Assign MBSS strata (BIBI [bugs] and FIBI [fish]) using the MBSS GIS shapefiles.
strata(data, col_lat = "lat", col_lon = "long")Data frame
Column name for latitude. Default = "lat"
Column name for longitude. Default = "lon"
Returns the input data frame with one column for each strata (bibi , fibi, and msw).
The results of this function are **provisional** and not official. Strata should be checked using GIS software (e.g., ArcGIS). GPS coordinates with low accuracy can affect the assignment of the correct strata.
Input is a data frame with columns for latitude and longitude. Coordinates should be decimal degrees. This function is intended for use in Maryland (USA) so longitudes will be converted to negative values.
Default point projection is: "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"
Locations outside of the strata GIS shapefiles will be coded as 'NA'.
The GIS shapefiles are available at:
https://github.com/leppott/MBSStools_SupportFiles
* BIBI, mbss_strata.shp
* FIBI, mbss_strata_coldstreams.shp converted to mbss_strata_fibi.ship
* BIBI, MSW, mbss_strata_msw.shp (from mbss_strata.shp)
The FIBI shapefile was a line layer that has been converted to a polygon layer using the catchment shapefile from NHDplus version 2 and clipped to the boundaries of the BIBI shapefile.
# random points
myN <- 250
latitude <- runif(myN, min = 37+53/60, max = 39+43/60)
longitude <- runif(myN, min = -(79+29/60), max = -(75+3/60))
data <- as.data.frame(cbind(longitude, latitude))
col_lat <- "latitude"
col_lon <- "longitude"
# Run Function
data_strata <- strata(data, col_lat, col_lon)
# View Results
head(data_strata)
#> longitude latitude strata_bibi strata_fibi strata_msw
#> 1 -79.37748 39.38003 Highland Cold NCP
#> 2 -76.09964 38.10507 Coastal Coastal CP
#> 3 -79.24849 38.76337 <NA> <NA> <NA>
#> 4 -76.65264 38.62310 Coastal Coastal CP
#> 5 -78.72006 38.33784 <NA> <NA> <NA>
#> 6 -78.91057 38.00940 <NA> <NA> <NA>
table(data_strata$strata_bibi, data_strata$strata_fibi, useNA = "ifany")
#>
#> Coastal Cold EPiedmont Highland <NA>
#> Coastal 62 0 0 0 0
#> EPiedmont 0 0 14 0 0
#> Highland 0 7 0 14 0
#> <NA> 0 0 0 0 153
# Plot
if (FALSE) {
library(rgdal)
## subset sites
sites_CP <- data_strata[data_strata[, "strata_fibi"] == "Coastal", ]
sites_EP <- data_strata[data_strata[, "strata_fibi"] == "EPiedmont", ]
sites_Hi <- data_strata[data_strata[, "strata_fibi"] == "Highland", ]
sites_Cold <- data_strata[data_strata[, "strata_fibi"] == "Cold", ]
## Plot
plot(shp_strata_fish
, col = "white"
, border = "darkslategray"
, lwd = 0.5)
pts_col <- "black"
pts_cex <- 1.0
pts_pch <- 21
pts_bg <- c("gray", "green", "purple", "orange", "blue")
graphics::points(data[, col_lon]
, data[, col_lat]
, pch = pts_pch
, col = pts_col
, bg = pts_bg[1]
, cex = pts_cex)
graphics::points(sites_CP[, col_lon]
, sites_CP[, col_lat]
, pch = pts_pch
, col = pts_col
, bg = pts_bg[2]
, cex = pts_cex)
graphics::points(sites_EP[, col_lon]
, sites_EP[, col_lat]
, pch = pts_pch
, col = pts_col
, bg = pts_bg[3]
, cex = pts_cex)
graphics::points(sites_Hi[, col_lon]
, sites_Hi[, col_lat]
, pch = pts_pch
, col = pts_col
, bg = pts_bg[4]
, cex = pts_cex)
graphics::points(sites_Cold[, col_lon]
, sites_Cold[, col_lat]
, pch = pts_pch
, col = pts_col
, bg = pts_bg[5]
, cex = pts_cex)
legend("bottomleft"
, legend = c("NA", "Coastal", "EPiedmont", "Highland", "Coldwater")
, col = pts_col
, pch = pts_pch
, pt.bg = pts_bg
, cex = pts_cex
, title = "Strata"
, box.lty = 0
, bg = "white")
title(main = "Assignment of MBSS strata"
, sub = paste0(myN, " random points using MBSStools::strata()"))
}