R/AGBChave2005Wet.R

In GabrielaLopez/BiomasaFP: Tools for analysing data downloaded from ForestPlots.net

#' @title Function to estimate biomass of individual tree records for wet forests (Chave et al., 2005). Uses diameter and wood density to estimate biomass.
#' 
#' @description Function to estimate tree biomass using Chave et al. (2005) equation for wet forests.The function adds columns to the dataset with the biomass information for all alive trees.
#' This function needs a dataset with the following information: PlotViewID, PlotID, TreeID, CensusNo, Diameter (DBH1-DBH4), Wood density (WD). The function assumes that the diameter used is DBH4, unless other DBH is selected.
#' See ForestPlots.net downloads documentation for more information.
#' @references Chave J, Andalo C, Brown, et al. 2005. Tree allometry and improved estimation of carbon stocks and balance in tropical forests. Oecologia 145 (1):87-99. doi:10.1007/s00442-005-0100-x.
#' 
#' Chave J, Coomes DA, Jansen S, Lewis SL, Swenson NG, Zanne AE. 2009. Towards a worldwide wood economics spectrum. Ecology Letters 12(4): 351-366. http://dx.doi.org/10.1111/j.1461-0248.2009.01285.x
#' 
#' Zanne AE, Lopez-Gonzalez G, Coomes DA et al. 2009. Data from: Towards a worldwide wood economics spectrum. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.234

#' @param xdataset a dataset for estimating biomass
#' @param dbh a diameter (in mm). 
#' @export

AGBChv05W <- function (xdataset, dbh = "D4",height.data=NULL,param.type=NULL){
        cdf <- xdataset
        ## Clean file 
        cdf <- CleaningCensusInfo(xdataset) 
        dbh_d <- paste(dbh,"_D", sep="") 
        
        cdf$AGBind <- ifelse(cdf$D1>0 & cdf$Alive == 1 & (cdf$CensusStemDied>cdf$Census.No | is.na(cdf$IsSnapped)),
                             cdf$WD * exp (-1.239 + (1.980*log(cdf[,dbh]/10))+ (0.207*(log(cdf[,dbh]/10))^2)- (0.0281*(log(cdf[,dbh]/10))^3))/1000, NA)
        #cdf$AGBAl <-  ifelse(cdf$Alive == 1, cdf$AGBind, NA)
        #The code below was removed as it is difficult to find recruits with the current download format
        #cdf$AGBRec <- ifelse(cdf$NewRecruit == 1, cdf$AGBind, NA)
        #The code below was removed and would be implemented later
        cdf$AGBDead<-ifelse(cdf$CensusStemDied==cdf$Census.No, 
                            cdf$WD * exp (-1.239 + (1.980*log(cdf[,dbh_d]/10))+ (0.207*(log(cdf[,dbh_d]/10))^2)- (0.0281*(log(cdf[,dbh_d]/10))^3))/1000                    
         , NA)
        
        cdf     
}