CTFS.groupcats {CTFS}R Documentation

Overview of Functions that Create Categories for Grouping Trees

Description

Provides an overview of a variety of functions that create vectors which contain values for each tree that indicate which "group" it belongs to. For instance, dbh class, species name, habitat type, quadrate, growth form.

Details

FUNCTIONS FOR CREATING CATEGORIES

There are a variety of ways of creating a vector of categories for individual trees which can be used for analysis of dynamics by those categories. The functions described here create vectors of category values for each tree based on characteristics of the tree (species, dbh size, growth form, etc.) or a location in the plot (quadrate, habitat). For instance, one can compute the mortality of a species by habitat by making 2 vectors, one for species and one for habitat.

sep.quadinfo
Creates a Vector of Quadrate Characteristics for each Tree in a Dataset.
sep.sppinfo
Creates a Vector of Species Characteristics for each Tree in a Dataset.
sep.dbh
Creates a Vector of DBH Classes for each Tree in a Dataset.

MAKING VECTORS FOR GROUPING TREES FOR ANALYSIS

These examples use a test dataset tst.bci90.full

        dim(tst.bci90.full)
        [1] 12421    14
        
        unique(tst.bci90.full$sp)
        [1] "alsebl" "psycde" "socrex"
1. Vector of species names same length as datafile
        sppname.vct <- tst.bci90.full$sp
        
        length(sppname.vct)
        [1] 12421
        
        sppname.vct[1:5]
        [1] "alsebl" "alsebl" "alsebl" "alsebl" "alsebl"

NOTE: computing growth for each species by dbh classes can be done using growth.eachspp

2. Vector of dbh classes same length as datafile. cut returns a vector of factors and Levels are provided

        dbh.vct <- sep.dbh(tst.bci90.full)
        
        dbh.vct[1:5]
        [1]  <NA>      300.10000 100.300   100.300   100.300  
        Levels: 10.100 100.300 300.10000

        dbh.vct <- sep.dbh(tst.bci90.full,dbhclass=c(10,20,30,40,50))
        
        dbh.vct[1:5]
        [1] <NA>     50.10000 50.10000 50.10000 50.10000
        Levels: 10.20 20.30 30.40 40.50 50.10000
        
        table(dbh.vct)
        dbh.vct
        10.20    20.30    30.40    40.50 50.10000 
    4115     1512      753      436     2337 

NOTE: computing growth for each dbh class with growth.dbh.

3. Vector of habitat location of trees

        habitat.vct <- sep.quadinfo(tst.bci90.full,bciquad.info,by.col="hab")
        
        length(habitat.vct)
        [1] 12421
        
        habitat.vct[1:10]
        [1] NA  5  6  7  7  7  5  5  6  6

4. Vector of growth form of species

        grform.vct <- sep.grform(tst.bci90.full,bcispp.info,by.col="grform")

        length(grform.vct)
        [1] 12421

        table(grform.vct)
        grform.vct
        M     S     T 
        1133   160 11128 
        
        length(grform.vct)
        [1] 12421

Note

For developers: the functions described here are found in “readandwrite.R”

Author(s)

Pamela Hall

See Also

CTFS.abundance, CTFS.basalarea, CTFS.diversity, CTFS.growth, CTFS.mortality, CTFS.recruitment, CTFS.quadfunctions, CTFS.readwrite, CTFS.utilities


[Package CTFS version 1.00 Index]