diff --git a/NAMESPACE b/NAMESPACE
index a41500c..6292bcf 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,15 @@
 # Generated by roxygen2: do not edit by hand
 
+export(aggregate_area)
+export(aggregate_gear)
+export(assign_area)
+export(calc_DK)
 export(comland)
+export(disaggregate_skates_hakes)
+export(get_comdisc_raw_data)
+export(get_comland_data)
+export(get_comland_raw_data)
+export(get_herring_data)
 export(get_areas)
 export(get_comland_data)
 export(get_foreign_data)
diff --git a/R/adjust_inflation.R b/R/adjust_inflation.R
index 9cd6f97..f15b0db 100644
--- a/R/adjust_inflation.R
+++ b/R/adjust_inflation.R
@@ -6,8 +6,8 @@
 #'
 #'
 #'@param comland Data frame. master data frame containing species landings
-#'@param refmonth Integer. Reference month
-#'@param refyear Integer. Reference year
+#'@param refMonth Integer. Reference month
+#'@param refYear Integer. Reference year
 #'
 #'@return comland data frame adjusted for inflation
 #'
@@ -16,7 +16,17 @@
 
 
 
-adjust_inflation <- function(comland,refyear,refmonth){
+adjust_inflation <- function(comland, refYear, refMonth){
+  
+  call <- c(comland$call, capture_function_call())
+  
+  #Pulling data
+  message("Adjusting for inflation ...")
+  
+  #pull out comland data
+  sql <- comland$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))
@@ -37,5 +47,9 @@ adjust_inflation <- function(comland,refyear,refmonth){
 
   #Remove extra column
   comland[, PPI := NULL]
-  return(comland)
+  
+  return(list(comland      = comland[], 
+              sql          = sql,
+              pullDate     = date(),
+              functionCall = call))
 }
diff --git a/R/aggregate_area.R b/R/aggregate_area.R
new file mode 100644
index 0000000..bac11b8
--- /dev/null
+++ b/R/aggregate_area.R
@@ -0,0 +1,60 @@
+#' Assign landing records to an aggregated area
+#'
+#' Takes the output from \code{get_comland_data} and further aggregates from NAFO 
+#' statistical areas to a user defined area.  Allows for species to be assigned by
+#' proportions to more than two user defined areas from one stat area
+#'
+#'@param comland Data set generated by \code{get_comland_data}
+#'@param userAreas Data frame. Definitions to aggregate statistical areas to user defined
+#'                 areas
+#'@param areaDescription Character. Name of column in userAreas that defines the new
+#'                       area.
+#'@param propDescription Character. Name of column in userAreas that defines the 
+#'                       proportions of landings assigned to new area.
+#'
+#'@export
+
+aggregate_area <- function(comland, userAreas, areaDescription, propDescription,
+                           applyPropValue = T){
+  
+  #Pulling data
+  message("Aggregating Areas ...")
+  
+  #Grab just the data
+  comData <- comland$comland
+  
+  call <- dbutils::capture_function_call()
+  
+  #Convert userAreas to data.table
+  areas <- data.table::as.data.table(userAreas)
+  data.table::setnames(areas, c(areaDescription, propDescription), c('newarea', 'prop'))
+  
+  #Merge new area descriptions to landings
+  new.area <- merge(comData, areas, by = c('NESPP3', 'AREA'), all.x = T, allow.cartesian=TRUE)
+  
+  #If no proportion assume 100% in
+  new.area[is.na(prop), prop := 1]
+  
+  #Proportion landings to new areas
+  new.area[, newspplivmt := SPPLIVMT * prop]
+  if(applyPropValue) new.area[, newsppvalue := SPPVALUE * prop]
+  
+  #Drop extra columns and rename
+  if(applyPropValue){
+    new.area[, c('SPPLIVMT', 'SPPVALUE', 'prop') := NULL]
+    data.table::setnames(new.area, c('newarea', 'newspplivmt', 'newsppvalue'), 
+                         c(areaDescription, 'SPPLIVMT', 'SPPVALUE'))
+  } else {
+    new.area[, c('SPPLIVMT', 'prop') := NULL]
+    data.table::setnames(new.area, c('newarea', 'newspplivmt'), 
+                         c(areaDescription, 'SPPLIVMT'))
+  }
+
+  
+  #Add changes back into comland
+   comland$comland <- new.area[]
+   comland$call <- c(comland$call, call)
+   comland$userAreas <- userAreas
+  
+  return(comland[])
+}                 
diff --git a/R/aggregate_gear.R b/R/aggregate_gear.R
new file mode 100644
index 0000000..a33d1e0
--- /dev/null
+++ b/R/aggregate_gear.R
@@ -0,0 +1,54 @@
+#' Assign landing records to an aggregated area
+#'
+#' Takes the output from \code{get_comland_data} and further aggregates from NAFO 
+#' statistical areas to a user defined area.  Allows for species to be assigned by
+#' proportions to more than two user defined areas from one stat area
+#'
+#'@param comland Data set generated by \code{get_comland_data}
+#'@param userAreas Data frame. Definitions to aggregate statistical areas to user defined
+#'                 areas
+#'@param areaDescription Character. Name of column in userAreas that defines the new
+#'                       area.
+#'@param propDescription Character. Name of column in userAreas that defines the 
+#'                       proportions of landings assigned to new area.
+#'
+#'@export
+
+aggregate_gear <- function(comData, userGears, fleetDescription){
+  
+  call <- dbutils::capture_function_call()
+  
+  #Convert userGears to data.table
+  gears <- data.table::as.data.table(userGears)
+  gears <- data.table::setnames(gears, fleetDescription, 'fleet')
+  
+  #Assign gears to fleets
+  #Generate NEGEAR2 codes from NEGEAR
+  if(is.numeric(comData$NEGEAR)){
+    comData[NEGEAR < 100, NEGEAR3 := paste0(0, NEGEAR)]
+    comData[NEGEAR >= 100, NEGEAR3 := NEGEAR]
+    comData[, NEGEAR2 := as.numeric(substr(NEGEAR3, 1, 2))]
+  } else {
+    comData[, NEGEAR2 := as.numeric(substr(NEGEAR, 1, 2))]
+  }
+  
+  fleets <- unique(gears$fleet)
+  
+  for(ifleet in 1:length(fleets)){
+    fleet.gear <- gears[fleet == fleets[ifleet], NEGEAR2]
+    fleet.mesh <- unique(gears[fleet == fleets[ifleet], MESHCAT])
+    #Check if there is a mesh characteristic associated with this gear
+    if(is.na(fleet.mesh)){
+      comData[NEGEAR2 %in% fleet.gear, fleet := fleets[ifleet]]
+    } else {
+      comData[NEGEAR2 %in% fleet.gear & MESHCAT == fleet.mesh, fleet := fleets[ifleet]]
+    }
+  }
+  
+  comData[, fleet := as.factor(fleet)]
+  
+  #Rename columns
+  data.table::setnames(comData, 'fleet', fleetDescription)
+  
+  return(comData[])
+}                 
diff --git a/R/assign_area.R b/R/assign_area.R
new file mode 100644
index 0000000..a08e902
--- /dev/null
+++ b/R/assign_area.R
@@ -0,0 +1,70 @@
+#' Assigns points to polygon
+#'
+#' Assign observer data (points, lat and lon) to designated regions (polygons) from a shape file.
+#'
+#'
+# @inheritParams strat_prep
+#' @param na.keep Boolean. Logical value to indicate whether original strata names
+#'  should be retained.
+#'
+#' @return Returns a \code{comdiscData} data.table with one additional column labeled
+#'  with the value of \code{areaDescription}
+#'
+#' \item{areaDescription}{The name of the region (found in \code{areaPolygon})
+#'  that a record in \code{surveyData} is assigned to}
+#'
+#' @importFrom magrittr "%>%"
+#'
+#'@family comdisc
+#'
+#' @export
+
+
+assign_area <- function (comdiscData, areaPolygon, areaDescription, na.keep = F) {
+
+    # transform Regional Shape file using lambert conformal conic coordinate ref system
+    crs <- "+proj=lcc +lat_1=20 +lat_2=60 +lat_0=40 +lon_0=-72 +x_0=0 +y_0=0 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"
+    
+    areas <- areaPolygon %>%
+    dplyr::rename(areaDescription = areaDescription) %>%
+    sf::st_transform(., crs)
+
+    #Need unique link3, lat lon column to make this work
+    comdiscData[, linkLL := paste0(LINK3, LAT, LON)]
+    #Should probably do this in the raw data pull
+    #remove stations missing lat or lon
+    comdiscData <- comdiscData[!is.na(LAT), ]
+    comdiscData <- comdiscData[!is.na(LON), ]
+    
+    # find unique stations and transform to required crs
+    locations <- comdiscData %>%
+    dplyr::select(linkLL, LAT, LON) %>%
+    dplyr::distinct() %>%
+    sf::st_as_sf(., coords = c("LON","LAT"), crs=4326) %>%
+    sf::st_transform(., crs)
+
+
+    # Intersect the locations with the polygon
+    # Assigns locations with polygons
+    location_area <- sf::st_join(locations, areas, join = sf::st_intersects) %>%
+    dplyr::select(names(locations), areaDescription) %>%
+    sf::st_drop_geometry() %>%
+    dplyr::arrange(linkLL)
+
+    # Join observer data with locations (which now are assigned to an area based on the shape file)
+    master <- base::merge(comdiscData, location_area, by = c("linkLL")) %>%
+    dplyr::rename(!!areaDescription := areaDescription)
+
+    # check to see if we want to keep points that fall outside of all of the polygons found in the shape file
+    if (!(na.keep)) { # removes all points that fall outside of the areas defined by the polygons in stratum
+    master <- master %>%
+        dplyr::filter(!is.na(get(areaDescription))) %>%
+        data.table::as.data.table()
+  }
+    #Drop linkLL column
+    master[, linkLL := NULL]
+
+  return(master[])
+
+}
+
diff --git a/R/calc_DK.R b/R/calc_DK.R
new file mode 100644
index 0000000..8b79047
--- /dev/null
+++ b/R/calc_DK.R
@@ -0,0 +1,62 @@
+#' Calculate discard to kept ratio
+#'
+#' Use observer data to calculate the ratio of discards to kept by species.
