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Summary

This script calculates mean annual net primary production values globally from 2003 to 2015. This data is used to standardize commercial fishing catch to produce fishing pressure layers for OHI and Cumulative Human Impacts.

Data Source

Reference: Behrenfeld, M.J. and Falkowski, P.G., 1997. Photosynthetic rates derived from satellite‐based chlorophyll concentration. Limnology and oceanography, 42(1), pp.1-20.

Downloaded: July 30, 2016

Description: Monthly Net Primary Production (mg C / m2 / day)

Native data resolution: 0.083 x 0.083 degree grid

Time range: 2002 - 2015, monthly. Only partial data provided for 2002. OHI uses 2003 - 2015.

Format: XYZ format

Setup

library(fields)
library(raster)
library(doParallel)
library(foreach)
library(parallel)
library(RColorBrewer)

source("~/github/ohiprep/src/R/common.R")
source('vgpm_func.R')

cols = rev(colorRampPalette(brewer.pal(11, 'Spectral'))(255)) # rainbow color scheme

#paths

dir_git <- file.path(dir_M,'git-annex/globalprep/prs_fish/v2016/VGPM_primary_productivity')
#unzip all files
tars <- list.files(file.path(dir_M,'git-annex/globalprep/_raw_data/VGPM_primary_productivity/d2016'),full.names=T, pattern = '.tar')

lapply(tars,untar, exdir = file.path(dir_M,'git-annex/globalprep/_raw_data/VGPM_primary_productivity/d2016'))

.xyz to .tiff

This code sources a function, vgpm.raster that transforms the raw .xyz files into GeoTIFFs.

files = list.files(file.path(dir_M,'git-annex/globalprep/_raw_data/VGPM_primary_productivity/d2016'), full.names=TRUE, pattern = '.gz')

registerDoParallel(12)

foreach (file = files) %dopar%{
  
  print(file)
  vgpm.raster(file, w.lon, e.lon, n.lat, s.lat, log = TRUE, 
              color = tim.colors(30))
}

Calculate mean annual NPP

Calculate the mean annual Net Primary Production per year and save as rasters.

#global ocean raster at 1km

ocean = raster(file.path(dir_M,'model/GL-NCEAS-Halpern2008/tmp/ocean.tif'))


# set mollweide projection
moll_crs = CRS("+proj=moll +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +units=m +no_defs")

registerDoParallel(7)

foreach (i = 2004:2015) %dopar%{
  
  print(i)
  
  l    = list.files(file.path(dir_git,'int/rasterized_rawdata'),pattern=as.character(i),full.names=T)%>%
          stack()%>%
          calc(fun=function(x){mean(x,na.rm=T)})%>%
            projectRaster(.,crs=moll_crs, over = T,filename = paste0(file.path(dir_git,'int/annual_npp/annual_mean_npp_'),i,'.tif',sep=''),overwrite=T)
  
  
  out  = raster::resample(l,ocean,method='ngb',
                 filename=paste0(file.path(dir_git,'int/annual_npp/annual_mean_npp_moll_1km_'),i,'.tif',sep=''),overwrite=T)
  
}

Output

raster(file.path(dir_M,'git-annex/globalprep/prs_fish/v2016/VGPM_primary_productivity/int/annual_npp/annual_mean_npp_moll_1km_2015.tif'))%>%plot(col=cols,box=F,axes=F,main = 'Mean Net Primary Productivity (mg C/m2/day)')

Citation information

Behrenfeld, M.J. and Falkowski, P.G., 1997. Photosynthetic rates derived from satellite‐based chlorophyll concentration. Limnology and oceanography, 42(1), pp.1-20.

Downloaded from http://www.science.oregonstate.edu/ocean.productivity/standard.product.php