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plot_aligned_nn_fluxnet2015.R
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plot_aligned_nn_fluxnet2015 <- function( sitename, nam_target="lue_obs_evi", bysm=FALSE, use_fapar=FALSE, use_weights=FALSE, makepdf=TRUE, verbose=FALSE ){
# ## Debug ----------------
# sitename = "FR-Pue"
# nam_target = "lue_obs_evi"
# use_weights= FALSE
# use_fapar = FALSE
# makepdf = TRUE
# verbose = TRUE
# ##--------------------------
require(dplyr)
source( "add_alpha.R" )
## check and override if necessary
if ( nam_target=="lue_obs" || nam_target=="lue_obs_evi" || nam_target=="lue_obs_fpar" ){
plotlue <- TRUE
if (nam_target=="lue_obs_evi"){
fapar_data <- "evi"
} else if (nam_target=="lue_obs_fpar"){
fapar_data <- "fpar"
}
if (use_fapar){
print("WARNING: setting use_fapar to FALSE")
use_fapar <- FALSE
}
}
## identifier for output files
if (use_fapar){
if (nam_target=="lue_obs_evi"){
char_fapar <- "_withEVI"
} else if (nam_target=="lue_obs_fpar"){
char_fapar <- "_withFPAR"
} else {
print("ERROR: PROVIDE VALID FAPAR DATA!")
}
} else {
char_fapar <- ""
}
if (bysm){
char_bysm <- "_bysm"
} else {
char_bysm <- ""
}
before <- 30
after <- 100
siteinfo <- read.csv( "soilm_data_usability_fluxnet2015.csv", as.is=TRUE )
##------------------------------------------------
## Load data
##------------------------------------------------
if (verbose) print("loading nn_fVAR file ...")
dir <- "./data/fvar/"
infil <- paste( dir, "nn_fluxnet2015_", sitename, "_", nam_target, char_fapar, ".Rdata", sep="" )
load( infil ) ## gets list 'nn_fluxnet'
df <- as.data.frame( nn_fluxnet[[ sitename ]]$nice )
## Get drought events. Default defined by fLUE, alternative (bysm=TRUE) defined by soil moisture threshold 0.5 (see 'nn_fVAR_fluxnet2015.R')
if (bysm){
## Get soil moisture droughts
print("get drought events ...")
df$is_drought_bysoilm <- ( df$soilm_mean < 0.5 )
droughts <- get_consecutive(
df$is_drought_bysoilm,
leng_threshold = 3,
do_merge = FALSE
)
} else {
droughts <- nn_fluxnet[[ sitename ]]$droughts
}
load( paste( "data/aligned_", sitename, char_bysm, ".Rdata", sep="" ) ) # loads data_alg_dry, names_alg, fvarbins, faparbins, iwuebins, before, after, bincentres_fvar, bincentres_fapar, bincentres_iwue
load( paste( "data/df_dday_aggbydday_", sitename, char_bysm, ".Rdata", sep="" ) ) # loads 'df_dday_aggbydday'
filn <- paste( "data/aligned_modis_", sitename, ".Rdata", sep="" )
if (file.exists(filn)) {
error <- try( load( filn ) ) # loads data_alg_dry_modis, df_dday_modis, df_dday_aggbydday_modis, names_alg_modis, after_modis, before_modis
if (class(error)=="try-error") avl_modis <- FALSE else avl_modis <- TRUE
} else {
avl_modis <- FALSE
}
filn <- paste( "data/aligned_mte_", sitename, ".Rdata", sep="" )
if (file.exists(filn)) {
error <- try( load( filn ) ) # loads data_alg_dry_mte, df_dday_mte, df_dday_aggbydday_mte, names_alg_mte, after_mte, before_mte
if (class(error)=="try-error") avl_mte <- FALSE else avl_mte <- TRUE
} else {
avl_mte <- FALSE
}
##------------------------------------------------
## PLOT MULTIPANEL
##------------------------------------------------
if (verbose) print("plotting muiltipanel ...")
