assemble.demography {CTFS}R Documentation

Reformat the Output from Demographic Functions from List to Dataframe

Description

This function reformats the list of lists output from the demographic functions mortality, recruitment, growth and abundance.change.

Usage

assemble.demography(output, type = "g", whichdbhcat = 1, 
    datefirst = "1980-1-1")

Arguments

output file containing the results from one of the demographic functions
type type of demographic function with values:
“g” output from growth
“a” output from abundance.change
“m” output from mortality
“r” output from recruitment
whichdbhcat number indicating how many dbh categories to include, cannot exceed the number of categories in output
datefirst date of first enumeration at site, format: yyyy-mm-dd

Details

The results of the demographic functions (growth, mortality, recruitment, abundance and related functions are lists. This is a very convenient format for further analysis but is not the easiest way to view the results of these functions. assemble.demography reformats the list output into a dataframe so that is resembles a table.

The columns of the dataframe are always composed of the values computed by the demographic function. The rows are the categories provided by the first split variable used in the demographic function. If a second split varible is used, then the argument whichdbhcat determines which category of the second spit variable is put into the dataframe.

Returned Values

assemble.demography returns a dataframe.

For growth the following values are returned:

$rate
the annual growth rate in mm per year or % per year, type determined by the argument method are provided for growth
$clim
the 95% confidence limit based on a normal distribution
$N0
the number of trees used to compute growth rate
$dbhmean
the mean dbh in mm for trees used to compute growth rate
$meanyrs
mean number of years between census for trees used in growth rate computation.
$date0
mean date of first census
$date1
mean date of second census

For mortality the following values are returned:

$rate
the mortality in %/year
$upper
the upper 95% confidence interval based on a normal distribution
$lower
the lower 95% confidence interval based on a normal distribution
$N0
the number of living trees at the first census
$S
the number of survivors from the first to second census
$dbhmean
the mean dbh in mm for trees used to compute growth rate
$meanyrs
mean number of years between census for trees used in growth rate computation.
$date0
mean date of first census
$date1
mean date of second census

For recruitment the following values are returned:

$rate
the recruitment in %/year
$upper
the upper 95% confidence interval based on a normal distribution
$lower
the lower 95% confidence interval based on a normal distribution
$N1
the number of living trees at the second census
$R
the number of recruits from the first to second census
$meanyrs
mean number of years between census for trees used in growth rate computation.
$date0
mean date of first census
$date1
mean date of second census

For abundance.change the following values are returned:

$rate
the change in abundance in %/year
$prob
the prob N0 == N1
$N0
the number of living trees at the first census
$N1
the number of living trees at the second census
$D
the number of trees that died from the first to second census
$R
the number of recruits from the first to second census
$meanyrs
mean number of years between census for trees used in growth rate computation.
$date0
mean date of first census
$date1
mean date of second census

Author(s)

Rick Condit and Pamela Hall

See Also

assemble.table.each

Examples

## Not run: 
1. Run the demographic function

dbh.vct <- sep.dbh(tst.bci90.full,dbhclass=c(10,50,100,200,300,400,500))
growth.dbh <- growth(tst.bci90.full,tst.bcio95.full)
growth.dbh.out

2. Reformat the output into a dataframe.  Note there is only one row in 
this dataframe because no split variable was used in growth()

assemble.demography(growth.out)

3.  Run the demographic functions with two split variables, species 
names and dbh classes. Only the first list of the output is shown.
## End(Not run)

[Package CTFS version 1.00 Index]