+#' 
+#'
+# @inheritParams strat_prep
+#' @param na.keep Boolean. Logical value to indicate whether original strata names
+#'  should be retained.
+#'
+#' @return Returns a \code{comdiscData} data.table with one additional column labeled
+#'  with the value of \code{areaDescription}
+#'
+#' \item{areaDescription}{The name of the region (found in \code{areaPolygon})
+#'  that a record in \code{surveyData} is assigned to}
+#'
+#' @importFrom magrittr "%>%"
+#'
+#'@family comdisc
+#'
+#' @export
+
+
+calc_DK <- function(comdiscData, areaDescription, fleetDescription){
+  
+  #Standardize column names
+  comdiscData <- data.table::setnames(comdiscData, c(areaDescription, 
+                                                     fleetDescription), 
+                                      c('area', 'fleet'))
+  
+  #sum catch by species/disposition/area/fleet
+  ob.sums <- comdiscData[, sum(SPPLIVMT), by = c('YEAR', 'area', 'fleet', 'NESPP3',
+                                                 'CATDISP')]
+  #identify discards
+  ob.discard <- ob.sums[CATDISP == 0, ]
+  
+  setnames(ob.discard, "V1", "DISCARD")
+  ob.discard[, CATDISP := NULL]
+  
+  #Sum kept by area/fleet
+  ob.kept <- ob.sums[CATDISP == 1, sum(V1), by = c('YEAR', 'area', 'fleet')]
+  
+  setnames(ob.kept, "V1", "KEPT.ALL")
+  
+  #Merge discards and kept
+  dk <- merge(ob.kept, ob.discard, by = c('YEAR', 'area', 'fleet'))
+  
+  #Calculate ratio
+  dk[, DK := DISCARD / KEPT.ALL]
+  #NAs result if divide by 0 so set DK to 1 (all discards)
+  dk[is.na(DK), DK := 1.0]
+  
+  #Remove extra columns
+  dk[, c('KEPT.ALL', 'DISCARD') := NULL]
+  
+  #Replace standard column names
+  #Standardize column names
+  data.table::setnames(dk, c('area', 'fleet'), 
+                       c(areaDescription, fleetDescription))
+  
+  return(dk[])
+}
+  
\ No newline at end of file
diff --git a/R/disaggregate_skates_hakes.R b/R/disaggregate_skates_hakes.R
new file mode 100644
index 0000000..c54dc86
--- /dev/null
+++ b/R/disaggregate_skates_hakes.R
@@ -0,0 +1,202 @@
+#'#Disaggregate skates and hakes
+#'
+#'Determine proportion of little/winter skates and silver hake in landings data 7/13
+#'SML
+#'
+#'@param comland Data frame. Master data frame containing species landings
+#'@param skate.hake.us Data frame. Landings of skates and hakes in USA
+#'
+#'@return updated comland
+#'
+#'@importFrom data.table ":=" "key"
+#'
+#' @noRd
+#' @export
+
+disaggregate_skates_hakes <- function(comland, channel, filterByYear, filterByArea) {
+        
+        message("Grabbing survey data to disaggregate skates and hakes ... ")
+        
+        #Grab survey data from NEFSC bottom trawl survey
+        survey <- survdat::get_survdat_data(channel, filterByYear, getLengths = F)
+        
+        #Skates----
+        message("Disaggregating little and winter skates from skates(ns) ... ")
+        skates <- 22:28
+        skate.survey <- survey$survdat[SVSPP %in% skates, ]
+        
+        #Identify Stat areas catch occured in
+        Stat.areas <- sf::st_read(dsn=system.file("extdata","Statistical_Areas_2010.shp",
+                                                  package="comlandr"), quiet = T)
+        skate.survey <- survdat::post_strat(skate.survey, Stat.areas, 'Id')
+        data.table::setnames(skate.survey, 'Id', 'AREA')
+        
+        #Filter By Area
+        if(!is.na(filterByArea[1])) skate.survey <- skate.survey[AREA %in% filterByArea, ]
+        
+        #Figure out proportion of skates
+        data.table::setkey(skate.survey, YEAR, SEASON, AREA)
+        
+        skates.prop <- skate.survey[, .(skates.all = sum(BIOMASS)), 
+                                    by = key(skate.survey)]
+        
+        little <- skate.survey[SVSPP == 26, .(little = sum(BIOMASS)), 
+                               by = key(skate.survey)]
+        
+        skates.prop <- merge(skates.prop, little, by = key(skate.survey), all = T)
+        
+        winter <- skate.survey[SVSPP == 23, .(winter = sum(BIOMASS)), 
+                               by = key(skate.survey)]
+        
+        skates.prop <- merge(skates.prop, winter, by = key(skate.survey), all = T)
+        
+        skates.prop[, little.per := little/skates.all]
+        skates.prop[, winter.per := winter/skates.all]
+        
+        #Drop extra columns and fix NAs
+        skates.prop[, c('skates.all', 'little', 'winter') := NULL]
+        skates.prop[is.na(little.per), little.per := 0]
+        skates.prop[is.na(winter.per), winter.per := 0]
+        
+        #disaggregate little and winter skates from skates(ns) - use survey in half years
+        #Generate season variable in comland
+        comland.skates <- comland$comland[NESPP3 == 365, ]
+        comland.skates[MONTH %in% 1:6,  SEASON := 'SPRING']
+        comland.skates[MONTH %in% 7:12, SEASON := 'FALL']
+
+        comland.skates <- merge(comland.skates, skates.prop, 
+                                by = c('YEAR', 'SEASON', 'AREA'), all.x = T)
+        
+        #Fix NAs
+        comland.skates[is.na(little.per), little.per := 0]
+        comland.skates[is.na(winter.per), winter.per := 0]
+
+        #Disaggregate
+        comland.skates[, little       := little.per * SPPLIVMT]
+        comland.skates[, little.value := round(little.per * SPPVALUE)]
+
+        comland.skates[, winter       := winter.per * SPPLIVMT]
+        comland.skates[, winter.value := round(winter.per * SPPVALUE)]
+
+        comland.skates[, other.skate       := SPPLIVMT - (little       + winter)]
+        comland.skates[, other.skate.value := SPPVALUE - (little.value + winter.value)]
+
+        #Little (366), winter (367), skates(ns) (365)
+        #put skates in comland format to merge back
+        little <- comland.skates[, list(YEAR, AREA, MONTH, NEGEAR,
+                                        TONCL1, NESPP3, UTILCD, MESHCAT, MKTCAT, 
+                                        little, little.value)]
+        little[, NESPP3 := 366]
+        data.table::setnames(little, c('little', 'little.value'), c('SPPLIVMT', 'SPPVALUE'))
+        little <- little[SPPLIVMT > 0, ]
+
+        winter <- comland.skates[, list(YEAR, AREA, MONTH, NEGEAR,
+                                        TONCL1, NESPP3, UTILCD, MESHCAT, MKTCAT, 
+                                        winter, winter.value)]
+        winter[, NESPP3 := 367]
+        data.table::setnames(winter, c('winter', 'winter.value'), c('SPPLIVMT', 'SPPVALUE'))
+        winter <- winter[SPPLIVMT > 0, ]
+
+        other <- comland.skates[, list(YEAR, AREA, MONTH, NEGEAR,
+                                       TONCL1, NESPP3, UTILCD, MESHCAT, MKTCAT, 
+                                       other.skate, other.skate.value)]
+        other[, NESPP3 := 365]
+        data.table::setnames(other, c('other.skate', 'other.skate.value'), c('SPPLIVMT', 'SPPVALUE'))
+        other <- other[SPPLIVMT > 0, ]
+
+        #merge all three and reformat for comland
+        skates.add.back <- data.table::rbindlist(list(little, winter, other))
+
+        data.table::setcolorder(skates.add.back, names(comland$comland))
+
+        comland$comland <- data.table::rbindlist(list(comland$comland[NESPP3 != 365, ],
+                                                      skates.add.back))
+
+        #Hakes ----
+        message("Disaggregating silver and offshore hake from whiting ... ")
+        
+        #Grab hake data from NEFSC bottom trawl survey
+        hake <- c(69, 72)
+        hake.survey <- survey$survdat[SVSPP %in% hake, ]
+        
+        #Identify Stat areas catch occured in
+        hake.survey <- survdat::post_strat(hake.survey, Stat.areas, 'Id')
+        data.table::setnames(hake.survey, 'Id', 'AREA')
+        
+        #Filter By Area
+        if(!is.na(filterByArea[1])) hake.survey <- hake.survey[AREA %in% filterByArea, ]
+        
+        #Figure out proportion of skates
+        data.table::setkey(hake.survey, YEAR, SEASON, AREA)
+        
+        hake.prop <- hake.survey[, .(hake.all = sum(BIOMASS, na.rm = T)), 
+                                 by = key(hake.survey)]
+        
+        silvers <- hake.survey[SVSPP == 72, .(silver = sum(BIOMASS, na.rm = T)), 
+                               by = key(hake.survey)]
+        
+        hake.prop <- merge(hake.prop, silvers, all = T)
+        hake.prop[is.na(silver), silver := 0]
+        
+        hake.prop[, silver.per := silver / hake.all]
+        
+        hake.prop[, offshore.per := 1 - silver.per]
+        hake.prop[, c('hake.all', 'silver') := NULL]
+        
+        #disaggregate silver and offshore hake from whiting - use survey in half years
+        #Generate season variable in comland
+        comland.hakes <- comland$comland[NESPP3 == 507, ]
+        comland.hakes[MONTH %in% 1:6,  SEASON := 'SPRING']
+        comland.hakes[MONTH %in% 7:12, SEASON := 'FALL']
+        
+        comland.hakes <- merge(comland.hakes, hake.prop, 
+                               by = c('YEAR', 'SEASON', 'AREA'), all.x = T)
+        
+        #Fix NAs
