CTFS R-Format Tables

R. Condit

Stem Tables

Download Stem Table Documention File (PDF)

These tables are stored in files Plotname.stem#.rdata, where # refers to the census number. The R object with is a dataframe of the same name. There is one file and one dataframe fro each census.

All the stem dataframes from one plot have exactly the same number of rows, with one row for every stem ever found in any census, in exactly the same order. Stems thus appear before they recruit, while they are alive, and after they die. See the description of the full table, which has a similar structure, but for trees, not stems.

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.
countPOMThe number of POMs (HOMs) for the same stem in this census.
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.

Note on DFStatus: Status of stems is not as clear-cut as for trees. Stems have status dead (D) only if the entire tree is dead. Stems are alive (A) only if the tree is alive and the stem has a dbh. Status = 'lost_stem' indicates that the stem was broken in the given census, while the tree has no other stem. Status = 'missing' (M) are cases where dbh and codes for a tree were not recorded (or lost), so it is not certain whether the tree was alive or dead. Status = 'prior' (P) indicates a tree had not yet recruited into the plot during the census. An additional status for stems is gone (G), in cases where a tree is alive and a stem which formerly had a measurement does not in this census. This happens in some plots, where individual stems do not have tags and cannot be tracked.