incorporating changes and suggestions from this summer into a package…

… state so we can look at how all of the changes work together

DESCRIPTION

@@ -29,7 +29,7 @@ LazyDataCompression: xz
 Imports: 
     stats, 
     utils
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests: 
     knitr,
     rmarkdown

R/public_data.R

@@ -1,34 +1,9 @@
 #' @title Presence-only public data from FOSS
-#' @description 
+#' @description Positive catch and effort from GAP_PRODUCTS.CPUE with associated taxonomic confidence. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 12 September 2024.
 #' @usage data('public_data')
 #' @author Emily Markowitz (Emily.Markowitz AT noaa.gov)
-#' @format A data frame with 939197 observations on the following 37 variables.
+#' @format A data frame with 890349 observations on the following 37 variables.
 #' \describe{
-#'   \item{\code{area_swept_km2}}{Area swept (km). The area the net covered while the net was fishing (kilometers squared), defined as the distance fished times the net width.}
-#'   \item{\code{bottom_temperature_c}}{Bottom temperature (degrees Celsius). Bottom temperature (tenths of a degree Celsius); NA indicates removed or missing values.}
-#'   \item{\code{common_name}}{Taxon common name. The common name of the marine organism associated with the 'scientific_name' and 'species_code' columns. For a complete species list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
-#'   \item{\code{count}}{Taxon count. Total whole number of individuals caught in haul or samples collected.}
-#'   \item{\code{cpue_kgkm2}}{Weight CPUE (kg/km2). Catch weight (kilograms) per unit effort (area swept by the net, units square kilometers).}
-#'   \item{\code{cpue_nokm2}}{Number CPUE (no/km2). Numerical catch per unit effort (area swept by the net, units square kilometers).}
-#'   \item{\code{cruise}}{Cruise Name. This is a six-digit integer identifying the cruise number of the form: YYYY99 (where YYYY = year of the cruise; 99 = 2-digit number and is sequential; 01 denotes the first cruise that vessel made in this year, 02 is the second, etc.).}
-#'   \item{\code{cruisejoin}}{Cruise ID. Unique integer ID assigned to each survey, vessel, and year combination.}
-#'   \item{\code{net_height_m}}{Net height (m). Measured or estimated distance (meters) between footrope and headrope of the trawl.}
-#'   \item{\code{net_width_m}}{Net width (m). Measured or estimated distance (meters) between wingtips of the trawl.}
-#'   \item{\code{performance}}{Haul performance code. This denotes what, if any, issues arose during the haul. For more information, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
-#'   \item{\code{scientific_name}}{Taxon scientific name. The scientific name of the organism associated with the 'common_name' and 'species_code' columns. For a complete taxon list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
-#'   \item{\code{species_code}}{Taxon code. The species code of the organism associated with the 'common_name' and 'scientific_name' columns. For a complete species list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
-#'   \item{\code{srvy}}{Survey abbreviation. Abbreviated survey names. The column 'srvy' is associated with the 'survey' and 'survey_definition_id' columns. Northern Bering Sea (NBS), Southeastern Bering Sea (EBS), Bering Sea Slope (BSS), Gulf of Alaska (GOA), Aleutian Islands (AI).}
-#'   \item{\code{station}}{Station ID. Alpha-numeric designation for the station established in the design of a survey.}
-#'   \item{\code{stratum}}{Stratum ID. RACE database statistical area for analyzing data. Strata were designed using bathymetry and other geographic and habitat-related elements. The strata are unique to each survey region. Stratum of value 0 indicates experimental tows.}
-#'   \item{\code{surface_temperature_c}}{Surface temperature (degrees Celsius). Surface temperature (tenths of a degree Celsius); NA indicates removed or missing values.}
-#'   \item{\code{survey}}{Survey name. Name and description of survey. The column 'survey' is associated with the 'srvy' and 'survey_definition_id' columns.}
-#'   \item{\code{survey_definition_id}}{Survey ID. The survey definition ID key code uniquely identifies a survey/survey design. Integer code that uniquely identifies survey. Full list of survey definition IDs are in RACE_DATA.SURVEY_DEFINITIONS. IDs used in GAP_PRODUCTS are: 47 (Gulf of Alaska); 52 (Aleutian Islands); 78 (Bering Sea Slope); 98 (Eastern Bering Sea Shelf); 143 (Northern Bering Sea Shelf). The column 'survey_definition_id' is associated with the 'srvy' and 'survey' columns. For a complete list of surveys, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