+        comland.hakes[is.na(silver.per), silver.per := 0]
+        comland.hakes[is.na(offshore.per), offshore.per := 0]
+        
+        #Disaggregate
+        comland.hakes[, silver       := silver.per * SPPLIVMT]
+        comland.hakes[, silver.value := round(silver.per * SPPVALUE)]
+        
+        comland.hakes[, offshore       := offshore.per * SPPLIVMT]
+        comland.hakes[, offshore.value := round(offshore.per * SPPVALUE)]
+        
+        comland.hakes[, other.hakes       := SPPLIVMT - (silver       + offshore)]
+        comland.hakes[, other.hakes.value := SPPVALUE - (silver.value + offshore.value)]
+        
+        #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, 
+                                       silver, silver.value)]
+        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, 
+                                         offshore, offshore.value)]
+        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, 
+                                      other.hakes, other.hakes.value)]
+        other[, NESPP3 := 507]
+        data.table::setnames(other, c('other.hakes', 'other.hakes.value'), c('SPPLIVMT', 'SPPVALUE'))
+        other <- other[SPPLIVMT > 0, ]
+        
+        #merge all three and reformat for comland
+        hakes.add.back <- data.table::rbindlist(list(silver, offshore, other))
+        
+        data.table::setcolorder(hakes.add.back, names(comland$comland))
+        
+        comland$comland <- data.table::rbindlist(list(comland$comland[NESPP3 != 507, ],
+                                                      hakes.add.back))
+        
+        return(comland)
+
+}
diff --git a/R/get_comdisc_raw_data.R b/R/get_comdisc_raw_data.R
new file mode 100644
index 0000000..df81af0
--- /dev/null
+++ b/R/get_comdisc_raw_data.R
@@ -0,0 +1,168 @@
+#' Extracts observer data from Database
+#'
+#' Connects to obdbs and pulls fields from OBSPP, OBINC, ASMSPP, and ASMINC
+#'
+#'@inheritParams get_comlands_raw_data
+#'
+#'@return Data frame (data.table) (n x 10)
+#'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{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{UTILCD}{Utilization code}
+#'\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.}
+#'
+#'@section File Creation:
+#'
+#'A file containing the data.table above will also be saved to the users machine in the directory provided
+#'
+#'@export 
+
+get_comdisc_raw_data <- function(channel, filterByYear){
+  
+  message("Pulling observer data from database. This could take a while (> 1 hour) ... ")
+  
+  #output objects
+  comdisc <- c()
+  sql <- c()
+  
+  #Create year vector
+  if(is.na(filterByYear[1])){
+    years <- ">= 1989"
+  }else{
+    years <- paste0("in (", comlandr:::sqltext(filterByYear), ")")
+  }
+  
+  ob.qry <- paste0("select year, month, area, negear, nespp4, hailwt, catdisp, drflag, 
+          tripid, haulnum, lathbeg, lonhbeg, link3
+          from OBSPP
+          where obsrflag = 1
+          and program not in ('127', '900', '250', '160')
+          and year ", years,
+                   "\n union
+          select year, month, area, negear, nespp4, hailwt, catdisp, drflag, 
+          tripid, haulnum, lathbeg, lonhbeg, link3
+          from ASMSPP
+          where obsrflag = 1
+          and program not in ('127', '900', '250', '160')
+          and year ", years)
+  
+  ob <- data.table::as.data.table(DBI::dbGetQuery(channel, ob.qry))
+  sql <- c(sql, ob.qry)
+  
+  #Add protected species here
+  mammal.qry <- paste0("select distinct a.year, a.month, b.area, b.negear, a.nespp4, 
+               1 as hailwt, 0 as catdisp, 1 as drflag, a.tripid, a.haulnum, 
+               b.lathbeg, b.lonhbeg, a.link3
+               from obinc a, obspp b
+               where a.tripid = b.tripid
+               and a.year ", years,
+                       "\n union
+               select distinct a.year, a.month, b.area, b.negear, a.nespp4, 
+               1 as hailwt, 0 as catdisp, 1 as drflag, a.tripid, a.haulnum, 
+               b.lathbeg, b.lonhbeg, a.link3
+               from asminc a, asmspp b
+               where a.tripid = b.tripid
+               and a.year ", years)
+  
+  mammal <- data.table::as.data.table(DBI::dbGetQuery(channel, mammal.qry))
+  sql <- c(sql, mammal.qry)
+  
+  ob <- data.table::rbindlist(list(ob, mammal))
+  
+  #Grab otter trawl gear tables to get mesh size for small verses large mesh
+  mesh.qry <- paste0("select link3, codmsize
+             from OBOTGH
+             where year ", years)
+  mesh <- data.table::as.data.table(DBI::dbGetQuery(channel, mesh.qry))
+  sql <- c(sql, mesh.qry)
+  
+  #Convert mesh size from mm to inches
+  mesh[, CODMSIZE := CODMSIZE * 0.0393701]
+  mesh[CODMSIZE <= 3, MESHCAT := 'SM']
+  mesh[CODMSIZE >  3, MESHCAT := 'LG']
+  mesh[, CODMSIZE := NULL]
+  
+  ob <- merge(ob, mesh, by = 'LINK3', all.x = T)
+  
+  #Clean up data set
+  #Remove those with unknown disposition
+  ob <- ob[CATDISP != 9, ]
+  
+  #remove record if weight is missing
+  ob <- ob[!is.na(HAILWT), ]    
+  
+  #remove non-living items (clappers and stomach contents) and unknown living matter
+  ob <- ob[!(NESPP4 %in% c(0, 6800:6802, 6805, 6810, 6820, 6830, 6850:6857, 6882, 
+                           6883, 6894:6897))]  
+  
+  #Convert lat/lon to decimal degrees
+  ob[, LAT := as.numeric(substr(LATHBEG, 1, 2)) + ((as.numeric(substr(LATHBEG, 3, 4))
+                                                  + as.numeric(substr(LATHBEG, 5, 6)))
+                                                  /60)]
+  ob[, LON := (as.numeric(substr(LONHBEG, 1, 2)) + ((as.numeric(substr(LONHBEG, 3, 4))
+                                                  + as.numeric(substr(LONHBEG, 5, 6)))
+                                                  /60)) * -1]
+  ob[, c('LATHBEG', 'LONHBEG') := NULL]
+  
+  #Convert weights
+  convert.qry <- "select nespp4_obs, catdisp_code, drflag_code, cf_lndlb_livlb, cf_rptqty_lndlb  
+                from obspecconv"
+  convert <- data.table::as.data.table(DBI::dbGetQuery(channel, convert.qry))
+  sql <- c(sql, convert.qry)
+  
+  setnames(convert,
+           c('NESPP4_OBS', 'CATDISP_CODE', 'DRFLAG_CODE'),
+           c('NESPP4',     'CATDISP',      'DRFLAG'))
+  
+  setkey(convert,
+         NESPP4,
+         CATDISP,
+         DRFLAG)
+  
+  ob.code <- merge(ob, convert, by = key(convert), all.x = T) 
+  
+  #missing cf's will be set to 1 Assume living
+  ob.code[is.na(CF_LNDLB_LIVLB), CF_LNDLB_LIVLB := 1]
+  ob.code[is.na(CF_RPTQTY_LNDLB), CF_RPTQTY_LNDLB := 1]
+  
+  ob.code[, C.HAILWT := HAILWT * CF_RPTQTY_LNDLB * CF_LNDLB_LIVLB] 
+  
+  #Grab PR flags
+  prflag.qry <- "select NESPP4, cetacean, turtle, pinniped
+                from obspec"
+  
+  prflag <- data.table::as.data.table(DBI::dbGetQuery(channel, prflag.qry))
+  sql <- c(sql, prflag.qry)
+  
+  prflag[CETACEAN == 1 | TURTLE == 1 | PINNIPED == 1, PR := 1]
+  prflag[is.na(PR), PR := 0]
+  prflag[, c('CETACEAN', 'TURTLE', 'PINNIPED') := NULL]
+  
+  comdisc <- merge(ob.code, prflag, by = 'NESPP4', all.x = T)
+  
+  #Convert to metric tons to align with commercial landings data
+  comdisc[PR == 0, SPPLIVMT := C.HAILWT * 0.00045359237]
+  
+  #Change to NESPP3 to combine market categories
+  comdisc[PR == 0, NESPP3 := substring(NESPP4, 1, 3)]
+  #Birds, mammals, etc don't have unique NESPP3 codes
+  comdisc[is.na(NESPP3), NESPP3 := NESPP4] 
+  
+  comdisc[PR == 0, MKTCAT := as.numeric(substring(NESPP4, 4, 4))]
+  comdisc[is.na(MKTCAT), MKTCAT := 0]
+  
+  #drop extra columns NESPP4
+  comdisc[, c('DRFLAG', 'CF_LNDLB_LIVLB', 'CF_RPTQTY_LNDLB', 'HAILWT', 'C.HAILWT',
+              'NESPP4') := NULL]
+  
+  return(list(comdisc = comdisc[], 
+              sql     = sql))
+}
+
diff --git a/R/get_comland_data.R b/R/get_comland_data.R
index a59dae7..c1cfa58 100644
--- a/R/get_comland_data.R
+++ b/R/get_comland_data.R
@@ -27,75 +27,48 @@
 #'
 #'A file containing the data.table above will also be saved to the users machine in the directory provided
 #'
+#'
 #'@export
 
-get_comland_data <- function(channel,landed,endyear,out.dir) {
-
-
-  message("Pulling landings data from database. This could take a while (> 1 hour) ... ")
-  #Landings
-  tables <- c(paste0('WOLANDS', 64:81),
-              paste0('WODETS',  82:93),
-              paste0('CFDETS',  1994:endyear, 'AA'))
-
-  #Generate one table
-  comland <- c()
-  for(i in 1:length(tables)){
-    landings.qry <- paste("select year, month, negear, toncl1, nespp3, nespp4, area,
-                           spplivlb, spplndlb, sppvalue, utilcd
-                           from", tables[i])
-
-    comland.yr <- as.data.table(DBI::dbGetQuery(channel, landings.qry))
-
-    data.table::setkey(comland.yr,
-                       YEAR,
-                       MONTH,
-                       NEGEAR,
-                       TONCL1,
-                       NESPP3,
-                       NESPP4,
-                       AREA,
-                       UTILCD)
-
-    message("Pulled data from ",tables[i]," ...")