lue <- TRUE
panelfiln <- paste( "fig_nn_fluxnet2015/aligned/aligned_potentialgpp_", sitename, "_", nam_target, char_fapar, char_bysm, ".pdf", sep="")
alpha <- 0.3/(nrow(droughts))
xvals <- (-before:after)+1
magn <- 2.4
ncols <- 1
# if (avl_pri) { nrows <- 4 } else { nrows <- 3 }
nrows <- 2
# heights <- rep(1,nrows)*magn
heights <- c(1,1.4)*magn
widths <- rep(1.8,ncols)*magn
if (makepdf) pdf( panelfiln, width=sum(widths), height=sum(heights), bg="white" )
panel <- layout(
matrix(c(1:(nrows*ncols)),nrows,ncols,byrow=TRUE),
# matrix( order, nrows, ncols, byrow=TRUE ),
widths=widths,
heights=heights,
TRUE
)
# layout.show( panel )
##--------------------------------------------------------
## SOIL MOISTURE
##--------------------------------------------------------
if (verbose) print("plot 1/5")
xvals <- (-before:after)+1
par( las=1, mar=c(0,4,1,4), xpd=FALSE )
plot( c(-before,after), c(0,1.4), type="n", xlab="day after drought onset", ylab="soil water content (fraction)", axes=FALSE ) # , col.lab="blue"
# axis( 2, col="blue", col.axis="blue" )
axis( 2 )
# axis( 4 )
abline( h=1.0, col='grey40', lwd=0.5 )
# mtext( "soil water content (fraction)", side=2, line=3, col="blue", cex=0.65, las=0 )
rect( 0, -99, droughts$len, 99, col=rgb(0,0,0,alpha), border=NA )
upper <- approx( df_dday_aggbydday$dday, df_dday_aggbydday$soilm_upp, xout=xvals )$y
lower <- approx( df_dday_aggbydday$dday, df_dday_aggbydday$soilm_low, xout=xvals )$y
mid <- approx( df_dday_aggbydday$dday, df_dday_aggbydday$soilm_med, xout=xvals )$y
idxs <- which( !is.na(upper) & !is.na(lower) )
# ylim <- range( upper, lower, na.rm=TRUE )
# par( las=1, mar=c(0,4,0,4), xpd=FALSE )
# plot( (-before:after), (-before:after), type="n", xlab="day after drought", ylab"soil water content (fraction)", ylim=c(0,1), axes=FALSE )
# axis( 2 )
# axis( 4 )
# boxplot( dplyr::select( dplyr::filter( df_dday, dday==1 ), soilm_mean ), at=1, add=TRUE, outline=FALSE, boxwex=10, axes=FALSE )
# for ( idx in 1:nrow(droughts) ){
# lines( xvals, data_alg_dry[,which(names_alg=="soilm_mean"),idx], col=rgb(0,0,1,0.2) , lwd=1 ) #col=rgb(0,1,0,0.6)
# }
## plot polygon for soil moisture
polygon( c( xvals[idxs], rev(xvals[idxs])), c( lower[idxs], rev(upper[idxs])), col=add_alpha('blue', 0.3), border=NA )
lines( xvals, mid, col="blue", lwd=1 )
##--------------------------------------------------------
## Relative VPD change (in same panel as soil moisture)
##--------------------------------------------------------
par( new=TRUE )
xvals <- (-before:after)+1
upper <- 1 / ( approx( df_dday_aggbydday$dday, df_dday_aggbydday$dvpd_upp, xout=xvals )$y )
lower <- 1 / ( approx( df_dday_aggbydday$dday, df_dday_aggbydday$dvpd_low, xout=xvals )$y )
mid <- 1 / ( approx( df_dday_aggbydday$dday, df_dday_aggbydday$dvpd_med, xout=xvals )$y )
idxs <- which( !is.na(upper) & !is.na(lower) )
# ylim <- range( upper, lower, na.rm=TRUE )
# plot( c(-before,after), ylim, type="n", xlab="", ylab="", axes=FALSE )
# axis( 4, col="darkgoldenrod4", col.axis="darkgoldenrod4" )
# mtext( expression( paste( Delta, "VPD", "/VPD"[0] ) ), side=4, line=2.5, las=0, cex=0.7, col="darkgoldenrod4" )
# for ( idx in 1:nrow(droughts) ){
# lines( xvals, data_alg_dry[,which(names_alg=="vpd"),idx], col=rgb(0,0,1,0.2) , lwd=1 ) #col=rgb(0,1,0,0.6)
# }
## plot polygon for soil moisture
polygon( c( xvals[idxs], rev(xvals[idxs])), c( lower[idxs], rev(upper[idxs])), col=add_alpha('steelblue3', 0.3), border=NA )
