Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, cache = TRUE)
test <- TRUE
CACHE <- TRUE
require(knitr)
require(BIOMASS)
## ---- eval=F------------------------------------------------------------------
# install.packages("BIOMASS")
## ---- eval=F------------------------------------------------------------------
# require(BIOMASS)
# require(knitr) # To build tables in this document
## ---- cache=CACHE-------------------------------------------------------------
data(KarnatakaForest)
str(KarnatakaForest)
#
data(NouraguesHD)
str(NouraguesHD)
## ---- cache=CACHE-------------------------------------------------------------
selecPlot <- KarnatakaForest$plotId %in% c("BSP2", "BSP12", "BSP14", "BSP26", "BSP28", "BSP30", "BSP34", "BSP44", "BSP63", "BSP65")
KarnatakaForestsub <- droplevels(KarnatakaForest[selecPlot, ])
## ----eval=test, cache=CACHE---------------------------------------------------
Taxo <- correctTaxo(genus = KarnatakaForestsub$genus, species = KarnatakaForestsub$species, useCache = FALSE, verbose = FALSE)
KarnatakaForestsub$genusCorr <- Taxo$genusCorrected
KarnatakaForestsub$speciesCorr <- Taxo$speciesCorrected
## ----eval=test, cache=CACHE---------------------------------------------------
APG <- getTaxonomy(KarnatakaForestsub$genusCorr, findOrder = TRUE)
KarnatakaForestsub$familyAPG <- APG$family
KarnatakaForestsub$orderAPG <- APG$order
## ----eval=test, cache=CACHE---------------------------------------------------
dataWD <- getWoodDensity(
genus = KarnatakaForestsub$genusCorr,
species = KarnatakaForestsub$speciesCorr,
stand = KarnatakaForestsub$plotId
)
## ----eval=test, cache=CACHE---------------------------------------------------
LocalWoodDensity <- data.frame(
genus = c("Ziziphus", "Terminalia", "Garcinia"),
species = c("oenopolia", "bellirica", "indica"),
wd = c(0.65, 0.72, 0.65)
)
dataWD <- getWoodDensity(
genus = KarnatakaForestsub$genusCorr,
species = KarnatakaForestsub$speciesCorr,
family = KarnatakaForestsub$familyAPG,
stand = KarnatakaForestsub$plotID,
addWoodDensityData = LocalWoodDensity
)
## ----eval=test, cache=CACHE---------------------------------------------------
# At species level
sum(dataWD$levelWD == "species")
# At genus level
sum(dataWD$levelWD == "genus")
# At plot level
sum(!dataWD$levelWD %in% c("genus", "species"))
## ----echo=TRUE, cache=CACHE---------------------------------------------------
result <- modelHD(
D = NouraguesHD$D,
H = NouraguesHD$H,
useWeight = TRUE
)
kable(result)
## ---- cache=CACHE-------------------------------------------------------------
HDmodel <- modelHD(
D = NouraguesHD$D,
H = NouraguesHD$H,
method = "log2",
useWeight = TRUE
)
## ---- cache=CACHE-------------------------------------------------------------
HDmodelPerPlot <- modelHD(
D = NouraguesHD$D, H = NouraguesHD$H, method = "weibull",
useWeight = TRUE, plot = NouraguesHD$plotId
)
ResHD <- t(sapply(HDmodelPerPlot, function(x) c(coef(x$model), RSE = x$RSE)))
kable(ResHD, row.names = TRUE, digits = 3)
## ---- cache=CACHE-------------------------------------------------------------
dataHlocal <- retrieveH(
D = KarnatakaForestsub$D,
model = HDmodel
)
## ---- cache=CACHE-------------------------------------------------------------
dataHfeld <- retrieveH(
D = KarnatakaForestsub$D,
region = "SEAsia"
)
## ---- eval=F, cache=CACHE-----------------------------------------------------
# dataHchave <- retrieveH(
# D = KarnatakaForestsub$D,
# coord = KarnatakaForestsub[, c("long", "lat")]
# )
## ---- cache=CACHE-------------------------------------------------------------
KarnatakaForestsub$WD <- dataWD$meanWD
KarnatakaForestsub$H <- dataHlocal$H
KarnatakaForestsub$Hfeld <- dataHfeld$H