-
-    # Use landed weight instead of live weight for shellfish
-    if(landed == 'y') {comland.yr[NESPP3 %in% 743:800, SPPLIVLB := SPPLNDLB]}
-
-    #Sum landings and value
-    #landings
-    comland.yr[, V1 := sum(SPPLIVLB), by = key(comland.yr)]
-    #value
-    #Fix null values
-    comland.yr[is.na(SPPVALUE), SPPVALUE := 0]
-    comland.yr[, V2 := sum(SPPVALUE), by = key(comland.yr)]
-
-    #Remove extra rows/columns
-    comland.yr <- unique(comland.yr, by = key(comland.yr))
-    comland.yr[, c('SPPLIVLB', 'SPPLNDLB', 'SPPVALUE') := NULL]
-
-    #Rename summed columns
-    data.table::setnames(comland.yr, c('V1', 'V2'), c('SPPLIVLB', 'SPPVALUE'))
-
-    comland <- data.table::rbindlist(list(comland, comland.yr))
-  }
-
-  # save in RODBC format
-  comland$YEAR <- as.integer(comland$YEAR)
-  comland$MONTH <- as.integer(comland$MONTH)
-  comland$NEGEAR <- as.integer(comland$NEGEAR)
-  comland$TONCL1 <- as.integer(comland$TONCL1)
-  comland$NESPP3 <- as.integer(comland$NESPP3)
-  comland$NESPP4 <- as.integer(comland$NESPP4)
-  comland$UTILCD <- as.integer(comland$UTILCD)
-  comland$AREA <- as.factor(comland$AREA)
-
-
-
-  # Save file.
-  if(landed == 'n') saveRDS(comland, file = file.path(out.dir, paste0("comland_raw_US_livewt.RDS")))
-  if(landed == 'y') saveRDS(comland, file = file.path(out.dir, paste0("comland_raw_US_meatwt.RDS")))
-
+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', 
+                             aggGear = F, userGears = comlandr::mykeyGears,
+                             fleetDescription = 'Fleet') {
+  
+  call <- dbutils::capture_function_call()
+  
+  #Pull raw data
+  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(channel, comland, 
+                                                            filterByYear, filterByArea)
+  
+  #Pull foreign landings
+  if(useForeign) comland <- comlandr::get_foreign_data(channel, comland, filterByYear,
+                                                       filterByArea)
+  
+  #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, channel, 
+                                                            filterByYear, filterByArea)
+  
+  #Aggregate areas
+  if(aggArea) comland <- aggregate_area(comland, userAreas, areaDescription, 
+                                          propDescription)
+  
+  #Aggregate gears
+  if(aggGear) comland <- aggregate_gear(comland, userGears, fleetDescription)
+  
+  comland$call <- call
+  
+  message("Some data may be CONFIDENTIAL ... DO NOT disseminate without proper Non-disclosure agreement.")  
   return(comland)
 
 }
diff --git a/R/get_comland_raw_data.R b/R/get_comland_raw_data.R
new file mode 100644
index 0000000..4b3cdd2
--- /dev/null
+++ b/R/get_comland_raw_data.R
@@ -0,0 +1,154 @@
+#' Extracts commercial data from Database
+#'
+#' Connects to cfdbs and pulls fields from WOLANDS, WODETS, CFDETS
+#'
+#'@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
+#'
+#'
+#'@return Data frame (data.table) (n x 10)
+#'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{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{UTILCD}{Utilization code}
+#'\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.}
+#'
+#'@section File Creation:
+#'
+#'A file containing the data.table above will also be saved to the users machine in the directory provided
+#'
+#'@export
+
+get_comland_raw_data <- function(channel, filterByYear = NA, filterByArea = NA, 
+                                 useLanded = T, removeParts = T){
+  
+  #If not specifying a year default to 1964 - 2019
+  if(is.na(filterByYear)) filterByYear <- 1964:2019
+  
+  message(paste0("Pulling landings data from ",
+  filterByYear[1], " to ", filterByYear[length(filterByYear)],
+  ". This could take a while (> 1 hour) ... "))
+  
+  #Generate vector of tables to loop through
+  if(any(filterByYear < 1964)) stop("Landings data start in 1964")
+  
+  tables <- as.numeric(c(substr(filterByYear[which(filterByYear <= 1993)], 3, 4),
+              filterByYear[which(filterByYear >  1993)]))
+  tables[which(tables > 1993)] <- paste0('CFDETS',  tables[which(tables > 1993)], 'AA')
+  tables[which(tables > 63 & tables <= 81)] <- paste0('WOLANDS', tables[which(tables > 63 & tables <= 81)])
+  tables[which(tables > 81 & tables <= 93)] <- paste0('WODETS',  tables[which(tables > 81 & tables <= 93)])
+  
+  #output objects
+  comland <- c()
+  sql <- c()
+  
+  for(itab in 1:length(tables)){
+    #Data query
+    #Need to add mesh data post 1981
+    if(substr(tables[itab], 1, 3) == 'WOL'){
+      landings.qry <- paste("select year, month, negear, toncl1, nespp3, nespp4, area,
+                           spplivlb, spplndlb, sppvalue, utilcd
+                           from", tables[itab])
+      if(!is.na(filterByArea[1])){
+        landings.qry <- paste0(landings.qry, " where area in (", survdat:::sqltext(filterByArea), ")
+                               order by area")
+      }
+      comland.yr <- data.table::as.data.table(DBI::dbGetQuery(channel, landings.qry))
+      comland.yr[, MESH := 5] #Identify all as large mesh
+    } else {
+      if(filterByYear[itab] > 1993){
+        trip.table <- paste0('CFDETT',  filterByYear[itab], 'AA')
+      } 
+      if(filterByYear[itab] > 1981 & filterByYear[itab] <= 1993){
+        trip.table <- paste0('WODETT',  substr(filterByYear[itab], 3, 4))
+      }
+      landings.qry <- paste("select a.year, a.month, a.negear, a.toncl1, a.nespp3, 
+                           a.nespp4, a.area, a.spplivlb, a.spplndlb, a.sppvalue, 
+                           a.utilcd, b.mesh
+                           from", tables[itab], "a,", trip.table, "b
+                           where a.link = b.link")
+      if(!is.na(filterByArea[1])){
+        landings.qry <- paste0(landings.qry, " and a.area in (", survdat:::sqltext(filterByArea), ")
+                               order by area")
+      }
+      comland.yr <- data.table::as.data.table(DBI::dbGetQuery(channel, landings.qry))
+    }
+    sql <- c(sql, landings.qry)
+
+    #Identify small/large mesh fisheries
+    comland.yr[MESH <= 3, MESHCAT := 'SM']
+    comland.yr[MESH >  3, MESHCAT := 'LG']
+    comland.yr[, MESH := NULL]
+    
+    # Use landed weight instead of live weight for shellfish
+    if(useLanded) {comland.yr[NESPP3 %in% 743:800, SPPLIVLB := SPPLNDLB]}
+    
+    # Remove fish parts so live weight is not double counted
+    if(removeParts){
+      comland.yr <- comland.yr[!NESPP4 %in% c('0119', '0123', '0125', '0127', 
+                                              '0812', '0819', '0828', '0829', 
+                                              '1731', '2351', '2690', '2699', 
+                                              '3472', paste0(348:359, 8), 
+                                              '3868', paste0(469:471, 4),
+                                              paste0(480:499, 8), '5018', 
+                                              '5039', '5261', '5265'), ]
+    }
+    
+    #Sum landings and value
+    data.table::setkey(comland.yr,
+                       YEAR,
+                       MONTH,
+                       NEGEAR,
+                       MESHCAT,
+                       TONCL1,
+                       NESPP3,
+                       AREA,
+                       UTILCD)
+    #landings
+    comland.yr[, V1 := sum(SPPLIVLB, na.rm = T), by = key(comland.yr)]
+    #value
+    comland.yr[, V2 := sum(SPPVALUE, na.rm = T), by = key(comland.yr)]
+    
+    #Create market category
+    comland.yr[, MKTCAT := substr(NESPP4, 4, 4)]
+    
+    #Remove extra rows/columns
+    comland.yr <- unique(comland.yr, by = key(comland.yr))
+    comland.yr[, c('SPPLIVLB', 'SPPLNDLB', 'SPPVALUE', 'NESPP4') := NULL]
+
+    #Rename summed columns
+    data.table::setnames(comland.yr, c('V1', 'V2'), c('SPPLIVLB', 'SPPVALUE'))
+
+    comland <- data.table::rbindlist(list(comland, comland.yr))
+    
+    message("Pulled data from ",tables[itab]," ...")