-#'   \item{\code{taxon_confidence}}{Taxon confidence rating. Confidence in the ability of the survey team to correctly identify the taxon to the specified level, based solely on identification skill (e.g., not likelihood of a taxon being caught at that station on a location-by-location basis). Quality codes follow: **'High'**: High confidence and consistency. Taxonomy is stable and reliable at this level, and field identification characteristics are well known and reliable. **'Moderate'**: Moderate confidence. Taxonomy may be questionable at this level, or field identification characteristics may be variable and difficult to assess consistently. **'Low'**: Low confidence. Taxonomy is incompletely known, or reliable field identification characteristics are unknown. Documentation: [Species identification confidence in the eastern Bering Sea shelf survey (1982-2008)](http://apps-afsc.fisheries.noaa.gov/Publications/ProcRpt/PR2009-04.pdf), [Species identification confidence in the eastern Bering Sea slope survey (1976-2010)](http://apps-afsc.fisheries.noaa.gov/Publications/ProcRpt/PR2014-05.pdf), and [Species identification confidence in the Gulf of Alaska and Aleutian Islands surveys (1980-2011)](http://apps-afsc.fisheries.noaa.gov/Publications/ProcRpt/PR2014-01.pdf).}
-#'   \item{\code{vessel_id}}{Vessel ID. ID number of the vessel used to collect data for that haul. The column 'vessel_id' is associated with the 'vessel_name' column. Note that it is possible for a vessel to have a new name but the same vessel id number. For a complete list of vessel ID key codes, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
-#'   \item{\code{vessel_name}}{Vessel name. Name of the vessel used to collect data for that haul. The column 'vessel_name' is associated with the 'vessel_id' column. Note that it is possible for a vessel to have a new name but the same vessel id number. For a complete list of vessel ID key codes, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
-#'   \item{\code{weight_kg}}{Sample or taxon weight (kg). Weight (thousandths of a kilogram) of individuals in a haul by taxon.}
-#'   \item{\code{worms}}{World register of marine species (WoRMS) taxonomic serial number. Species code as identified in the World Register of Marine Species (WoRMS) (https://www.marinespecies.org/).}
-#'   \item{\code{year}}{Survey year. Year the observation (survey) was collected.}
 #'   \item{\code{date_time}}{Date and time. The date (MM/DD/YYYY) and time (HH:MM) of the haul. All dates and times are in Alaska time (AKDT) of Anchorage, AK, USA (UTC/GMT -8 hours).}
 #'   \item{\code{depth_m}}{Depth (m). Bottom depth (meters).}
 #'   \item{\code{distance_fished_km}}{Distance fished (km). Distance the net fished (thousands of kilometers).}
@@ -40,7 +15,32 @@
 #'   \item{\code{latitude_dd_end}}{End latitude (decimal degrees). Latitude (one hundred thousandth of a decimal degree) of the end of the haul.}
 #'   \item{\code{latitude_dd_start}}{Start latitude (decimal degrees). Latitude (one hundred thousandth of a decimal degree) of the start of the haul.}
 #'   \item{\code{longitude_dd_end}}{End longitude (decimal degrees). Longitude (one hundred thousandth of a decimal degree) of the end of the haul.}
-#'   \item{\code{longitude_dd_start}}{Start longitude (decimal degrees). Longitude (one hundred thousandth of a decimal degree) of the start of the haul.}#'   }
+#'   \item{\code{longitude_dd_start}}{Start longitude (decimal degrees). Longitude (one hundred thousandth of a decimal degree) of the start of the haul.}
+#'   \item{\code{net_height_m}}{Net height (m). Measured or estimated distance (meters) between footrope and headrope of the trawl.}
+#'   \item{\code{net_width_m}}{Net width (m). Measured or estimated distance (meters) between wingtips of the trawl.}
+#'   \item{\code{performance}}{Haul performance code. This denotes what, if any, issues arose during the haul. For more information, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
+#'   \item{\code{scientific_name}}{Taxon scientific name. The scientific name of the organism associated with the common_name and species_code columns. For a complete taxon list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
+#'   \item{\code{species_code}}{Taxon code. The species code of the organism associated with the common_name and scientific_name columns. For a complete species list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
+#'   \item{\code{srvy}}{Survey abbreviation. Abbreviated survey names. The column srvy is associated with the survey and survey_definition_id columns. Northern Bering Sea (NBS), Southeastern Bering Sea (EBS), Bering Sea Slope (BSS), Gulf of Alaska (GOA), Aleutian Islands (AI).}
+#'   \item{\code{station}}{Station ID. Alpha-numeric designation for the station established in the design of a survey.}
