# The CTFS Large Plot Forest Dynamics Analyses

## Documentation for package `CTFS' version 1.00

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C E F G I L M N P R S T

## -- A --

abund.ch.prob | Calculation of Probability of Change in Population size
abundance | Abundance of Trees by Categories (User Defined Groups)
abundance.change | Annual Change in Population Size by Categories (User Defined Groups
abundance.change.calculation | Calculation of Annual Change in Population Size and Probability that Population Size has Changed
abundance.change.dbh | Annual Change in Population Size by DBH
abundance.quad | Abundance of Trees by Species and User Defined Quadrates
abundance.spp | Abundance of Trees by Species and DBH Classes
agb.ind | Computes Above Growth Biomass for Individual Tree
agb.mult | Computes Above Growth Biomass for Individual Tree
assemble.demography | Reformat the Output from Demographic Functions from List to Dataframe
assemble.table.each | Reformat the Output from Demographic Functions from List to Dataframe

## -- B --

ba | Basal Area of Trees
ba.change | Annual Change in Basal Area by Categories (User Defined Group)
ba.indiv | Basal Area of Individual Trees, including Mulitiple Stems
badgrowth.tree | Identify Trees for which DBH was Estimated for Biomass Calculation
basal.area | Basal Area by Categories (User defined groups)
basum | Basal Area of Trees
bcielev.info | Dataset of elevation for 5 x 5 m points in the BCI CTFS Plot
bciquad.info | Dataset of Information for each 20 by 20 m quadrate in the BCI 50 ha plot
bcispp.info | Dataset of Information on each Species found in the BCI 50 HA plot
bcitopo.info | Topographic Data for CTFS Plot : Elevation, Convexity and Slope
biomass | Compute Above Ground Biomass for Trees for 2 Censuses using Wood Specific Gravity for Species
biomass.change | Biomass Dynamics

## -- C --

convert.ba.mult | Compute Basal Area for All Stems of an Individual Tree using Census Dataset and Multi-Stem Dataset
countdens.1quad | Create File of Neighbor Attributes for a Single Species
countdens.1tree | Create File of Neighbor Attributes for a Single Species
create.status | Create STATUS variable for CTFS Datasets
CTFS.abundance | Overview of Analysis of Abundance and Rate of Change in Population Size in Tropical Tree Populations
CTFS.basalarea | Overview of Analysis of the Change in Basal Area of Tropical Tree Populations
CTFS.biomass | Overview of Analysis of the Biomass Dynamics of Tropical Tree Populations
CTFS.datafiles | Overview of Data File Structure for CTFS Package
CTFS.densdepend | Counting Neighbors and their Attributes - Investigating Density Dependence
CTFS.diversity | Analysis of the number of Species, Genera, and Families in Samples of the Plot
CTFS.groupcats | Overview of Functions that Create Categories for Grouping Trees
CTFS.growth | Overview of Analysis of Growth Rates in Tropical Tree Populations
CTFS.main | Center for Tropical Forest Science (CTFS) : Analysis of Long Term Forest Plot of Large Size
CTFS.manual | CTFS Manuals : Overview
CTFS.maps | Making Maps of Tree Positions, Topography and Area Characteristics
CTFS.mortality | Overview of Analysis of Mortality Rates in Tropical Tree Populations
CTFS.quadfunctions | Overview of Functions that provide Information on the location of trees in a Plot
CTFS.readwrite | Overview of Functions that Read, Write and Restructure CTFS data files
CTFS.recruitment | Overview of Analysis of Recruitment Rates in Tropical Tree Populations
CTFS.utilities | Overview of Functions that are CTFS Utilities

## -- E --

elev.to.list | Converts a Dataframe of Elevation Values to a Matrix

## -- F --

find.climits | Computes 95% CI for a Survivorship
findborderquads | Returns Indices of Neighboring Quadrats Given a Quadrat Index
fromjulian | Converts Calendar Dates to Julian Dates and Back

## -- G --

getwsg.vct | Computes Above Growth Biomass for Individual Tree
gr.raw | Unadjusted, Untrimmed Annual DBH Increment for Individual Trees
growth | Annual Growth Rates by Categories (User defined groups)
growth.dbh | Annual Growth Rate for DBH Classes
growth.eachspp | Annual Growth Rate for Species by DBH Class
growth.indiv | Annual Growth Rates for Individual Trees (3 methods of growth rate computation provided)
gxgy.to.hectindex | Converts GX GY Coordinates to a Hectare Number
gxgy.to.index | Converts GX GY Coordinates to a Quadrate Number
gxgy.to.rowcol | Converts a GX GY Coordinates to Row and Column Numbers

