CTFS R-Format Tables

R. Condit

Full Tree Tables

Download Full Tree Table Documention File (PDF)

These tables are stored in files Plotname.full#.rdata, where # refers to the census number. The R object within is a dataframe of the same name. There is one le and one dataframe for each census.

All the full dataframes from one plot have exactly the same number of rows, with one row for every tree ever found in any census, in exactly the same order. Trees thus appear before they recruit, while they are alive, and after they die. Because rows match, it is convenient to work with multiple censuses, as if all the data were in one table. Additionally, because tables from every census have precisely the same format, identical analyses can easily be repeated on more than one census, and demographic rates can be calculated between any pair of censuses.

Description of columns in the full R format tables. Each row is data from a single tree. If a tree has multiple stems, the dbh of only one is given. Usually, the same stem of a tree appears in this table in successive censuses, unless that stem was lost or damaged. The stemID is used to determine whether the stem changed. Usually, the largest stem is the one whose dbh is given, but not always (see the stem for all dbh's). The biomass in this table, though, is for the entire tree, or the sum of the biomass of each stem.

Column nameDescription
tagTag number used in the field.
StemTagTag number on the individual stem, if present.
treeIDThe unique tree identifier in CTFS database. Useful to be certain in matching trees.
stemIDThe unique stem identifier in CTFS database. Useful to be certain in matching stems.
spThe species mnemonic. Full Latin name can be found in the R Analytical Species Table (spptable) for each plot, or in the Taxonomy Report at http:/ctfs.arnarb.harvard.edu/CTFSReports. This mnemonic is crucial in joining various databases, for instance The Full Tree and Stem tables to the Species tables and Wood Density Table
quadratQuadrat designation
gxThe x coordinate within the plot, relative to one edge of the plot.
gyThe y coordinate within the plot, relative to one edge of the plot.
MeasureIDThe unique identifier of a single measurement in the CTFS database.
CensusIDThe numeric identifier of the census.
dbhDiameter of the stem.
pomThe point-of-measure, where the diameter was taken, identical to hom, but a character variable with only 2 decimal places.
ExactDateThe date on which the steam was measured.
DFstatusThe status taken from the DFtemp table of the CTFS database: alive, dead, lost_stem, missing, or prior
codesThe codes for the measurement as recorded in the field.
statusAn abbreviated version of status, for compatibility with earlier versions of functions in the CTFS R package; A, D, M, P
dateThe julian date, for date arithmetic.
agbAbove-ground-biomass of the stem, in Mg (= metric tons or 10^6 grams). Some are NA.
homThe height-of-measure, identical to pom but a numeric variable with full precision.
nostemsThe number of living stems on the date of measurement.

Note on DFStatus: Alive (A) and dead (D) refer to the entire tree, so if any stem is alive, the tree is alive, and a tree is only dead when every stem is dead. Status = 'lost_stem' indicates that the stem had the associated code; it usually means the was broken in the given census, while the tree had no other stem. Status = 'missing' (M) are cases where dbh are codes for a tree were not given, so it is not certain whether the tree was alive or dead. Status = 'prior' (P) indicates a tree had not yet recruited at this census. The lost_stem status is now deprecated, since it should always be safer to check stemID to determine whether a tree's measurement changed stems between censuses.