+    
+    }
+
+  #Convert number fields from chr to num
+  numberCols <- c('YEAR', 'MONTH', 'NEGEAR', 'TONCL1', 'NESPP3', 'UTILCD', 'AREA',
+                  'MKTCAT')
+  comland[, (numberCols):= lapply(.SD, as.numeric), .SDcols = numberCols][]
+  
+  #Adjust pounds to metric tons
+  comland[, SPPLIVMT := SPPLIVLB * 0.00045359237]
+  comland[, SPPLIVLB := NULL]
+  
+  #standardize YEAR field
+  comland[YEAR < 100, YEAR := YEAR + 1900L]
+
+  
+  return(list(comland = comland[], 
+              sql     = sql))
+}
+
diff --git a/R/get_discard_data.R b/R/get_discard_data.R
new file mode 100644
index 0000000..db52015
--- /dev/null
+++ b/R/get_discard_data.R
@@ -0,0 +1,447 @@
+# #Comdisc.r 
+# library(here); library(data.table); library(comlandr)
+# 
+# #channel <- dbutils::connect_to_database(server="nova",uid="slucey")
+# 
+# #get_observer_data <- function(channel, filterByYear, )
+# endyear <- 2017
+# 
+# strat.var <- c('YEAR', 'QY', 'EPU', 'GEAR')
+# haullevel <- F #Toggle whether to save haul by haul data or not
+# landings.file <- 'comland_meatwt_deflated.RData'
+# 
+# 
+# 
+# #-------------------------------------------------------------------------------
+# #User created functions 
+# #Sums the number of occurances
+# count<-function(x){
+#   num<-rep(1,length(x))
+#   out<-sum(num)
+#   return(out)
+#   }
+#   
+# #-------------------------------------------------------------------------------
+# 
+# filterByYear <- 1989
+# 
+# #Create year vector
+# if(is.na(filterByYear[1])){
+#   years <- ">= 1989"
+# }else{
+#   years <- paste0("in (", survdat:::sqltext(filterByYear), ")")
+# }
+# 
+# ob.qry <- paste0("select year, month, area, negear, nespp4, hailwt, catdisp, drflag, 
+#           tripid, haulnum, lathbeg, lonhbeg, link3
+#           from OBSPP
+#           where obsrflag = 1
+#           and program not in ('127', '900', '250', '160')
+#           and year ", years,
+#           "\n union
+#           select year, month, area, negear, nespp4, hailwt, catdisp, drflag, 
+#           tripid, haulnum, lathbeg, lonhbeg, link3
+#           from ASMSPP
+#           where obsrflag = 1
+#           and program not in ('127', '900', '250', '160')
+#           and year ", years)
+# 
+# ob <- data.table::as.data.table(DBI::dbGetQuery(channel, ob.qry))
+# 
+# #Add protected species here
+# mammal.qry <- paste0("select distinct a.year, a.month, b.area, b.negear, a.nespp4, 
+#                1 as hailwt, 0 as catdisp, 1 as drflag, a.tripid, a.haulnum, 
+#                b.lathbeg, b.lonhbeg, a.link3
+#                from obinc a, obspp b
+#                where a.tripid = b.tripid
+#                and a.year ", years,
+#                "\n union
+#                select distinct a.year, a.month, b.area, b.negear, a.nespp4, 
+#                1 as hailwt, 0 as catdisp, 1 as drflag, a.tripid, a.haulnum, 
+#                b.lathbeg, b.lonhbeg, a.link3
+#                from asminc a, asmspp b
+#                where a.tripid = b.tripid
+#                and a.year ", years)
+#                
+# mammal <- data.table::as.data.table(DBI::dbGetQuery(channel, mammal.qry))
+# 
+# ob <- rbindlist(list(ob, mammal))
+# 
+# #Grab otter trawl gear tables to get mesh size for small verses large mesh
+# mesh.qry <- paste0("select link3, codmsize
+#              from OBOTGH
+#              where year ", years)
+# mesh <- data.table::as.data.table(DBI::dbGetQuery(channel, mesh.qry))
+# 
+# #Convert mesh size from mm to inches
+# mesh[, CODMSIZE := CODMSIZE * 0.0393701]
+# mesh[CODMSIZE <= 3, MESHCAT := 'SM']
+# mesh[CODMSIZE >  3, MESHCAT := 'LG']
+# mesh[, CODMSIZE := NULL]
+# 
+# ob <- merge(ob, mesh, by = 'LINK3', all.x = T)
+# 
+# #Clean up data set
+# #Remove those with unknown disposition
+# ob <- ob[CATDISP != 9, ]
+#  
+# #remove record if weight is missing
+# ob <- ob[!is.na(HAILWT), ]    
+#  
+# #remove non-living items (clappers and stomach contents) and unknown living matter
+# ob <- ob[!(NESPP4 %in% c(0, 6800:6802, 6805, 6810, 6820, 6830, 6850:6857, 6882, 6883, 6894:6897))]  
+# 
+# #Convert lat/lon to decimal degrees
+# ob[, LATDD := substr(LATHBEG, 1, 2) + ((substr(LATHBEG, 3, 4) + substr(LATHBEG, 5, 6))
+#    / 60)]
+# 
+# #Convert weights
+# convert.qry <- "select nespp4_obs, catdisp_code, drflag_code, cf_lndlb_livlb, cf_rptqty_lndlb  
+#                 from obspecconv"
+# convert <- data.table::as.data.table(DBI::dbGetQuery(channel, convert.qry))
+# 
+# setnames(convert,
+#         c('NESPP4_OBS', 'CATDISP_CODE', 'DRFLAG_CODE'),
+#         c('NESPP4',     'CATDISP',      'DRFLAG'))
+# 
+# setkey(convert,
+#       NESPP4,
+#       CATDISP,
+#       DRFLAG)
+# 
+# ob.code <- merge(ob, convert, by = key(convert), all.x = T) 
+# 
+# #missing cf's will be set to 1 Assume living
+# ob.code[is.na(CF_LNDLB_LIVLB), CF_LNDLB_LIVLB := 1]
+# ob.code[is.na(CF_RPTQTY_LNDLB), CF_RPTQTY_LNDLB := 1]
+#  
+# ob.code[, C.HAILWT := HAILWT * CF_RPTQTY_LNDLB * CF_LNDLB_LIVLB] 
+# 
+# #Grab common name and PR flags
+# comname.qry <- "select NESPP4, comname, sciname, cetacean, turtle, pinniped
+#                 from obspec"
+# 
+# comname <- data.table::as.data.table(DBI::dbGetQuery(channel, comname.qry))
+# comname[CETACEAN == 1 | TURTLE == 1 | PINNIPED == 1, PR := 1]
+# comname[is.na(PR), PR := 0]
+# comname[, c('CETACEAN', 'TURTLE', 'PINNIPED') := NULL]
+# 
+# ob.code <- merge(comname, ob.code, by = 'NESPP4')
+# 
+# #Convert to metric tons to align with commercial landings data
+# ob.code[PR == 0, C.HAILWT := C.HAILWT * 0.00045359237]
+# 
+# #Change to NESPP3 to combine market categories
+# ob.code[, NESPP3 := substring(NESPP4, 1, 3)]
+# #Birds, mammals, etc don't have unique NESPP3 codes
+# ob.code[is.na(NESPP3), NESPP3 := NESPP4] 
+# 
+# ob.code[, MKTCAT := as.numeric(substring(NESPP4, 4, 4))]
+# 
+# #drop NESPP4
+# ob.code[, NESPP4 := NULL]
+# 
+# #Deal with skate(ns) for little and winter skates
+# source(file.path(data.dir.2, 'Comland_skates_hakes.R'))
+# 
+# #get little skates and winter skates from skates(ns) - use survey in half years
+# #Generate Half year variable in comland
+# ob.skates <- ob.code[NESPP3 == 365, ]
+# ob.skates[MONTH %in% 1:6,  Half := 1]
+# ob.skates[MONTH %in% 7:12, Half := 2]
+# 
+# setkey(skate.hake.us,
+#        YEAR,
+#        Half,
+#        AREA)
+# 
+# ob.skates <- merge(ob.skates, skate.hake.us, by = key(skate.hake.us), all.x = T)
+# 
+# ob.skates[NESPP3 == 365, little := little.per * C.HAILWT]
+# ob.skates[is.na(little), little := 0]
+# 
+# ob.skates[NESPP3 == 365, winter := winter.per * C.HAILWT]
+# ob.skates[is.na(winter), winter := 0]
+# 
+# ob.skates[NESPP3 == 365, other.skate := C.HAILWT - (little + winter)]
+# 
+# #Little (366), winter (367), skates(ns) (365)
+# #put skates in ob.code format to merge back
+# little <- ob.skates[, list(COMNAME, SCINAME, PR, CATDISP, DRFLAG,
+#                            YEAR, MONTH, AREA, NEGEAR, HAILWT, 
+#                            TRIPID, HAULNUM, LINK1, LINK3, CF_LNDLB_LIVLB, 
+#                            CF_RPTQTY_LNDLB, little, NESPP3, MKTCAT)]
+# little[, NESPP3 := 366]
+# setnames(little, "little", "C.HAILWT")
+# little <- little[C.HAILWT > 0, ]
+# 
+# winter <- ob.skates[, list(COMNAME, SCINAME, PR, CATDISP, DRFLAG,
+#                            YEAR, MONTH, AREA, NEGEAR, HAILWT, 
+#                            TRIPID, HAULNUM, LINK1, LINK3, CF_LNDLB_LIVLB, 