## -- I --

index.to.gxgy | Converts a Quadrate Number to GX GY Coordinates
index.to.rowcol | Converts a Quadrate Number (Indext) to Row and Column Numbers

## -- L --

load.species | Separate One or More Dataframes of Tree Records from a List

## -- M --

map | Plot of the Spatial Location of Trees of a Species
map1species | Plot of the Spatial Location of Trees of a Species
maptopo | Plot a Contour Map of Topography of a CTFS Plot
meaninterval.quad | Mean Interval Between Census for Quadrates
meantopo.quad | Mean Topographic Values for Quadrates
mergecensus | Merging Two Censuses of CTFS Plot Data
mortality | Annual Mortality Rates by Categories (User defined groups)
mortality.calculation | Compute Annual Mortality Rates and Confidence Limits given N, S and Time
mortality.dbh | Annual Mortality Rates for DBH Classes
mortality.eachspp | Annual Mortality Rate for Species by DBH Class

## -- N --

neighbordens.1quad | Create File of Neighbor Attributes for a Single Species
neighbordens.1sp | Create File of Neighbor Attributes for a Single Species

## -- P --

pick.dbh | Determine the Appropriate DBH to Use for Computation of Above Ground Biomass

## -- R --

readelevdata | Read a Text or RData Dataframe and Make a Matrix, Specifically for Elevation Data
recruitment | Annual Recruitment Rate by Categories (User defined groups)
recruitment.calculation | Compute Annual Recruitment Rates and Confidence Limits given N, S and Time
recruitment.eachspp | Annual Recruitment Rate for Species
rowcol.to.index | Converts a Row and Column to a Quadrate Number

## -- S --

select.randquad | Randomly Select the Coordinates of Quadrate
sep.data | Re-structures a Dataframe into a List of Dataframes by Values in a Vector
sep.dbh | Creates a Vector of DBH Classes for each Tree in a Dataset
sep.quadinfo | Creates a Vector of Quadrate Characteristics for each Tree in a Dataset
sep.species | Separate One or More Dataframes of Tree Records from a List
sep.sppinfo | Creates a Vector of Species Characteristics for each Tree in a Dataset
sep.vct.data | Re-structures a Dataframe into a List of Dataframes by Values in a Vector
sgf.area | Number of Species, Genera and Families for a single defined Area
sgf.meanarea | Mean Number of Species, Genera and Families for Replicates of Randomly Selected Areas
sgf.meanarea.range | Mean Number of Species, Genera and Families for Replicates of Randomly Selected Areas of a Given Range of Area Sizes and Shapes
sgf.randarea | Number of Species, Genera and Families for Randomly Selected Area
socrex90.neigh | Structure of Datasets for Density Dependence Analysis
splitdata | Re-structures a Dataframe into a List of Dataframes by values of a Column in the Dataframe
spp.randarea.range | Number of Species in Randomly Selected Areas of Various Shapes and Sizes

## -- T --

texttordata | Creates CTFS R dataset from any tab delimited text file
tojulian | Converts Calendar Dates to Julian Dates and Back
trim.growth | Determines if the Growth Rate of a Tree is Within Defined Limits
tst.bci90.full | Structure of CTFS Long Term Forest Data Set for a Single Census
tst.bci90.mult | Structure of the CTFS Long Term Forest Data Set Multiple Stem dataset for a single census
tst.bci90.quad | Structure of CTFS Long Term Forest Data Set for a Single Census
tst.bci90.spp | Structure of CTFS Long Term Forest Data Set for a Single Census
tst.bci95.full | Structure of CTFS Long Term Forest Data Set for a Single Census
tst.bci95.mult | Structure of the CTFS Long Term Forest Data Set Multiple Stem dataset for a single census
tst.bci95.quad | Structure of CTFS Long Term Forest Data Set for a Single Census
tst.bci95.spp | Structure of CTFS Long Term Forest Data Set for a Single Census
tst.ctfs.wsg | Wood Specific Gravity for Tropical Tree Species