The CTFS Large Plot Forest Dynamics Analyses


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Documentation for package ‘CTFS’ version 1.00

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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