lines( xvals, mid, col=add_alpha('steelblue3', 1), lwd=1 )
# try( lines( smooth.spline( xvals, mid, spar=0.3 ), col="steelblue3", lwd=1 ) )
text( -before, 1.2, sitename, cex=1.2, adj=c(0,0), font=2 )
# text( -before, 1.1, dplyr::filter( siteinfo, siteinfo$mysitename==sitename )$classid, cex=1.2, adj=c(0,0), font=1 )
legend( "bottomleft", c("soil water content (fraction)", expression( paste( "VPD"^{-1}, " (relative change)" ) ) ), bty="n", lty=1, lwd=2, col=c("blue", "steelblue3"), cex=1.0 )
##--------------------------------------------------------
## fLUE
##--------------------------------------------------------
if (verbose) print("plot 2/5")
par( las=1, mar=c(4,4,0,4), xpd=FALSE )
plot( c(-before,after), c(0,1.3), type="n", xlab="day after drought onset", ylab="unitless", axes=FALSE )
axis( 1, xlab="days after drought onset" )
axis( 2 )
# axis( 4 )
abline( h=1.0, col='grey40', lwd=0.5 )
# title( paste( sitename ) )
# ## boxplot for levels within bins
# bp1 <- boxplot( fvar ~ infvarbin,
# data = df_dday,
# at = bincentres_fvar,
# outline = FALSE,
# na.rm = TRUE,
# add = TRUE,
# axes = FALSE,
# boxwex = 5,
# border = "grey50",
# lwd = 0.5
# )
## GPP over drought aligned
# for ( idx in 1:nrow(droughts) ){
# frac <- data_alg_dry[,which( names_alg=="fvar"),idx]
# lines( xvals, frac, col=rgb(0,0,0,0.2) )
# }
rect( 0, -99, droughts$len, 99, col=rgb(0,0,0,alpha), border=NA )
## plot polygon for fvar
upper <- approx( df_dday_aggbydday$dday, df_dday_aggbydday$fvar_upp, xout=xvals )$y
lower <- approx( df_dday_aggbydday$dday, df_dday_aggbydday$fvar_low, xout=xvals )$y
mid <- approx( df_dday_aggbydday$dday, df_dday_aggbydday$fvar_med, xout=xvals )$y
idxs <- which( !is.na(upper) & !is.na(lower) )
polygon( c( xvals[idxs], rev(xvals[idxs])), c( lower[idxs], rev(upper[idxs])), col=add_alpha("tomato", 0.4), border=NA )
lines( xvals, mid, col="tomato" )
# ## create new aligned data frame
# df_aligned_stat <- data.frame( day=xvals, fvar=mid )
##--------------------------------------------------------
## FAPAR into same panel as above
##--------------------------------------------------------
if (verbose) print("plot 3/5")
xvals <- (-before:after)+1
for ( idx in 1:nrow(droughts) ){
lines( xvals, data_alg_dry[,which(names_alg==fapar_data),idx], col=add_alpha("springgreen4", 0.2) , lwd=1 ) #col=rgb(0,1,0,0.6)
}
# ## boxplot for levels within bins
# bp1 <- boxplot( df_dday[[ fapar_data ]] ~ infaparbin,
# data = df_dday,
# at = bincentres_fapar,
# outline = FALSE,
# na.rm = TRUE,
# add = TRUE,
# axes = FALSE,
# boxwex = 10,
# border = "grey50",
# lwd = 0.5
# )
## plot polygon for EVI
upper <- approx( df_dday_aggbydday$dday, df_dday_aggbydday$evi_upp, xout=xvals )$y
lower <- approx( df_dday_aggbydday$dday, df_dday_aggbydday$evi_low, xout=xvals )$y
mid <- approx( df_dday_aggbydday$dday, df_dday_aggbydday$evi_med, xout=xvals )$y
polygon( c( xvals, rev(xvals)), c( lower, rev(upper)), col=add_alpha('springgreen4', 0.3), border=NA )
lines( xvals, mid, col="springgreen4", lwd=2 )
# ## attach to aligned data frame
# df_aligned_stat[[ fapar_data ]] <- mid
legend( "left", c("fLUE", "EVI"), bty="n", lty=1, lwd=2, col=c("tomato", "springgreen4"), cex=1.0 )
if (makepdf) dev.off()
}