set_select: set_select

In Maritimes/Mar.utils: A suite of functions used by a variety of Maritimes packages

set_select

Description

This function randomly selects stations within particular strata. A specified number of stations of 3 different categories can be selected, and the minimum distance required between the stations can be specified. Additional details about each set can be added (such as which NAFO zones or marine protected area a set falls in) can be added through provision of sf files to the parameters addExtData1_sf and/or addExtData2_sf. Additionally, certain areas can be set to exclude stations the inclusion of an additional sf object.

Usage

set_select(
  stationData = NULL,
  stationDataField = NULL,
  strata_sf = NULL,
  strataField = NULL,
  addExtData1_sf = NULL,
  addExtDataFields1 = NULL,
  addExtData2_sf = NULL,
  addExtDataFields2 = NULL,
  avoid_sf = NULL,
  outName = NULL,
  writexls = TRUE,
  writegpkg = TRUE,
  localCRS = 2961,
  minDistNM = 4,
  tryXTimes = 100
)

Arguments

stationData	default is NULL. This is either 1) the path to a csv file or 2) an existing r dataframe containing the all of the strata for which stations should be generated . In addition to the strata, this file must also include the fields "PRIMARY", "SECONDARY", and "ALTERNATE". These three fields should contain integers corresponding with how many of that type of station should be generated. If no stations of a particular type should be generated, a value of NA should be present. Strata where PRIMARY is set to NA will not have any stations generated. Below is an example of how this file might look: > head(stationFile) STRATUM PRIMARY ALTERNATE SECONDARY 5Z1 6 3 4 5Z2 11 6 NA 5Z3 5 2 2 5Z4 4 2 2
stationDataField	default is "STRATUM". This is just the name of the field that contains the strata. For the example above, this would be "STRATUM".
strata_sf	default is NULL. This should point to an sf object the strata to use. This object must have a field that has values identical to those found in the "stationDataField" within the "stationData" file.
strataField	default is NULL. This is the name of the field within strata_sf that contains the identifier for the strata. Continuing with the example above, this field would contain values including "5Z1", "5Z2", "5Z3" and "5Z4".
addExtData1_sf	default is NULL. If additional information should be added to the output for each set, an sf object can be provided here. For example, one might provide a file of NAFO zones or special fishing areas.
addExtDataFields1	default is NULL. If a value is provided to addExtData1_sf, this should correspond with one or more fields within that file. If a set falls within a particular polygon, the value for that polygon from these fields will be provided as part of the output.
addExtData2_sf	default is NULL. This is identical to addExtData1_sf, but allows for including information from an additional sf object.
addExtDataFields2	default is NULL. If a value is provided to addExtData2_sf, this should correspond with one or more fields within that file. If a set falls within a particular polygon, the value for that polygon from these fields will be provided as part of the output.
avoid_sf	default is NULL. This is and sf object containing polygons of the areas where stations should not be located. For example, one might populate a file with areas known to contain unexploded ordinance, or areas where bottom contact is forbidden. No stations will be generated where polygons exist in this file.
outName	This is the name of the output file excel that will be generated and/or the name of a layer withing a gpkg file.
writexls	default is TRUE. Write the results to an excel file in your working directory?
writegpkg	default is TRUE. Write the results to a spatial gpkg file in your working directory? (for use in a)
localCRS	default is 2961. In order to create sampling stations, the function reprojects any spatial data to a locally appropriate projection. The default value is UTM Zone 20N, and is appropriate only for Maritimes data. Any valid CRS can be entered here, and should be appropriate for your data.
minDistNM	default is 4. This is the minimum required distance between the sets. By default, sets will be no closer than 4 nautical miles from each other.
tryXTimes	default is 100 By default, the script will make this many attempts to fit the requested number of stations into each strata.

Author(s)

Mike McMahon, [e-mail]

Examples

## Not run: 
Spring_4X_2025 <- set_select(stationData = "c:/2025/Spring_4X_RM.csv",
                            outName =  "Spring_4X_2025",
                            stationDataField = "STRATUM",
                            strata_sf = Mar.data::Strata_Mar_sf, strataField = "StrataID", 
                            addExtData1_sf = Mar.data::NAFOSubunits_sf, addExtDataFields1 = "NAFO",
                            addExtData2_sf = oceans_areas_sf, 
                            addExtDataFields2 = c("NAME_E","ZONE_E"), 
                            avoid_sf = this_avoid_sf)


Georges_5Z_2025 <- set_select(stationData = "c:/2025/Georges_5Z_RM.csv.csv",
                             outName =  "Georges_5Z_2025",
                             stationDataField = "STRATUM",
                             strata_sf = Mar.data::Strata_Mar_sf, strataField = "StrataID", 
                             addExtData1_sf = Mar.data::NAFOSubunits_sf, addExtDataFields1 = "NAFO",
                             addExtData2_sf = oceans_areas_sf, 
                             addExtDataFields2 = c("NAME_E","ZONE_E"), 
                             avoid_sf = this_avoid_sf)
                       
## End(Not run)

Maritimes/Mar.utils documentation built on April 5, 2025, 1:47 p.m.