+#                            CF_RPTQTY_LNDLB, winter, NESPP3, MKTCAT)]
+# winter[, NESPP3 := 367]
+# setnames(winter, "winter", "C.HAILWT")
+# winter <- winter[C.HAILWT > 0, ]
+# 
+# other <- ob.skates[, list(COMNAME, SCINAME, PR, CATDISP, DRFLAG,
+#                           YEAR, MONTH, AREA, NEGEAR, HAILWT, 
+#                           TRIPID, HAULNUM, LINK1, LINK3, CF_LNDLB_LIVLB, 
+#                           CF_RPTQTY_LNDLB, other.skate, NESPP3, MKTCAT)]
+# other[, NESPP3 := 365]
+# setnames(other, "other.skate", "C.HAILWT")
+# other <- other[C.HAILWT > 0, ]
+# 
+# #merge all three and reformat for ob
+# skates.add.back <- rbindlist(list(little, winter, other))
+# 
+# setcolorder(skates.add.back, names(ob.code))
+# 
+# ob.code <- rbindlist(list(ob.code[NESPP3 != 365, ], skates.add.back))  
+# 
+# #Assign stat areas to EPUs
+# gom <- c(500,510,512:515)
+# gb  <- c(521:526,551,552,561,562)
+# mab <- c(537,539,600,612:616,621,622,625,626,631,632)
+# ss  <- c(463:467,511)
+# 
+# ob.code[AREA %in% gom, EPU := 'GOM']
+# ob.code[AREA %in% gb,  EPU := 'GB']
+# ob.code[AREA %in% mab, EPU := 'MAB']
+# ob.code[AREA %in% ss,  EPU := 'SS']
+# ob.code[is.na(EPU),    EPU := 'OTHER']
+# ob.code[, EPU := factor(EPU, levels = c('GOM', 'GB', 'MAB', 'SS', 'OTHER'))]
+# 
+# #Create quarter year variable
+# ob.code[MONTH %in% 1:3,   QY := 1]
+# ob.code[MONTH %in% 4:6,   QY := 2]
+# ob.code[MONTH %in% 7:9,   QY := 3]
+# ob.code[MONTH %in% 10:12, QY := 4]
+# 
+# #Aggregate Gear
+# otter     <- 50:59
+# dredge.sc <- 131:132
+# pot       <- c(189:190, 200:219, 300, 301)
+# longline  <- c(10, 40)
+# seine     <- c(70:79, 120:129, 360)
+# gillnet   <- c(100:119, 500, 510, 520)
+# midwater  <- c(170, 370)
+# dredge.o  <- c(281, 282, 380:400)
+# 
+# ob.code[NEGEAR %in% otter,     GEAR := 'otter']
+# ob.code[NEGEAR %in% dredge.sc, GEAR := 'dredge.sc']
+# ob.code[NEGEAR %in% pot,       GEAR := 'pot']
+# ob.code[NEGEAR %in% longline,  GEAR := 'longline']
+# ob.code[NEGEAR %in% seine,     GEAR := 'seine']
+# ob.code[NEGEAR %in% gillnet,   GEAR := 'gillnet']
+# ob.code[NEGEAR %in% midwater,  GEAR := 'midwater']
+# ob.code[NEGEAR %in% dredge.o,  GEAR := 'dredge.o']
+# ob.code[is.na(GEAR),           GEAR := 'other']
+# ob.code[, GEAR := as.factor(GEAR)]
+# 
+# ob.code[, c('DRFLAG', 'MONTH', 'AREA', 'NEGEAR', 
+#             'HAILWT', 'CF_LNDLB_LIVLB', 'CF_RPTQTY_LNDLB') := NULL]
+# 
+# setkeyv(ob.code, c(strat.var, 'NESPP3', 'CATDISP'))
+# 
+# if(haullevel == T){#This is broken
+#   ob.haul <- ob.code
+#   save(comdisc, file = file.path(out.dir, "Observer_Discards_by_Haul.RData"))
+# }
+# 
+# ob.sums <- ob.code[, sum(C.HAILWT), by = key(ob.code)]
+# 
+# #Make a new function
+# #Calculate kept and discards
+# ob.discard <- ob.sums[CATDISP == 0, ]
+# 
+# setnames(ob.discard,
+#         "V1",
+#         "DISCARD")
+# 
+# setkeyv(ob.sums, strat.var)
+#       
+# ob.kept <- ob.sums[CATDISP == 1, sum(V1), by = key(ob.sums)]
+# 
+# setnames(ob.kept,
+#         "V1",
+#         "KEPT.ALL")
+#         
+# ob.all <- merge(ob.kept, ob.discard, by = key(ob.sums))
+# 
+# ob.all[, CATDISP := NULL]
+# 
+# ob.all[, DK := DISCARD / KEPT.ALL]
+# ob.all[is.na(DK), DK := 1.0]
+# ob.all[, c('KEPT.ALL', 'DISCARD') := NULL]
+# 
+# #Get landings
+# load(file.path(data.dir, landings.file))
+# 
+# setkeyv(comland, strat.var)
+#       
+# tot.land <- comland[, sum(SPPLIVMT), by = key(comland)]
+# 
+# setnames(tot.land,
+#         "V1",
+#         "TOT.LAND")
+#         
+# comdisc <- merge(ob.all, tot.land, by = key(comland))
+# 
+# comdisc[, DISC := DK * TOT.LAND]
+# 
+# #Variance
+# #Need to add back individual trip data
+# rm(ob) #Free up memory
+# setkeyv(comdisc, c(strat.var, 'NESPP3'))
+# 
+# disc.var <- unique(comdisc, by = key(comdisc))
+# 
+# #Trip kept all
+# setkeyv(ob.code, c(strat.var, 'TRIPID'))
+#                  
+# trip.kept <- ob.code[CATDISP == 1, sum(C.HAILWT), by = key(ob.code)]                
+# setnames(trip.kept, "V1", "trip.k")
+# 
+# #Trip discard by species
+# setkeyv(ob.code, c(strat.var, 'TRIPID', 'NESPP3'))
+#                  
+# trip.disc <- ob.code[CATDISP == 0, sum(C.HAILWT), by = key(ob.code)]                
+# setnames(trip.disc, "V1", "trip.d")
+# 
+# trip.all <- merge(trip.disc, trip.kept, by = c(strat.var, 'TRIPID'), all = T)
+# trip.all[is.na(trip.k), trip.k := 0] 
+# 
+# disc.var <- merge(disc.var, trip.all, by = c(strat.var, 'NESPP3'))
+# 
+# #Calculate the number of observed trips
+# setkeyv(ob.code, c(strat.var, 'TRIPID'))
+#                 
+# trips <- unique(ob.code, by = key(ob.code))
+# 
+# trip.count <- trips[, count(TRIPID), by = strat.var]
+# 
+# setnames(trip.count, "V1", "n")
+# 
+# disc.var <- merge(disc.var, trip.count, by = strat.var)
+# 
+# #Calculate the total number of trips
+# #CFDBS is on sole - need to switch connection
+# odbcClose(channel)
+# if(Sys.info()['sysname']=="Windows"){
+#   channel <- odbcDriverConnect()
+# } else {
+#   channel <- odbcConnect('sole', uid, pwd)
+# }
+# 
+# tables <- c(paste('WODETS',  89:93, sep = ''), 
+#             paste('CFDETS',  1994:endyear, 'AA', sep = ''))
+#             
+# comtrip.qry <- "select year, month, area, negear, count(link) as N
+#                 from WODETS89
+#                 group by year, month, area, negear"
+# comtrip <- as.data.table(sqlQuery(channel, comtrip.qry))
+# 
+# for(i in 2:length(tables)){
+#   tripyr.qry <- paste("select year, month, area, negear, count(link) as N
+#                        from", tables[i],
+#                        "group by year, month, area, negear")
+#   tripyr <- as.data.table(sqlQuery(channel, tripyr.qry))
+# 
+#   comtrip <- rbindlist(list(comtrip, tripyr))
+#   }
+#   
+# comtrip[AREA %in% gom, EPU := 'GOM']
+# comtrip[AREA %in% gb,  EPU := 'GB']
+# comtrip[AREA %in% mab, EPU := 'MAB']
+# comtrip[AREA %in% ss,  EPU := 'SS']
+# comtrip[is.na(EPU),    EPU := 'OTHER']
+# comtrip[, EPU := factor(EPU, levels = c('GOM', 'GB', 'MAB', 'SS', 'OTHER'))]
+# 
+# comtrip[YEAR < 100, YEAR := YEAR + 1900]
+# 
+# comtrip[MONTH %in% 1:3,   QY := 1]
+# comtrip[MONTH %in% 4:6,   QY := 2]
+# comtrip[MONTH %in% 7:9,   QY := 3]
+# comtrip[MONTH %in% 10:12, QY := 4]
+# 
+# comtrip[NEGEAR %in% otter,     GEAR := 'otter']
+# comtrip[NEGEAR %in% dredge.sc, GEAR := 'dredge.sc']
+# comtrip[NEGEAR %in% pot,       GEAR := 'pot']
+# comtrip[NEGEAR %in% longline,  GEAR := 'longline']
+# comtrip[NEGEAR %in% seine,     GEAR := 'seine']
+# comtrip[NEGEAR %in% gillnet,   GEAR := 'gillnet']
+# comtrip[NEGEAR %in% midwater,  GEAR := 'midwater']
+# comtrip[NEGEAR %in% dredge.o,  GEAR := 'dredge.o']
+# comtrip[is.na(GEAR),           GEAR := 'other']
+# comtrip[, GEAR := as.factor(GEAR)]
+# 
+# setkeyv(comtrip, strat.var)
+# 
+# comtrip.count <- comtrip[, sum(N), by = key(comtrip)]
+# 
+# setnames(comtrip.count, "V1", "N")
+# 
+# disc.var <- merge(disc.var, comtrip.count, by = key(comtrip), all.x = T)
+# 
+# #Fix groups that don't line up properly - actual value of N not that important only relative size
+# N.avg <- disc.var[, mean(N, na.rm = T)]
+# disc.var[is.na(N), N := N.avg]
+# 
+# #Calculate variance
+# #Need to expand so zero discards by species are represented
+# setkeyv(disc.var, c(strat.var, 'TRIPID'))
+# var.trips <- unique(disc.var, by = key(disc.var))
+# #drop species specific data
+# var.trips[, c('NESPP3', 'DK', 'DISC', 'trip.d') := NULL]
+# 
+# #Get list of species
+# spp <- unique(disc.var[, NESPP3])