+#'   \item{\code{stratum}}{Stratum ID. RACE database statistical area for analyzing data. Strata were designed using bathymetry and other geographic and habitat-related elements. The strata are unique to each survey region. Stratum of value 0 indicates experimental tows.}
+#'   \item{\code{surface_temperature_c}}{Surface temperature (degrees Celsius). Surface temperature (tenths of a degree Celsius); NA indicates removed or missing values.}
+#'   \item{\code{survey}}{Survey name. Name and description of survey. The column survey is associated with the srvy and survey_definition_id columns.}
+#'   \item{\code{survey_definition_id}}{Survey ID. The survey definition ID key code is an integer that uniquely identifies a survey region/survey design. The column survey_definition_id is associated with the srvy and survey columns. Full list of survey definition IDs are in RACE_DATA.SURVEY_DEFINITIONS and in the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
+#'   \item{\code{taxon_confidence}}{Taxon confidence rating. Confidence in the ability of the survey team to correctly identify the taxon to the specified level, based solely on identification skill (e.g., not likelihood of a taxon being caught at that station on a location-by-location basis). Quality codes follow: **High**: High confidence and consistency. Taxonomy is stable and reliable at this level, and field identification characteristics are well known and reliable. **Moderate**: Moderate confidence. Taxonomy may be questionable at this level, or field identification characteristics may be variable and difficult to assess consistently. **Low**: Low confidence. Taxonomy is incompletely known, or reliable field identification characteristics are unknown. Documentation: [Species identification confidence in the eastern Bering Sea shelf survey (1982-2008)](http://apps-afsc.fisheries.noaa.gov/Publications/ProcRpt/PR2009-04.pdf), [Species identification confidence in the eastern Bering Sea slope survey (1976-2010)](http://apps-afsc.fisheries.noaa.gov/Publications/ProcRpt/PR2014-05.pdf), and [Species identification confidence in the Gulf of Alaska and Aleutian Islands surveys (1980-2011)](http://apps-afsc.fisheries.noaa.gov/Publications/ProcRpt/PR2014-01.pdf).}
+#'   \item{\code{vessel_id}}{Vessel ID. ID number of the vessel used to collect data for that haul. The column vessel_id is associated with the vessel_name column. Note that it is possible for a vessel to have a new name but the same vessel id number. For a complete list of vessel ID key codes, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
+#'   \item{\code{vessel_name}}{Vessel name. Name of the vessel used to collect data for that haul. The column vessel_name is associated with the vessel_id column. Note that it is possible for a vessel to have a new name but the same vessel id number. For a complete list of vessel ID key codes, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
+#'   \item{\code{weight_kg}}{Sample or taxon weight (kg). Weight (thousandths of a kilogram) of individuals in a haul by taxon.}
+#'   \item{\code{worms}}{World register of marine species (WoRMS) taxonomic serial number. Species code as identified in the World Register of Marine Species (WoRMS) (https://www.marinespecies.org/).}
+#'   \item{\code{year}}{Survey year. Year the observation (survey) was collected.}
+#'   \item{\code{area_swept_km2}}{Area swept (km). The area the net covered while the net was fishing (kilometers squared), defined as the distance fished times the net width.}
+#'   \item{\code{bottom_temperature_c}}{Bottom temperature (degrees Celsius). Bottom temperature (tenths of a degree Celsius); NA indicates removed or missing values.}
+#'   \item{\code{common_name}}{Taxon common name. The common name of the marine organism associated with the scientific_name and species_code columns. For a complete species list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
+#'   \item{\code{count}}{Taxon count. Total whole number of individuals caught in haul or samples collected.}
+#'   \item{\code{cpue_kgkm2}}{Weight CPUE (kg/km2). Catch weight (kilograms) per unit effort (area swept by the net, units square kilometers).}
+#'   \item{\code{cpue_nokm2}}{Number CPUE (no/km2). Numerical catch per unit effort (area swept by the net, units square kilometers).}
+#'   \item{\code{cruise}}{Cruise Name. This is a six-digit integer identifying the cruise number of the form: YYYY99 (where YYYY = year of the cruise; 99 = 2-digit number and is sequential; 01 denotes the first cruise that vessel made in this year, 02 is the second, etc.).}
+#'   \item{\code{cruisejoin}}{Cruise ID. Unique integer ID assigned to each survey, vessel, and year combination.}#'   }
 #' @source https://github.com/afsc-gap-products/gap_products and https://www.fisheries.noaa.gov/foss/f?p=215:28:14951401791129:::::
 #' @keywords species code data
 #' @examples

