### R code from vignette source 'expectedPlotOutcomes.Rnw'
###################################################
### code chunk number 1: expectedPlotOutcomes.Rnw:24-34
###################################################
library(MakeMyForests)
library(disperseR)
library(SortieIO)
head(ssdSeedlings)
head(expandedTrees)
###################################################
### code chunk number 2: expectedPlotOutcomes.Rnw:39-61
###################################################
## clean up
seedlings <- ssdSeedlings[which(ssdSeedlings$nSeedlings >0) ,]
seedlings <- aggregate(seedlings$nSeedlings, by=list(seedlings$plot,
seedlings$subplot,
seedlings$sppcode,
seedlings$year),
FUN=sum)
colnames(seedlings) <- c("plot", "subplot", "species", "measyear", "nSdl")
expandedSeedlings <- data.frame(species=seedlings$species,
plot=seedlings$plot, subplot=seedlings$subplot,
treeid=0, ingrowth=NA, firstrec=seedlings$measyear,
deathyear=NA, x=NA, y=NA,
measyear=seedlings$measyear, dbh=NA, stage="seedling",
basalarea=NA, mindbh=NA,
nSdl=seedlings$nSdl, stringsAsFactors=F)
## set up nSdl in expandedTrees so we can merge
expandedTrees$nSdl <- 1
head(expandedTrees)
expandedSeedlings <- rbind(expandedTrees, expandedSeedlings)
###################################################
### code chunk number 3: expectedPlotOutcomes.Rnw:67-137
###################################################
plotChars <- aggregate(expandedTrees$basalarea,
by=list(expandedTrees$plot,
expandedTrees$species,
expandedTrees$measyear,
expandedTrees$stage),
FUN=length)
colnames(plotChars) <- c("plot", "species", "year", "stage", "AbsDen")
## do the seedlings separately
plotSdls <- aggregate(expandedSeedlings$nSdl,
by=list(expandedSeedlings$plot,
expandedSeedlings$species,
expandedSeedlings$measyear),
FUN=sum)
colnames(plotSdls) <- c("plot", "species", "year", "nSdl")
test <- merge(plotSdls,
plotChars[plotChars$stage=="seedling",c(1,2,3,5)],
by=c("plot", "species", "year"),
all=T)
test[is.na(test$nSdl), "nSdl"] <- 0
test[is.na(test$AbsDen), "AbsDen"] <- 0
test$sum <- test$nSdl + test$AbsDen
test$AbsDen <- test$sum
test <- test[,c(1:3,5)]
test$stage <- "seedling"
rawr <- merge(test, plotChars,
by=c("plot", "species", "year", "stage"),
all=T)
rawr[rawr$stage=="seedling", "AbsDen.y"] <- rawr[rawr$stage=="seedling", "AbsDen.x"]
plotChars <- rawr[, c(1:4,6)]
colnames(plotChars) <- c("plot", "species", "year", "stage", "AbsDen")
absBA <- aggregate(expandedTrees$basalarea,
by=list(expandedTrees$plot,
expandedTrees$species,
expandedTrees$measyear,
expandedTrees$stage),
FUN=sum)
colnames(absBA) <- c("plot", "species", "year", "stage", "AbsBA")
plotChars <- merge(plotChars, absBA,
by=c("plot", "species", "year", "stage"), all=T)
## put in plot normalizer
plotChars <- merge(plotChars, ssdPlotDesc[,c(1,3)])
plotChars$AbsDenByHa <- plotChars$AbsDen/plotChars$size_ha
plotChars$AbsBAByHa <- plotChars$AbsBA/plotChars$size_ha
plotChars$year <- as.numeric(plotChars$year)
## prepping for input into big table
## making years into steps
uniqueplots <- unique(plotChars$plot)
for(i in 1:length(uniqueplots)){
plotChars[
plotChars$plot==uniqueplots[i], "year"] <- plotChars[
plotChars$plot==uniqueplots[i], "year"] -
ssdPlotDesc[ssdPlotDesc$plot==uniqueplots[i], "minYear"]
+ 1
}
## make fake plot names into real plot names
##
plotChars <- convertPlotNames(plotChars, "plot", F)
plotChars <- plotChars[!is.na(plotChars$plot),]
###################################################
### code chunk number 4: expectedPlotOutcomes.Rnw:142-183
###################################################
plotCharUniques <- unique(plotChars[, c("plot", "species", "year")])
## set up end table
## get ready to fill with the variables that we have
## change colnames to match some
colnames(plotChars)[c(1:3,9 )] <- c("Species", "Step", "Stage", "Plot")
AdultAbsBA <- subset(plotChars, Stage=="tree",
select=c("Plot", "Step", "Species", "AbsBA"))
SaplAbsBA <- subset(plotChars, Stage=="sapling",
select=c("Plot", "Step", "Species", "AbsBA"))
AdultAbsDen <- subset(plotChars, Stage=="tree",
select=c("Plot", "Step", "Species", "AbsDen"))
SdlAbsDen <- subset(plotChars, Stage=="seedling",
select=c("Plot", "Step", "Species", "AbsDen"))
SaplAbsDen <- subset(plotChars, Stage=="sapling",
select=c("Plot", "Step", "Species", "AbsDen"))
newRealPlots <- data.frame(Plot=plotCharUniques[,1],
Step=plotCharUniques[,3],
Species=plotCharUniques[,2],
stringsAsFactors=F)
newRealPlots <- merge(newRealPlots, AdultAbsBA, all=T)
newRealPlots <- merge(newRealPlots, AdultAbsDen, all=T)
colnames(newRealPlots)[4:5] <- c("AdultAbsBA", "AdultAbsDen")
newRealPlots <- merge(newRealPlots, SaplAbsBA, all=T)
newRealPlots <- merge(newRealPlots, SaplAbsDen, all=T)
colnames(newRealPlots)[6:7] <- c("SaplAbsBA", "SaplAbsDen")
newRealPlots <- merge(newRealPlots, SdlAbsDen, all=T)
colnames(newRealPlots)[8] <- c("SdlAbsDen")
head(newRealPlots)
tail(newRealPlots)
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