+# all.spp.var <- c()
+# for(i in 1:length(spp)){
+#   spp.trip <- disc.var[NESPP3 == spp[i], ]  
+#   #Get rid of extra data
+#   spp.trip[, c('TOT.LAND', 'DISC', 'trip.k', 'n', 'N') := NULL]
+#   
+#   spp.var <- merge(var.trips, spp.trip, by = c(strat.var, 'TRIPID'), all.x = T)
+#   
+#   #Fix NAs
+#   spp.var[is.na(NESPP3), NESPP3 := spp[i]]
+#   spp.var[is.na(trip.d), trip.d := 0]
+#   
+#   #Merge in DK ratios
+#   setkeyv(spp.trip, strat.var)
+#   spp.dk <- unique(spp.trip, by = key(spp.trip))
+#   spp.var[, DK := NULL]
+#   spp.dk[, c('NESPP3', 'TRIPID', 'trip.d') := NULL]
+#   spp.var <- merge(spp.var, spp.dk, by = strat.var, all.x = T)
+#   spp.var[is.na(DK), DK := 0]
+#   
+#   spp.var[, step.1 := (sum(trip.d^2 + DK^2 * trip.k^2 - 2 * DK * trip.d * trip.k)/(n - 1)), by = strat.var]
+# 
+#   setkeyv(spp.var, strat.var)
+#   spp.var <- unique(spp.var, by = key(spp.var))
+#   spp.var[, c('TRIPID', 'trip.d', 'trip.k', 'DK') := NULL]
+# 
+#   spp.var[, DISC.VAR :=  TOT.LAND^2 * ((N - n)/n*N) * (1/(TOT.LAND/n)^2) * step.1]
+#   spp.var[, c('TOT.LAND', 'n', 'N', 'step.1') := NULL]
+# 
+#   all.spp.var <- rbindlist(list(all.spp.var, spp.var))
+#   }
+# comdisc <- merge(comdisc, all.spp.var, by = c(strat.var, 'NESPP3'), all.x = T)
+# 
+# #Add species names
+# #Change to NESPP3 to combine market categories
+# comname[NESPP4 < 100,                        NESPP3 := as.numeric(substring(NESPP4, 1, 1))]
+# comname[NESPP4 > 99 & NESPP4 < 1000,         NESPP3 := as.numeric(substring(NESPP4, 1, 2))]
+# comname[(NESPP4 > 999 & NESPP4 < 6100) | 
+#         NESPP4 %in% c(7100:7109, 8020:8029), NESPP3 := as.numeric(substring(NESPP4, 1, 3))]
+# #Birds, mammals, etc don't have unique NESPP3 codes
+# comname[NESPP4 > 6099 & !NESPP4 %in% c(7100:7109, 8020:8029), NESPP3 := NESPP4]
+# 
+# setkey(comname, NESPP3)
+# comname <- unique(comname, by = key(comname))
+# comname[, c('NESPP4', 'SCINAME') := NULL]
+# 
+# comdisc <- merge(comname, comdisc, by = 'NESPP3')
+# 
+# save(comdisc, file = file.path(out.dir, "Comdisc.RData"))
diff --git a/R/get_herring_data.R b/R/get_herring_data.R
new file mode 100644
index 0000000..5f655a5
--- /dev/null
+++ b/R/get_herring_data.R
@@ -0,0 +1,126 @@
+#' Processes herring data
+#'
+#'Herring Data comes from the state of Maine.
+#'
+#'@param channel DBI object. connection object for database access
+#'@param comland Data frame. master data frame containing species landings
+#'
+#'@return Processed Herring data added to comland
+#'
+#'@importFrom data.table ":=" "key"
+#'
+#' @noRd
+#' @export
+
+get_herring_data <- function(channel, comland, filterByYear, filterByArea) {
+  
+  #Pulling data
+  message("Pulling Atlantic herring data from maine_herring_catch ...")
+  
+  if(is.na(filterByYear[1])){
+    years <- ">= 1963"
+  }else{
+    years <- paste0("in (", survdat:::sqltext(filterByYear), ")")
+  }
+  
+  herr.qry <- paste0("select year, month, stock_area, negear, gearname, keptmt, discmt
+                     from maine_herring_catch
+                     where year ", years)
+  if(!is.na(filterByArea[1])){
+    herr.qry <- paste0(herr.qry, " and stock_area in (", survdat:::sqltext(filterByArea), ")
+                               order by stock_area")
+  }
+  
+  sql <- c(comland$sql, herr.qry)
+  
+  #pull out comland data
+  comland <- comland$comland
+
+  herr.catch <- data.table::as.data.table(DBI::dbGetQuery(channel, herr.qry))
+  
+  #Convert number fields from chr to num
+  numberCols <- c('YEAR', 'MONTH', 'STOCK_AREA', 'NEGEAR', 'GEARNAME')
+  herr.catch[, (numberCols):= lapply(.SD, as.numeric), .SDcols = numberCols]
+
+  #Aggregate data
+  data.table::setkey(herr.catch, YEAR, MONTH, STOCK_AREA, NEGEAR)
+
+  herring <- herr.catch[, list(sum(KEPTMT, na.rm = T), sum(DISCMT, na.rm = T)), 
+                        by = key(herr.catch)]
+
+  data.table::setnames(herring, c('STOCK_AREA', 'V1', 'V2'),
+                       c('AREA', 'SPPLIVMT', 'DISCMT'))
+
+  #Using averages from comland to fill in categories
+  herring[, MKTCAT := 5]
+
+  herring[, TONCL1 := 3]
+
+  herring[, UTILCD := 0]
+  
+  herring[, MESHCAT := 'LG']
+
+  #compute price/utilization from CF tables
+  herring.comland <- comland[NESPP3 == 168, ]
+
+  #Price from comland
+  herring.price <- herring.comland[, (sum(SPPVALUE, na.rm = T) / sum(SPPLIVMT, na.rm = T)), 
+                                   by = c('YEAR', 'MONTH')]
+
+  data.table::setnames(herring.price, 'V1', 'price')
+
+  herring <- merge(herring, herring.price, by = c('YEAR', 'MONTH'), all.x = T)
+
+  #Use 1964 prices for < 1964
+  herring[YEAR < 1964, price := mean(herring[YEAR == 1964, price])]
+  #Calculate SPPVALUE from price
+  herring[, SPPVALUE := round(price * SPPLIVMT)]
+
+  #Utilization from comland
+  herring.util <- herring.comland[, sum(SPPLIVMT), by = c('YEAR', 'MONTH', 'UTILCD')]
+  data.table::setnames(herring.util, 'V1', 'SPPLIVMT')
+
+  herring.util[, SPPLIVMT.ALL := sum(SPPLIVMT), by = c('YEAR', 'MONTH')]
+
+  herring.util[, Prop := SPPLIVMT/SPPLIVMT.ALL]
+
+  data.table::setorder(herring.util, YEAR, MONTH, Prop)
+
+  herring.util[, cum.prop := cumsum(Prop), by = c('YEAR', 'MONTH')]
+
+  #Apply proportions to Maine data set
+  #Not pulled all the time - current through 2017
+  herring[, Total := sum(SPPLIVMT), by = c('YEAR', 'MONTH')]
+
+  herring[, Prop := SPPLIVMT / Total]
+
+  data.table::setorder(herring, YEAR, MONTH, Prop)
+  herring[, cum.prop := cumsum(Prop), by = c('YEAR', 'MONTH')]
+
+  for(iyear in unique(herring.util[, YEAR])){
+    for(imonth in unique(herring.util[YEAR == iyear, MONTH])){
+      cum.prop.low <- 0
+      for(iutil in herring.util[YEAR == iyear & MONTH == imonth, UTILCD]){
+        cum.prop.high <- herring.util[YEAR == iyear & MONTH == imonth &
+                                        UTILCD == iutil, cum.prop]
+        herring[YEAR == iyear & MONTH == imonth & cum.prop <= cum.prop.high &
+                  cum.prop > cum.prop.low, UTILCD := iutil]
+        cum.prop.low <- cum.prop.high
+      }
+    }
+  }
+
+  #fix column headings
+  herring[, c('Total', 'Prop', 'cum.prop', 'price', 'DISCMT') := NULL]
+  herring[, NESPP3 := 168]
+
+  data.table::setcolorder(herring, names(comland))
+
+  #remove herring from data pull and add in Maine numbers
+  comland <- data.table::rbindlist(list(comland[NESPP3 != 168, ], herring))
+
+
+  return(list(comland = comland[], 
+              sql     = sql))
+
+}
diff --git a/R/sqltext.R b/R/sqltext.R
new file mode 100644
index 0000000..4f143bf
--- /dev/null
+++ b/R/sqltext.R
@@ -0,0 +1,18 @@
+#'  Convert output to text for DB query
+#'
+#'  @param x
+#'
+#' Not exported
+#' @noRd
+
+sqltext <- function(x){
+  out <- x[1]
+  if(length(x) > 1){
+    for(i in 2:length(x)){
+      out <- paste(out, x[i], sep = "','")
+    }
+  }
+  out <- paste("'", out, "'", sep = '')
+  return(out)
+}
+
diff --git a/data-raw/All_Species_Proportions.rds b/data-raw/All_Species_Proportions.rds
new file mode 100644
index 0000000..94e7719
Binary files /dev/null and b/data-raw/All_Species_Proportions.rds differ
diff --git a/data-raw/aggregate_area_table.R b/data-raw/aggregate_area_table.R
new file mode 100644
index 0000000..4819127
--- /dev/null
+++ b/data-raw/aggregate_area_table.R
@@ -0,0 +1,17 @@
+#Aggregate areas table
+
+#The proportion of catch inside and outside was calculated from the MS Keyrun 
+#project for Georges Bank.  