R/species_data.R

@@ -1,12 +1,12 @@
 #' @title Subsetted species data
-#' @description species classification table
+#' @description Taxonomic classification information for the current list of SPECIES_CODE values. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 12 September 2024.
 #' @usage data('species_data')
 #' @author Sarah Friedman (sarah.friedman AT noaa.gov)
-#' @format A data frame with 2699 observations on the following 3 variables.
+#' @format A data frame with 2718 observations on the following 3 variables.
 #' \describe{
-#'   \item{\code{common_name}}{Taxon common name. The common name of the marine organism associated with the 'scientific_name' and 'species_code' columns. For a complete species list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
-#'   \item{\code{scientific_name}}{Taxon scientific name. The scientific name of the organism associated with the 'common_name' and 'species_code' columns. For a complete taxon list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
-#'   \item{\code{species_code}}{Taxon code. The species code of the organism associated with the 'common_name' and 'scientific_name' columns. For a complete species list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}#' }
+#'   \item{\code{scientific_name}}{Taxon scientific name. The scientific name of the organism associated with the common_name and species_code columns. For a complete taxon list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
+#'   \item{\code{species_code}}{Taxon code. The species code of the organism associated with the common_name and scientific_name columns. For a complete species list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}
+#'   \item{\code{common_name}}{Taxon common name. The common name of the marine organism associated with the scientific_name and species_code columns. For a complete species list, review the [code books](https://www.fisheries.noaa.gov/resource/document/groundfish-survey-species-code-manual-and-data-codes-manual).}#' }
 #' @source https://github.com/afsc-gap-products/gap_products
 #' @keywords species code data
 #' @examples

R/station_coords.R

@@ -4,10 +4,10 @@
 #' @author Sean Rohan (sean.rohan AT noaa.gov)
 #' @format A data frame with 31594 observations on the following 4 variables.
 #' \describe{
-#'   \item{\code{srvy}}{Survey abbreviation. Abbreviated survey names. The column 'srvy' is associated with the 'survey' and 'survey_definition_id' columns. Northern Bering Sea (NBS), Southeastern Bering Sea (EBS), Bering Sea Slope (BSS), Gulf of Alaska (GOA), Aleutian Islands (AI).}
-#'   \item{\code{station}}{Station ID. Alpha-numeric designation for the station established in the design of a survey.}
 #'   \item{\code{latitude_dd}}{Latitude (decimal degrees). Latitude (one hundred thousandth of a decimal degree).}
-#'   \item{\code{longitude_dd}}{Longitude (decimal degrees). Longitude (one hundred thousandth of a decimal degree).}#'   }
+#'   \item{\code{longitude_dd}}{Longitude (decimal degrees). Longitude (one hundred thousandth of a decimal degree).}
+#'   \item{\code{srvy}}{Survey abbreviation. Abbreviated survey names. The column srvy is associated with the survey and survey_definition_id columns. Northern Bering Sea (NBS), Southeastern Bering Sea (EBS), Bering Sea Slope (BSS), Gulf of Alaska (GOA), Aleutian Islands (AI).}
+#'   \item{\code{station}}{Station ID. Alpha-numeric designation for the station established in the design of a survey.}#'   }
 #' @source https://github.com/afsc-gap-products/akgfmaps
 #' @keywords station survey data
 #' @examples