in lbs}
 #'\item{SPPVALUE}{The value of landed catch to the nearest dollar (U.S.), paid to fisherman by dealer, for a given species.}
 #'
@@ -34,75 +52,75 @@
 #'@export
 
 
-get_comland_data <- function(channelSole, channelNova, filterByYear = NA, 
-                             filterByArea = NA, useLanded = T, removeParts = T, 
-                             useHerringMaine = T, useForeign = T, refYear = NA, 
-                             refMonth = NA, disagSkatesHakes = T, aggArea = F, 
-                             userAreas = comlandr::mskeyAreas, 
+get_comland_data <- function(channel, filterByYear = NA,
+                             filterByArea = NA, useLanded = T, removeParts = T,
+                             useHerringMaine = T, useForeign = T, refYear = NA,
+                             refMonth = NA, disagSkatesHakes = T, aggArea = F,
+                             userAreas = comlandr::mskeyAreas,
                              areaDescription = 'EPU', propDescription = 'MeanProp',
                              applyPropLand = T, applyPropValue = T,
                              aggGear = F, userGears = comlandr::mskeyGears,
-                             fleetDescription = 'Fleet', unkVar = 'AREA',
-                             knStrata = c('NESPP3', 'YEAR', 'HY', 'QY', 'MONTH',
-                                          'NEGEAR', 'TONCL1', 'AREA')) {
+                             fleetDescription = 'Fleet',
+                             unkVar = c('MONTH','NEGEAR','AREA'),
+                             knStrata = c('HY', 'QY','MONTH','NEGEAR', 'TONCL2', 'AREA')) {
+
 
-
 
   call <- dbutils::capture_function_call()
 
   #Pull raw data
-  comland <- comlandr::get_comland_raw_data(channelSole, channelNova, 
-                                            filterByYear, filterByArea, 
+  comland <- comlandr::get_comland_raw_data(channel,
+                                            filterByYear, filterByArea,
                                             useLanded, removeParts)
 
   #Pull herring data from the state of Maine
   if(useHerringMaine){
-    comland <- comlandr::get_herring_data(channelSole, comland,
-                                          filterByYear, filterByArea, 
+    comland <- comlandr::get_herring_data(channel, comland,
+                                          filterByYear, filterByArea,
                                           useForeign)
   }
 
   #Pull foreign landings
   if(useForeign){
     #Look up NAFO divisions that contain Stat areas
     if (all(!is.na(filterByArea))) {
-      NAFOAreas <- comlandr::get_areas(channelSole)$data %>%
+      NAFOAreas <- comlandr::get_areas(channel)$data %>%
         dplyr::select(AREA,NAFDVCD) %>%
         dplyr::filter(AREA %in% filterByArea) %>%
         dplyr::pull(NAFDVCD) %>%
         unique() %>%
         as.integer()
       filterByArea <- c(filterByArea, NAFOAreas)
     }
-    
+
     #Pull data and process to look like comland data
     comland.foreign <- comlandr::get_foreign_data(filterByYear, filterByArea)
-    comland.foreign <- comlandr::process_foreign_data(channelSole, comland.foreign, 
-                                                      useHerringMaine)
-   
+    comland.foreign <- comlandr::process_foreign_data(channel, comland.foreign,
+                                                      useLanded, useHerringMaine)
+
     #Combine foreign landings
-    comland$comland <- data.table::rbindlist(list(comland$comland, comland.foreign), 
+    comland$comland <- data.table::rbindlist(list(comland$comland, comland.foreign),
                                              use.names = T)
-  } 
-  
-  
+  }
+
+
   #Apply correction for inflation
   if(!is.na(refYear)) comland <- comlandr::adjust_inflation(comland, refYear, refMonth)
 
   #Disaggregate skates and hakes
-  if(disagSkatesHakes) comland <- comlandr::disaggregate_skates_hakes(comland, 
-                                                                      channelSole, 
+  if(disagSkatesHakes) comland <- comlandr::disaggregate_skates_hakes(comland,
+                                                                      channel,
                                                             filterByYear, filterByArea)
 
   #Aggregate areas
-  if(aggArea) comland <- comlandr::aggregate_area(comland, userAreas, 
+  if(aggArea) comland <- comlandr::aggregate_area(comland, userAreas,
                                                   areaDescription, propDescription,
-                                                  useForeign, channelSole, 
+                                                  useForeign, channel,
                                                   applyPropLand, applyPropValue)
 
   #Aggregate gears
   if(aggGear) comland <- comlandr::aggregate_gear(comland, userGears, fleetDescription)
-  
+
   #Impute unknown catch variables
   if(!is.null(unkVar)) comland <- comlandr::assign_unknown(comland, unkVar, knStrata)