add R file for working w/ datacube

this might be outdated but a good place to start

docs/working_with_datacube.R

@@ -0,0 +1,34 @@
+# set a path to the datacube
+mypath = paste0('/mnt/ExtraDrive1/Work/desktop_data/2022_papers/',
+	'HSsurv2023/data/')
+# load the datacube
+load(paste0(mypath, 'akpv_datacube.rda'))
+
+# check out the structure of the datacube
+class(akpv_datacube) # it is a list
+str(akpv_datacube[[1]]) # the first element is a 194 x 27 matrix
+length(akpv_datacube)  # there are 1000 list items, each element of which is 
+#  a 194 x 27 matrix
+attributes(akpv_datacube[[1]]) # notice the attributes of each matrix
+rownames(akpv_datacube[[1]]) # the polyid's are the row names
+colnames(akpv_datacube[[1]]) # the years are the column names
+attr(akpv_datacube[[1]], 'stockid') # there is an extra attribute for 
+#  stockid, which is equal to length as rownames, and in the same order
+
+# the datacube is composed of 1000 matrices, where each matrix is an MCMC sample
+# if we want to see the MCMC samples for the first year for the first site
+unlist(lapply(akpv_datacube,function(x){x[1,1]}))
+
+# we can also use names rather than numbers.  Here is polyid "OA00" for 1997
+unlist(lapply(akpv_datacube,function(x){x["OA00","1997"]}))
+
+# find all polyids for a given stock in any matrix using stockid attribute
+attr(akpv_datacube[[1]], 'stockid') == 6
+# make a subset of those for the first MCMC sample in year 1996
+akpv_datacube[[1]][attr(akpv_datacube[[1]], 'stockid') == 6, "1996"]
+# sum those to get the first MCMC sample for total abundance of stock 6 in 1996
+sum(akpv_datacube[[1]][attr(akpv_datacube[[1]], 'stockid') == 6, "1996"])
+# get the sum for the 2nd MCMC sample 
+i = 2 # MCMC sample
+sum(akpv_datacube[[i]][attr(akpv_datacube[[i]], 'stockid') == 6, "1996"])
+