## ----warning=F, cache=CACHE---------------------------------------------------
AGBtree <- computeAGB(
D = KarnatakaForestsub$D,
WD = KarnatakaForestsub$WD,
H = KarnatakaForestsub$H
)
## ----warning=F, cache=CACHE---------------------------------------------------
AGBplot <- summaryByPlot(AGBtree, KarnatakaForestsub$plotId)
## ----warning=F, eval=F, cache=CACHE-------------------------------------------
# AGBplotChave <- summaryByPlot(
# computeAGB(
# D = KarnatakaForestsub$D, WD = KarnatakaForestsub$WD,
# coord = KarnatakaForestsub[, c("long", "lat")]
# ),
# KarnatakaForestsub$plotId
# )
## ----warning=F, cache=CACHE---------------------------------------------------
AGBplotFeld <- summaryByPlot(
computeAGB(
D = KarnatakaForestsub$D, WD = KarnatakaForestsub$WD,
H = KarnatakaForestsub$Hfeld
),
plot = KarnatakaForestsub$plotId
)
## ---- cache=CACHE-------------------------------------------------------------
KarnatakaForestsub$sdWD <- dataWD$sdWD
KarnatakaForestsub$HfeldRSE <- dataHfeld$RSE
## ---- cache=CACHE-------------------------------------------------------------
resultMC <- AGBmonteCarlo(D = KarnatakaForestsub$D, WD = KarnatakaForestsub$WD, errWD = KarnatakaForestsub$sdWD, HDmodel = HDmodel, Dpropag = "chave2004")
Res <- summaryByPlot(resultMC$AGB_simu, KarnatakaForestsub$plotId)
Res <- Res[order(Res$AGB), ]
plot(Res$AGB, pch = 20, xlab = "Plots", ylab = "AGB", ylim = c(0, max(Res$Cred_97.5)), las = 1, cex.lab = 1.3)
segments(seq(nrow(Res)), Res$Cred_2.5, seq(nrow(Res)), Res$Cred_97.5, col = "red")
## ---- eval=F, cache=CACHE-----------------------------------------------------
# resultMC <- AGBmonteCarlo(
# D = KarnatakaForestsub$D,
# WD = KarnatakaForestsub$WD,
# errWD = KarnatakaForestsub$sdWD,
# H = KarnatakaForestsub$Hfeld,
# errH = KarnatakaForestsub$HfeldRSE,
# Dpropag = "chave2004"
# )
#
# Res <- summaryByPlot(resultMC$AGB_simu, KarnatakaForestsub$plotId)
# Res <- Res[order(Res$AGB), ]
# plot(Res$AGB, pch = 20, xlab = "Plots", ylab = "AGB", ylim = c(0, max(Res$Cred_97.5)), las = 1, cex.lab = 1.3)
# segments(seq(nrow(Res)), Res$Cred_2.5, seq(nrow(Res)), Res$Cred_97.5, col = "red")
## ---- eval=F,cache=CACHE------------------------------------------------------
# resultMC <- AGBmonteCarlo(
# D = KarnatakaForestsub$D,
# WD = KarnatakaForestsub$WD,
# errWD = KarnatakaForestsub$sdWD,
# coord = KarnatakaForestsub[, c("long", "lat")],
# Dpropag = "chave2004"
# )
# Res <- summaryByPlot(resultMC$AGB_simu, KarnatakaForestsub$plotId)
# Res <- Res[order(Res$AGB), ]
# plot(Res$AGB, pch = 20, xlab = "Plots", ylab = "AGB", ylim = c(0, max(Res$Cred_97.5)), las = 1, cex.lab = 1.3)
# segments(seq(nrow(Res)), Res$Cred_2.5, seq(nrow(Res)), Res$Cred_97.5, col = "red")
## ---- cache=CACHE-------------------------------------------------------------
NouraguesHD$Hmix <- NouraguesHD$H
NouraguesHD$RSEmix <- 0.5
filt <- is.na(NouraguesHD$Hmix)
NouraguesHD$Hmix[filt] <- retrieveH(NouraguesHD$D, model = HDmodel)$H[filt]
NouraguesHD$RSEmix[filt] <- HDmodel$RSE
## ----eval=F, cache=CACHE------------------------------------------------------
# wd <- getWoodDensity(NouraguesHD$genus, NouraguesHD$species)
# resultMC <- AGBmonteCarlo(
# D = NouraguesHD$D, WD = wd$meanWD, errWD = wd$sdWD,
# H = NouraguesHD$Hmix, errH = NouraguesHD$RSEmix,
# Dpropag = "chave2004"
# )
# Res <- summaryByPlot(resultMC$AGB_simu, NouraguesHD$plotId)
# Res <- Res[order(Res$AGB), ]
# plot(Res$AGB, pch = 20, xlab = "Plots", ylab = "AGB (Mg/ha)", ylim = c(0, max(Res$Cred_97.5)), las = 1, cex.lab = 1.3)
# segments(1:nrow(Res), Res$Cred_2.5, 1:nrow(Res), Res$Cred_97.5, col = "red")
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