fishboxes

R tools for working with NMFS-NEFSC One Degree, Quarter Degree and Ten Minute Squares (ODS, QDS, and TMS). Functions for downloading publically available shape files are alos provided.

NMFS-NEFSC assigns fish reports to a grid system as shown below.

Requirements

• R (>= 3.0)
• sp package

Installation

It's easy to install using Hadley Wickham's devtools.

library(devtools)
install_github('btupper/fishboxes')

Usage - One Degree Squares (ODS), Quarter Degrees Squares (QDS) and Ten Minute Squares (TMS)

Here is a simple example that generates two Quarter Degree Squares within the 42N, 69W One Degree Box. These are the lower left and upper right QDS.

library(sp)
library(raster)
library(fishboxes)

P <- decode_polygons(x = c(42692, 42693))
P
# class       : SpatialPolygonsDataFrame 
# features    : 2 
# extent      : -70, -69, 42, 43  (xmin, xmax, ymin, ymax)
# coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 
# variables   : 1
# names       :    ID 
# min values  : 42692 
# max values  : 42693  

These polygons can be saved as ESRI shapefiles using the rgdal package.

NMFS_QDS <- decode_polygons(x = out)
library(rgdal)
rgdal::writeOGR(NMFS_QDS, "NMFS_QDS", layer="NMFS_QDS", driver="ESRI Shapefile")

The show_fishboxes() function shows how to produce a completed set of nested squares.

show_fishboxes(x = 4269)

... that produces polygons as shown below.

The SpatialPolygon* objects produced by the can be used for extracting pixel values from a Raster* object. First we draw some squares - this time using ssp:spplot.

library(raster)
library(latticeExtra)

# read in an example raster that comes with the package
# The data is from [Ocean Color Web](http://oceancolor.gsfc.nasa.gov/cms/) 
# MODISA L3SMI daily monthly data selected at random.
   
filename <- system.file("NE-chlorophyl.grd", package = 'fishboxes')
r <- log10(raster::brick(filename))

# get a set of polygons (there are 6 - two pairs of three nested boxes)
P <- decode_polygons(x=c(426916, 42692, 4269, 387066, 38701, 3870))

# show them
sp::spplot(r) +
   sp::spplot(P, colorkey = FALSE, border = 'black', col.regions = NA)

Now we can make a One Degree Square and its 4 Quarter Degree Squares. We'll find the sum of the raster pixels within each and compare them. If all goes well, the sum of the 4 quarters will exactly equal the sum across the entore One Degree Square.

# make a One Degree Square
P <- decode_polygons(x = 4269)

# and it's 4 Quarter Degree Squares
P4 <- lapply(paste0('4269', 1:4), decode_polygons)

# get the raster mean from each
S <- raster::extract(r, P, fun = sum, na.rm = TRUE)
S4 <- sapply(P4, function(x) raster::extract(r, x, fun = sum, na.rm = TRUE))

# these is no difference! (S is a matrix, we need the first element at [1,1])
identical(S[1,1], sum(S4))
# [1] TRUE

Usage - downloading public data sets

NMFS-NEFSC serves various data sets as ESRI Shape Files. This package provides one function for downloading these for subsequent reading into R using the rgdal package.

ok <- download_nefsc_gis("EcoMon_Strata", dest = "/Users/ben/Downloads/EcoMon_Strata")
# ok
#    EcoMon_Strata.dbf     EcoMon_Strata.prj     EcoMon_Strata.sbn     EcoMon_Strata.sbx     EcoMon_Strata.shp EcoMon_Strata.shp.xml 
#                 TRUE                  TRUE                  TRUE                  TRUE                  TRUE                  TRUE 
#    EcoMon_Strata.shx 
#                 TRUE 
library(rgdal)
P <- readOGR("/Users/ben/Downloads/EcoMon_Strata", "EcoMon_Strata")
plot(P)
z <- getSpatialPolygonsLabelPoints(P)
text(z, 1:47)