Topic: Growth

Topic Description:

Functions for analyzing tree growth, designed for the standard CTFS R Analytical Tables.



File: growth/growth.r

View File Source Download File No help file available

Function: growth.indiv

Function Description: growth.indiv

This returns a complete table with growth rate of every individual, both relative and dbh-increment. The table also includes most other key pieces of information for every individual: species, dbh, coordinates. Growth is trimmed with trim.growth, and growth is returned as NA if the individual is excluded; note, though, that every individual tree is always included in the table, even if growth=NA. Arguments are the same as in growth().

Function Arguments:

ArgumentDefault Value
census1
census2
rounddownFALSE
mindbh10
dbhunit'mm'
err.limit4
maxgrow75

Sample Usage:

growth.table=growth.indiv(bci.full5,bci.full6)


Function Source:


growth.indiv=function(census1,census2,rounddown=FALSE,mindbh=10,dbhunit='mm',err.limit=4,maxgrow=75)
         {
if(is.null(census2$codes)) census2$codes=rep('.',length(census2$dbh))

time=(census2$date-census1$date)/365.25

if(rounddown)
{
sm=((census1$dbh<55 | census2$dbh<55) & !is.na(census1$dbh) & !is.na(census2$dbh))
census1$dbh[sm]=rndown5(census1$dbh[sm])
census2$dbh[sm]=rndown5(census2$dbh[sm])
}

incgrowth=(census2$dbh-census1$dbh)/time
expgrowth=(log(census2$dbh)-log(census1$dbh))/time

good=trim.growth(census1,census2,time,err.limit=err.limit,maxgrow=maxgrow,mindbh=mindbh,dbhunit=dbh
        unit) good[census1$dbh incgrowth[!good]=expgrowth[!good]=NA


growthdata=data.frame(treeID=census1$treeID,tag=I(census1$tag),sp=I(census1$sp),gx=census1$gx,gy=ce
        nsus1$gy,dbh1=census1$dbh,dbh2=census2$dbh,time=time,
incgr=incgrowth,expgr=expgrowth,status1=census1$status,status2=census2$status
        )
return(growthdata)
}