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mdsumnermdsumner
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add BeFa PP
1 parent 481ee64 commit f5e24c4

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‎DESCRIPTION

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@@ -11,14 +11,15 @@ Description: Work with data from NASA's ocean colour data, primarily the 'Level-
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License: GPL-3
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LazyLoad: yes
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Depends: dplyr
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Imports:
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Imports:
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geosphere,
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progress,
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sp,
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raster,
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rlang,
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rhdf5,
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tibble
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tibble,
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Rcpp
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Suggests:
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testthat,
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BiocInstaller,
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RoxygenNote: 6.0.1
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URL: https://github.com/sosoc/croc
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BugReports: https://github.com/sosoc/croc/issues
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LinkingTo:
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Rcpp

‎NAMESPACE

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export(initbin)
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export(lonlat2bin)
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export(lonlatFromCell)
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export(prod_BeFa)
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export(read_L3_file)
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export(read_binlist)
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export(read_compound)
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export(read_smi_image)
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importFrom(Rcpp,sourceCpp)
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importFrom(dplyr,"%>%")
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importFrom(dplyr,filter)
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importFrom(geosphere,gcIntermediate)
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importFrom(utils,download.file)
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importFrom(utils,tail)
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importMethodsFrom(raster,extent)
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useDynLib(croc, .registration = TRUE)

‎NEWS.md

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# croc 0.0.9
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* Add Behrenfeld-Falkowski production calculation.
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* updated web links for ocean colour site to https
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* added a c (renamed package) to avoid BioConductor/CRAN clash

‎R/RcppExports.R

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# Generated by using Rcpp::compileAttributes() -> do not edit by hand
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# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
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#' Primary production
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#'
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#' @export
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prod_BeFa <- function(chla, irrad, stemp, daylength) {
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.Call(`_croc_prod_BeFa`, chla, irrad, stemp, daylength)
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}
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‎R/croc-package.R

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#' @keywords internal
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"_PACKAGE"
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#' @useDynLib croc, .registration = TRUE
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#' @importFrom Rcpp sourceCpp
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NULL

‎man/croc-package.Rd

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‎man/prod_BeFa.Rd

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‎man/roc-package.Rd

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‎src/.gitignore

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*.o
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*.so
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*.dll

‎src/RcppExports.cpp

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// Generated by using Rcpp::compileAttributes() -> do not edit by hand
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// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
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#include <Rcpp.h>
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using namespace Rcpp;
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// prod_BeFa
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NumericVector prod_BeFa(NumericVector chla, NumericVector irrad, NumericVector stemp, NumericVector daylength);
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RcppExport SEXP _croc_prod_BeFa(SEXP chlaSEXP, SEXP irradSEXP, SEXP stempSEXP, SEXP daylengthSEXP) {
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BEGIN_RCPP
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Rcpp::RObject rcpp_result_gen;
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Rcpp::RNGScope rcpp_rngScope_gen;
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Rcpp::traits::input_parameter< NumericVector >::type chla(chlaSEXP);
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Rcpp::traits::input_parameter< NumericVector >::type irrad(irradSEXP);
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Rcpp::traits::input_parameter< NumericVector >::type stemp(stempSEXP);
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Rcpp::traits::input_parameter< NumericVector >::type daylength(daylengthSEXP);
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rcpp_result_gen = Rcpp::wrap(prod_BeFa(chla, irrad, stemp, daylength));
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return rcpp_result_gen;
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END_RCPP
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}
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static const R_CallMethodDef CallEntries[] = {
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{"_croc_prod_BeFa", (DL_FUNC) &_croc_prod_BeFa, 4},
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{NULL, NULL, 0}
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};
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RcppExport void R_init_croc(DllInfo *dll) {
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R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
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R_useDynamicSymbols(dll, FALSE);
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}

‎src/productivity.cpp

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#include <Rcpp.h>
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#include <math.h>
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using namespace Rcpp;
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// copied 2018-04-26 http://www.science.oregonstate.edu/ocean.productivity/vgpm.code.php
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double opp_befa( double chl,
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double irr,
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double sst,
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double dayL ) {
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/*
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!C--------------------------------------------------------------------------*\
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!Description: opp_befa - computes daily primary productivity using
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the Behrenfeld-Falkowski (BeFa) algorithm. The BeFa
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algorithm estimates productivity using surface chl
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(mg m-3), surface irradiance (Einsteins m-2 d-1),
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sea surface temperature (C), and day length (hours).
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Pb_opt is modelled as a polynomial function of SST.
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!Input Parameters:
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chl Chlorophyll_a surface concentration in milligrams
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chlorophyl per cubic meter
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irr Photosynthetically available radiation in Einsteins per
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day per square meter
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sst Sea surface temperature in degrees Centigrade
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dayL Length day in decimal hours.
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!Output Parameters:
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<return> Primary productivity in milligrams Carbon per square meter
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per day
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!Revision History:
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First programmed up by Monica Chen at Rutgers
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(1996)
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Revised by K. Turpie at NASA
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(August 1997)
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Maintained by Don Shea at NASA
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Now maintained by Robert O'Malley at Oregon State University
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(April, 2005 - present)
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!References and Credits
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Behrenfeld,M.J; Falkowski,P.G.; 1997. Photosynthetic Rates Derived
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from Satellite-Based Chlorophyll Concentration. Limnology and
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Oceanography, Volume 42, Number 1
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!END------------------------------------------------------------------------*\
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*/
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double chl_tot,
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z_eu,
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pb_opt,
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irrFunc,
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npp;
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/* Calculate euphotic depth (z_eu) with Morel's Case I model. */
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/* Calculate chl_tot from Satellite Surface Chlorophyll Data. */
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if (chl < 1.0L)
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chl_tot = 38.0L * pow( chl, 0.425L );
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else
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chl_tot = 40.2L * pow( chl, 0.507L );
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z_eu = 200.0L * pow( chl_tot, (-.293L) );
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if (z_eu <= 102.0L)
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z_eu = 568.2L * pow( chl_tot, (-.746L) );
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/* Calculate the Pb_opt from satellite sea surface temperature (sst). */
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if (sst < -10.0L)
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pb_opt = 0.00L;
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else if (sst < -1.0L)
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pb_opt = 1.13L;
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else if (sst > 28.5L)
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pb_opt = 4.00L;
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else {
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pb_opt = 1.2956 + 2.749e-1*sst + 6.17e-2*pow(sst,2) - 2.05e-2*pow(sst, 3)
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+ 2.462e-3*pow(sst,4) - 1.348e-4*pow(sst,5) + 3.4132e-6*pow(sst,6)
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- 3.27e-8*pow(sst,7);
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}
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/* calculate the irradiance function */
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irrFunc = 0.66125L * irr / ( irr + 4.1L );
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/* Return the primary production calculation. */
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npp = pb_opt * chl * dayL * irrFunc * z_eu;
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return npp;
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}
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//' Primary production
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//'
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//' @export
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// [[Rcpp::export]]
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NumericVector prod_BeFa(NumericVector chla, NumericVector irrad, NumericVector stemp, NumericVector daylength) {
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NumericVector out(chla.length());
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for (int i = 0; i < out.length(); i++) {
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out[i] = opp_befa(chla[i], irrad[i], stemp[i], daylength[i]);
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}
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return out;
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}

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