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| require(zoo) | ||
| graphics.off() | ||
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| error.bar <- function(x, y, upper, lower=upper, length=0.05,...){ | ||
| if(length(x) != length(y) | length(y) !=length(lower) | length(lower) != length(upper)) | ||
| stop("vectors must be same length") | ||
| arrows(x,y+upper, x, y, angle=90, code=3, length=length, ...) | ||
| } | ||
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| # compile code | ||
| system('gfortran -ffree-form -ffree-line-length-200 -g func.f90 inc.f90 phenograss.f90 sann.f90 main.f90 -o phenograss', wait = T) | ||
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| # run the code for the konza site, using site specific meteorological drivers | ||
| system('./a.out ./parameters/konza.txt r',wait = T) | ||
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| # local weather | ||
| drivers = read.table("data/drivers/konza_grass.csv") | ||
| drivers_year = drivers[,1] | ||
| precip = drivers[,7] | ||
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| # read konza yearly productivity measurements | ||
| df_bio = read.table('data/ancillary/konza_total_annual_biomass.csv',sep=',',header=T) | ||
| df_bio[is.na(df_bio)] = 0 | ||
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| # use florence soil: The Florence series consists of deep, well drained, moderately slowly permeable soils on uplands. | ||
| df_bio = df_bio[c(df_bio$SOILTYPE=="fl"),] | ||
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| # extract the dates on which the measurements are made as well as the DOY and the year | ||
| dates_bio = as.Date(paste(df_bio$RECYEAR,df_bio$RECMONTH,df_bio$RECDAY,sep='-'),"%Y-%m-%d") | ||
| doy = as.numeric(format(dates_bio,"%j")) | ||
| year = as.numeric(format(dates_bio,"%Y")) | ||
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| # make the variables human readable | ||
| grass = as.numeric(as.matrix(df_bio$LVGRASS)) | ||
| forbs = as.numeric(as.matrix(df_bio$FORBS)) | ||
| death_cur = as.numeric(as.matrix(df_bio$CUYRDEAD)) | ||
| woody = as.numeric(as.matrix(df_bio$WOODY)) | ||
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| death_prev = as.numeric(as.matrix(df_bio$PRYRDEAD)) | ||
| death_prev = as.numeric(c(death_prev[-1],NA)) | ||
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| # we will consider all biomass of perennial nature (death from this season or alive) | ||
| biomass = grass + forbs + death_cur | ||
| biomass = biomass * 10 # values are in g / 0.1 m2 | ||
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| # read in the modelled results | ||
| model= unlist(read.table('output/modelrun_01_fCover.txt')) | ||
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| # read in the input data to extract the dates vector | ||
| dates =as.Date(paste(drivers[,1],drivers[,2],sep='-'),"%Y-%j") | ||
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| bio_year = format(dates_bio,"%Y") | ||
| year = as.numeric(format(dates[order(dates)],"%Y")) | ||
| doy_drivers = as.numeric(format(dates[order(dates)],"%j")) | ||
| year_drivers = as.numeric(format(dates[order(dates)],"%Y")) | ||
| bio_doy = as.numeric( format(dates_bio,"%j")) | ||
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| growth = model | ||
| growth_increase = c(diff(growth),NA) | ||
| growth_increase[which(growth_increase < 0) ] = NA | ||
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| annual_model = by(growth,INDICES = list(year),function(x,...)sum(x[1:260],na.rm=T)) | ||
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| sums = by(biomass,INDICES=list(bio_year),FUN=mean,na.rm=T) | ||
| sds = by(biomass,INDICES=list(bio_year),FUN=sd,na.rm=T) | ||
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| model_names = names(annual_model) | ||
| bio_names = names(sums) | ||
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| pdf("output/Figure4.pdf",21,10) | ||
| par(mfrow=c(1,2),mar=c(5,5,3,1),tck=0.03,lwd=2.5,cex=2.5) | ||
| dd = cbind(sums,sds,annual_model[which(model_names %in% bio_names)]) | ||
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| plot(dd[,3],dd[,1], | ||
| xlab='Annual intergral of fCover', | ||
| col='olivedrab4', | ||
| ylab=expression("Biomass (g m" ^-2 *" yr" ^-1*")"), | ||
| pch=19, | ||
| bty='n', | ||
| xlim=c(60,120), | ||
| ylim=c(125,700), | ||
| yaxt='n', | ||
| xaxt='n', | ||
| xaxs='i', | ||
| yaxs='i') | ||
| axis(2,at=c(125,250,500),tck=0.03,lwd=2) | ||
| axis(1,tck=0.03,lwd=2) | ||
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| # omit first 10 years as spinup | ||
| fit = lm(dd[,1]~dd[,3]) | ||
| print(cor(dd[,3],dd[,1])) | ||
| print(summary(fit)) | ||
| abline(fit,lty=2,col='grey') | ||
| coef = round(fit$coefficients,2) | ||
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| text(65,550,expression("R" ^2 * "= 0.54; p < 0.001"),pos=4) | ||
| text(65,490,paste("y = ",coef[1]," + ",coef[2],"x",sep=""),pos=4) | ||
| legend('topright',legend="a",bty='n',cex=2) | ||
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| ## | ||
| par(mar=c(5,1,3,5)) | ||
| p <- barplot(t(dd[,1]),ylim=c(125,700),xpd=FALSE,col='wheat', | ||
| xlab="Year", | ||
| ylab="", | ||
| border=NA, | ||
| yaxt='n') | ||
| axis(2,at=c(125,250,500),tck=0.03,labels=FALSE,lwd=2) | ||
| #mtext(expression("Biomass (g m" ^-2 *" yr" ^-1*")"),2,3,adj=0.2) | ||
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| error.bar(p,dd[,1],dd[,2],col='wheat3') | ||
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| par(new=TRUE) | ||
| lines(p,-28.97+dd[,3]*4.25,type='b', | ||
| xaxt='n', | ||
| yaxt='n', | ||
| col='olivedrab4', | ||
| lwd=3, | ||
| xlab='', | ||
| ylab='', | ||
| lty=2, | ||
| cex=0.8, | ||
| pch=19) | ||
| axis(4,at=c(125,250,500),labels=round(c(125,250,500)/4.25),tck=0.03,lwd=2) | ||
| mtext("Annual integral of fCover",4,3,cex=2.5) | ||
| legend('topright',legend="b",bty='n',cex=2) | ||
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| graphics.off() |