+library(here); library(data.table)
+
+mskeyAreas <- readRDS(here::here('data-raw/All_Species_Proportions.rds')) 
+mskeyAreas[InOut == 'in', EPU := 'GB']
+mskeyAreas[AREA %in% c(521, 522, 551, 561) & InOut == 'out', EPU := 'GOM']  
+mskeyAreas[AREA %in% c(526, 537, 538)      & InOut == 'out', EPU := 'MAB']
+mskeyAreas[is.na(EPU), EPU := 'Other']
+
+#Drop InOut column
+mskeyAreas[, InOut := NULL]
+
+#Output to package
+usethis::use_data(mskeyAreas, overwrite = TRUE)
\ No newline at end of file
diff --git a/data-raw/aggregate_gears_table.R b/data-raw/aggregate_gears_table.R
new file mode 100644
index 0000000..cb9ea21
--- /dev/null
+++ b/data-raw/aggregate_gears_table.R
@@ -0,0 +1,29 @@
+#Aggregate gears table
+
+#Gear designations from the MS Keyrun project for Georges Bank.  
+
+library(data.table)
+
+#Create Gear table
+mskeyGears <- data.table(NEGEAR2 = c(5, 
+                                     5, 16, 32, 35, 36,
+                                     1, 2, 8, 10, 50, 52, 14, 26,
+                                     12, 17, 37,
+                                     18, 15, 19, 20, 21, 23, 30, 33, 53,
+                                     13,
+                                     40,
+                                     22, 25, 38, 41,
+                                     3, 4, 6, 11),
+                         MESHCAT = c('SM', rep('LG', 5), rep(NA, 30)),
+                         Fleet = c('SM Mesh',
+                                   rep('LG Mesh', 5),
+                                   rep('Fixed Gear', 8),
+                                   rep('Pelagic', 3),
+                                   rep('Trap', 9),
+                                   'Scallop Dredge',
+                                   'Clam Dredge',
+                                   rep('Other Dredge', 4),
+                                   rep('HMS', 4)))
+
+#Output to package
+usethis::use_data(mskeyGears, overwrite = TRUE)
\ No newline at end of file
diff --git a/data/mskeyAreas.rda b/data/mskeyAreas.rda
new file mode 100644
index 0000000..eb318df
Binary files /dev/null and b/data/mskeyAreas.rda differ
diff --git a/data/mskeyGears.rda b/data/mskeyGears.rda
new file mode 100644
index 0000000..a5fcb2e
Binary files /dev/null and b/data/mskeyGears.rda differ
diff --git a/man/aggregate_area.Rd b/man/aggregate_area.Rd
new file mode 100644
index 0000000..22ff63a
--- /dev/null
+++ b/man/aggregate_area.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/aggregate_area.R
+\name{aggregate_area}
+\alias{aggregate_area}
+\title{Assign landing records to an aggregated area}
+\usage{
+aggregate_area(
+  comland,
+  userAreas,
+  areaDescription,
+  propDescription,
+  applyPropValue = T
+)
+}
+\arguments{
+\item{comland}{Data set generated by \code{get_comland_data}}
+
+\item{userAreas}{Data frame. Definitions to aggregate statistical areas to user defined
+areas}
+
+\item{areaDescription}{Character. Name of column in userAreas that defines the new
+area.}
+
+\item{propDescription}{Character. Name of column in userAreas that defines the 
+proportions of landings assigned to new area.}
+}
+\description{
+Takes the output from \code{get_comland_data} and further aggregates from NAFO 
+statistical areas to a user defined area.  Allows for species to be assigned by
+proportions to more than two user defined areas from one stat area
+}
diff --git a/man/aggregate_gear.Rd b/man/aggregate_gear.Rd
new file mode 100644
index 0000000..a36efee
--- /dev/null
+++ b/man/aggregate_gear.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/aggregate_gear.R
+\name{aggregate_gear}
+\alias{aggregate_gear}
+\title{Assign landing records to an aggregated area}
+\usage{
+aggregate_gear(comData, userGears, fleetDescription)
+}
+\arguments{
+\item{comland}{Data set generated by \code{get_comland_data}}
+
+\item{userAreas}{Data frame. Definitions to aggregate statistical areas to user defined
+areas}
+
+\item{areaDescription}{Character. Name of column in userAreas that defines the new
+area.}
+
+\item{propDescription}{Character. Name of column in userAreas that defines the 
+proportions of landings assigned to new area.}
+}
+\description{
+Takes the output from \code{get_comland_data} and further aggregates from NAFO 
+statistical areas to a user defined area.  Allows for species to be assigned by
+proportions to more than two user defined areas from one stat area
+}
diff --git a/man/assign_area.Rd b/man/assign_area.Rd
new file mode 100644
index 0000000..bbb4302
--- /dev/null
+++ b/man/assign_area.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/assign_area.R
+\name{assign_area}
+\alias{assign_area}
+\title{Assigns points to polygon}
+\usage{
+assign_area(comdiscData, areaPolygon, areaDescription, na.keep = F)
+}
+\arguments{
+\item{na.keep}{Boolean. Logical value to indicate whether original strata names
+should be retained.}
+}
+\value{
+Returns a \code{comdiscData} data.table with one additional column labeled
+ with the value of \code{areaDescription}
+
+\item{areaDescription}{The name of the region (found in \code{areaPolygon})
+ that a record in \code{surveyData} is assigned to}
+}
+\description{
+Assign observer data (points, lat and lon) to designated regions (polygons) from a shape file.
+}
+\seealso{
+Other comdisc: 
+\code{\link{calc_DK}()}
+}
+\concept{comdisc}
diff --git a/man/calc_DK.Rd b/man/calc_DK.Rd
new file mode 100644
index 0000000..57b78d6
--- /dev/null
+++ b/man/calc_DK.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/calc_DK.R
+\name{calc_DK}
+\alias{calc_DK}
+\title{Calculate discard to kept ratio}
+\usage{
+calc_DK(comdiscData, areaDescription, fleetDescription)
+}
+\arguments{
+\item{na.keep}{Boolean. Logical value to indicate whether original strata names
+should be retained.}
+}
+\value{
+Returns a \code{comdiscData} data.table with one additional column labeled
+ with the value of \code{areaDescription}
+
+\item{areaDescription}{The name of the region (found in \code{areaPolygon})
+ that a record in \code{surveyData} is assigned to}
+}
+\description{
+Use observer data to calculate the ratio of discards to kept by species.
+}
+\seealso{
+Other comdisc: 
+\code{\link{assign_area}()}
+}
+\concept{comdisc}
diff --git a/man/get_comdisc_raw_data.Rd b/man/get_comdisc_raw_data.Rd
new file mode 100644
index 0000000..7c088fa
--- /dev/null
+++ b/man/get_comdisc_raw_data.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_comdisc_raw_data.R
+\name{get_comdisc_raw_data}
+\alias{get_comdisc_raw_data}
+\title{Extracts observer data from Database}
+\usage{
+get_comdisc_raw_data(channel, filterByYear)
+}
+\value{
+Data frame (data.table) (n x 10)
+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{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{UTILCD}{Utilization code}
+\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.}
+}
+\description{
+Connects to obdbs and pulls fields from OBSPP, OBINC, ASMSPP, and ASMINC
+}
+\section{File Creation}{
+
+
+A file containing the data.table above will also be saved to the users machine in the directory provided
+}
+
diff --git a/man/get_comland_data.Rd b/man/get_comland_data.Rd
index ceed4f2..bec04e6 100644
--- a/man/get_comland_data.Rd
+++ b/man/get_comland_data.Rd
@@ -4,16 +4,34 @@
 \alias{get_comland_data}
 \title{Extracts commercial data from Database}
 \usage{
-get_comland_data(channel, landed, endyear, out.dir)
+get_comland_data(
+  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",
+  aggGear = F,
+  userGears = comlandr::mykeyGears,
+  fleetDescription = "Fleet"
+)
 }
 \arguments{
 \item{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}})}
 
-\item{landed}{Character String. Use landed weight ("y" - meatwt) for scallops and clams instead of live weight ("n" - livewt).}
-
 \item{endyear}{Numeric Scalar. Final year of query.}
 
+\item{landed}{Character String. Use landed weight ("y" - meatwt) for scallops and clams instead of live weight ("n" - livewt).}
+
 \item{out.dir}{path to directory where final output will be saved}
 }
 \value{
diff --git a/man/get_comland_raw_data.Rd b/man/get_comland_raw_data.Rd
new file mode 100644
index 0000000..a75ceda
--- /dev/null
+++ b/man/get_comland_raw_data.Rd
@@ -0,0 +1,48 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_comland_raw_data.R
+\name{get_comland_raw_data}
+\alias{get_comland_raw_data}
+\title{Extracts commercial data from Database}
+\usage{
+get_comland_raw_data(
+  channel,
+  filterByYear = NA,
+  filterByArea = NA,
+  useLanded = T,
+  removeParts = T
+)
+}
+\arguments{
+\item{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}})}
+
+\item{endyear}{Numeric Scalar. Final year of query.}
+
+\item{landed}{Character String. Use landed weight ("y" - meatwt) for scallops and clams instead of live weight ("n" - livewt).}
+
+\item{out.dir}{path to directory where final output will be saved}
+}
+\value{
+Data frame (data.table) (n x 10)
+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{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{UTILCD}{Utilization code}
+\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.}
+}
+\description{
+Connects to cfdbs and pulls fields from WOLANDS, WODETS, CFDETS
+}
+\section{File Creation}{
+
+
+A file containing the data.table above will also be saved to the users machine in the directory provided
+}
+