strata: Assign MBSS strata

In leppott/MBSStools: MBSS tool suite for calculations and data manipulation

Assign MBSS strata

Description

Assign MBSS strata (BIBI [bugs] and FIBI [fish]) using the MBSS GIS shapefiles.

Usage

strata(data, col_lat = "lat", col_lon = "long")

Arguments

data	Data frame
col_lat	Column name for latitude. Default = "lat"
col_lon	Column name for longitude. Default = "lon"

Details

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.

Value

Returns the input data frame with one column for each strata (bibi , fibi, and msw).

Examples

# 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)
table(data_strata$strata_bibi, data_strata$strata_fibi, useNA = "ifany")

# Plot
## Not run: 
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()"))

## End(Not run)

leppott/MBSStools documentation built on April 8, 2024, 9:57 p.m.