bug soil plots

R/plot_internals.R

@@ -594,47 +594,47 @@
  if(!is.null(dates)) PsiM = PsiM[row.names(PsiM) %in% as.character(dates),,drop = FALSE]
  if(!is.null(summary.freq)) PsiM = .temporalSummary(PsiM, summary.freq, mean, na.rm=TRUE)
  return(.multiple_dynamics(as.matrix(PsiM), xlab = xlab, ylab = ylab, ylim = ylim,
- labels = c("Overall", paste("Layer", 1:nlayers))))
+ labels = c(paste("Layer", 1:nlayers), "Overall")))
  } 
  else if(type=="SoilTheta") {
  SWCM = as.data.frame(Soil$SWC)
  if(!is.null(dates)) SWCM = SWCM[row.names(SWCM) %in% as.character(dates),,drop = FALSE]
  if(!is.null(summary.freq)) SWCM = .temporalSummary(SWCM, summary.freq, mean, na.rm=TRUE)
  if(is.null(ylab)) ylab = "Soil water content (% volume)"
  return(.multiple_dynamics(as.matrix(SWCM), xlab = xlab, ylab = ylab, ylim = ylim,
- labels = c("Overall", paste("Layer", 1:nlayers))))
+ labels = c(paste("Layer", 1:nlayers), "Overall")))
  } 
  else if(type=="SoilREW") {
  REWM = as.data.frame(100*Soil$REW)
  if(!is.null(dates)) REWM = REWM[row.names(REWM) %in% as.character(dates),,drop = FALSE]
  if(!is.null(summary.freq)) REWM = .temporalSummary(REWM, summary.freq, mean, na.rm=TRUE)
  if(is.null(ylab)) ylab = "Relative extractable water (%)"
  return(.multiple_dynamics(as.matrix(REWM), xlab = xlab, ylab = ylab, ylim = ylim,
- labels = c("Overall", paste("Layer", 1:nlayers))))
+ labels = c(paste("Layer", 1:nlayers), "Overall")))
  } 
  else if(type=="SoilRWC") {
  RWCM = as.data.frame(100*Soil$RWC)
  if(!is.null(dates)) RWCM = RWCM[row.names(RWCM) %in% as.character(dates),,drop = FALSE]
  if(!is.null(summary.freq)) RWCM = .temporalSummary(RWCM, summary.freq, mean, na.rm=TRUE)
  if(is.null(ylab)) ylab = "Relative water content (% field capacity)"
  return(.multiple_dynamics(as.matrix(RWCM), xlab = xlab, ylab = ylab, ylim = ylim,
- labels = c("Overall", paste("Layer", 1:nlayers))))
+ labels = c(paste("Layer", 1:nlayers), "Overall")))
  } 
  else if(type=="SoilVol") {
  if(is.null(ylab)) ylab = "Soil water content (mm)"
  MLM = as.data.frame(Soil$ML)
  if(!is.null(dates)) MLM = MLM[row.names(MLM) %in% as.character(dates),]
  if(!is.null(summary.freq)) MLM = .temporalSummary(MLM, summary.freq, mean, na.rm=TRUE)
  return(.multiple_dynamics(as.matrix(MLM), ylab = ylab, ylim = ylim,
- xlab=xlab, labels = c("Overall", paste("Layer", 1:nlayers))))
+ xlab=xlab, labels = c(paste("Layer", 1:nlayers), "Overall")))
  } 
  else if(type=="PlantExtraction") {
- extrBal = as.data.frame(100*Soil$PlantExt)
+ extrBal = as.data.frame(Soil$PlantExt)
  if(!is.null(dates)) extrBal = extrBal[row.names(extrBal) %in% as.character(dates),,drop = FALSE]
  if(is.null(ylab)) ylab = .getYLab(type)
  if(!is.null(summary.freq)) extrBal = .temporalSummary(extrBal, summary.freq, sum, na.rm=TRUE)
  g<-.multiple_dynamics(as.matrix(extrBal), xlab = xlab, ylab = ylab, ylim = ylim,
- labels = c("Overall", paste("Layer", 1:nlayers)))
+ labels = c(paste("Layer", 1:nlayers), "Overall"))
  g<-g+geom_abline(slope=0, intercept=0, col="gray")
  return(g)
  } 
@@ -644,7 +644,7 @@
  if(is.null(ylab)) ylab = "Hydraulic input (mm)" 
  if(!is.null(summary.freq)) hydrIn = .temporalSummary(hydrIn, summary.freq, sum, na.rm=TRUE)
  return(.multiple_dynamics(as.matrix(hydrIn), xlab = xlab, ylab = ylab, ylim = ylim,
- labels = c("Overall", paste("Layer", 1:nlayers))))
+ labels = c(paste("Layer", 1:nlayers), "Overall")))
  } 
 }
 .plot_stand<-function(Stand, type, 

vignettes/workedexamples/PlantWaterPools.Rmd

@@ -99,7 +99,7 @@ cowplot::plot_grid(fb_sperry_plot, fb_sureau_plot,
 ## Simulations
 As target forest stands we take five experimental plots whose data was already used when presenting the water balance model in De Cáceres et al. (2021). An evaluation of model performance in these experimental plots is given in [*Stand-level evaluation*](https://emf-creaf.github.io/medfate/articles/evaluation/StandLevelEvaluation.html). 
 
-For each of these plots we performed two simulations with the advanced water balance model (`transpirationMode = "Sperry"`), one using the default assumption of complete rhizosphere overlap (`rhizosphereOverlap = "total"`) and the other assuming complete independence of water pools (`rhizosphereOverlap = "none"`). Recovery from embolism was assumed to depend on soil moisture (`cavitationRefill = "rate"`). We performed a burn-in simulation for the available weather of the forest plot (1 to 3 years, depending on the plot), so that soil moisture, plant water potentials and xylem percent loss conductance (PLC) could be equilibrated. After this burn-in period, we run again the model for one year only, to simplify the examination of the results.
+For each of these plots we performed two simulations with the advanced water balance model (`transpirationMode = "Sperry"`), one using the default assumption of complete rhizosphere overlap (`rhizosphereOverlap = "total"`) and the other assuming complete independence of water pools (`rhizosphereOverlap = "none"`). Recovery from embolism was assumed to depend on soil moisture (`stemCavitationRecovery = "rate"` and `leafCavitationRecovery = "rate"`). We performed a burn-in simulation for the available weather of the forest plot (1 to 3 years, depending on the plot), so that soil moisture, plant water potentials and xylem percent loss conductance (PLC) could be equilibrated. After this burn-in period, we run again the model for one year only, to simplify the examination of the results.
 
 
 ## Results