diff --git a/R/plot_internals.R b/R/plot_internals.R index 8d51c5d93..9d82aad8b 100644 --- a/R/plot_internals.R +++ b/R/plot_internals.R @@ -594,7 +594,7 @@ 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$SWC) @@ -602,7 +602,7 @@ if(!is.null(summary.freq)) SWCM = .temporalSummary(SWCM, summary.freq, mean, na.rm=TRUE) if(is.null(ylab)) ylab = "Soil water content (% volume)" return(.multiple_dynamics(as.matrix(SWCM), xlab = xlab, ylab = ylab, ylim = ylim, - labels = c("Overall", paste("Layer", 1:nlayers)))) + labels = c(paste("Layer", 1:nlayers), "Overall"))) } else if(type=="SoilREW") { REWM = as.data.frame(100*Soil$REW) @@ -610,7 +610,7 @@ 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$RWC) @@ -618,7 +618,7 @@ if(!is.null(summary.freq)) RWCM = .temporalSummary(RWCM, summary.freq, mean, na.rm=TRUE) if(is.null(ylab)) ylab = "Relative water content (% field capacity)" return(.multiple_dynamics(as.matrix(RWCM), xlab = xlab, ylab = ylab, ylim = ylim, - labels = c("Overall", paste("Layer", 1:nlayers)))) + labels = c(paste("Layer", 1:nlayers), "Overall"))) } else if(type=="SoilVol") { if(is.null(ylab)) ylab = "Soil water content (mm)" @@ -626,15 +626,15 @@ if(!is.null(dates)) MLM = MLM[row.names(MLM) %in% as.character(dates),] if(!is.null(summary.freq)) MLM = .temporalSummary(MLM, summary.freq, mean, na.rm=TRUE) return(.multiple_dynamics(as.matrix(MLM), ylab = ylab, ylim = ylim, - xlab=xlab, labels = c("Overall", paste("Layer", 1:nlayers)))) + xlab=xlab, labels = c(paste("Layer", 1:nlayers), "Overall"))) } else if(type=="PlantExtraction") { - extrBal = as.data.frame(100*Soil$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, diff --git a/man/defaultControl.Rd b/man/defaultControl.Rd index 647193708..7b684c3d4 100644 --- a/man/defaultControl.Rd +++ b/man/defaultControl.Rd @@ -70,7 +70,7 @@ A list, with the following options (default values in brackets): } } \item{\code{cavitationRecoveryMaximumRate [= 0.05]}: Maximum rate of daily refilling of embolized conduits as sapwood area per leaf area (in cm2·m-2·day-1).} - \item{\code{lfmcComponent [= "leaf"]}: Plant component used to estimate LFMC, either "leaf" or "fine" (for fine fuel).} + \item{\code{lfmcComponent [= "fine"]}: Plant component used to estimate LFMC, either "leaf" or "fine" (for fine fuel).} } \bold{Water balance} (functions \code{\link{spwb}}, \code{\link{pwb}} or \code{\link{spwb_day}} when \code{traspirationMode = "Granier"} only): \itemize{ diff --git a/vignettes/workedexamples/PlantWaterPools.Rmd b/vignettes/workedexamples/PlantWaterPools.Rmd index 737b1712f..a0f5d4a9e 100644 --- a/vignettes/workedexamples/PlantWaterPools.Rmd +++ b/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