Description of the data and file structure

Data from sonic tomography (Picus 3, Argus Electronic GmbH) of 1744 live tree on the 50-ha Forest Dynamics Plot (FDP) on Barro Colorado Island, Republic of Panama, (2012-2014) to evaluate the extent of internal wood decay. The data are in a spreadsheet in .csv format.

Files and variables

File: ScannedTreeCleanData_20160510.csv

This file contains all of the data we used in our analyses.

Variables

• tag: Unique tag number for each tree on the FDP.
• code6: Six-letter tree species code used on the FDP.
• Qx: Position of quadrat (20m x 20m) in easterly direction on FDP where tree found.
• Qy: Position of quadrat (20m x 20m) in northerly direction on FDP where tree found.
• lx: Tree distance (m) east of the south-west corner of the quadrat.
• ly: Tree distance (m) north of the south-west corner of the quadrat.
• dbh2010: Diameter (mm) of tree at 1.3 m height in 2010 census of the FDP. Measured with a fabric diameter tape.
• circum: Circumference of the tree at 1 m height measured at time of tomography. Measured with a fabric measuring tape stretched around trunk, so measurement is a convex hull.
• perim: Perimeter of the tree at 1 m height measured at time of tomography. Fabric measuring tape follows the contour of the trunk, rather than stretching tight as for circum.
• irreg: Ratio of perim to circum. The larger the value, the more irregular the shape of the trunk.
• clavoNorth: The identification number of the nail positioned on the north side of the tree for tomography. Allows for comparison of tomogram image to specific position on tree.
• species: Genus and species name of tree.
• scandate: Date of tomography given as month/day/year.
• clavoPole1: The identification number of the nail used as pole 1 for tomography.
• clavoPole2: The identification number of the nail used as pole 2 for tomography.
• status: Tree status codes at time of tomography. S = apparently healthy, H = trunk hollow, Y = trunk fallen with roots exposed, Q = trunk broken, DC = trunk dead and fallen, DS = trunk dead and standing.
• healthy: Categorical notation of whether trunk is healthy (corresponds to status = S) or not_healthy (any other status, but still alive).
• hollow: Categorical notation of whether trunk is visibly hollow or not_hollow (based on if status = H)
• fallen: Categorical notation of whether trunk is fallen but alive (based on status = Y).
• broken: Categorical notation of whether trunk is broken but alive (based on status = Q).
• associados: List of visible associates of trunk. N = no associates, F = macroscopic reproductive structures of wood-decay fungi, H = ant nest, C = termite nest or trails, L = lianas or epiphytic plants on tree trunk.
• termites: Categorical notation of whether trunk has termite associates from associados = C.
• fungi: Categorical notation of whether trunk has macroscopic reproductive structure of wood-decay fungi, from associados = H.
• ants: Categorical notation of whether trunk has ant associates from associados = H.
• lianas: Categorical notation of whether trunk has liana or epiphytic plant associates on trunk, from associados = L.
• associates: Categorical notation of whether trunk has any noted associates (associados = F, H, C, or L) or not (no_associates) from associados = N.
• gx: Global coordinates of tree in m east from south-west corner of FDP. Calculated as Qx x 20 + lx.
• gy: Global coordinates of tree in m north from south-west corner of FDP. Calculated as Qy x 20 + ly.
• abund1cm: Abundance of stems (larger that 1 cm diameter) of that species across the entire 50-ha FDP as reported in the 2010 FDP census.
• abund20cm: Abundance of stems (larger that 20 cm diameter) of that species across the entire 50-ha FDP as reported in the 2010 FDP census.
• BA_m2: Total basal area (in meters squared) of that species across the entire 50-ha FDP as reported in the 2010 FDP census.
• meanDBHmm: Mean diameter (mm) of all stems of that species across the entire 50-ha FDP as reported in the 2010 FDP census.
• medianDBHmm: Median diameter (mm) of all stems of that species across the entire 50-ha FDP as reported in the 2010 FDP census.
• maxDBHmm: Maximum diameter (mm) of all stems of that species across the entire 50-ha FDP as reported in the 2010 FDP census.
• filename: Name of spreadsheet with all field-collected data for tomography of that tree.
• scanned: Designation that the tomography of that tree was completed (scanned = completed). All trees in this data set were scanned.
• pitAssess: Visual assessment of whether internal decay was present in the tree based on examination of the tomogram image. healthy = no decay visible on tomogram, decay = decay visible on tomogram.
• Decay: Binary coding of pitAssess; 1 = decay visible on tomogram, 0 = decay not visible on tomogram.
• full_area: Cross-sectional area of the trunk in the tomography in square cm.
• decay_area: Cross-sectional area showing decay (green, blue, magenta) in the tomography in square cm.
• severe_area: Cross-sectional area showing severe decay (blue and magenta) in the tomography in square cm.
• outline_area: Area of tomography image with annotations including the blue outline of the trunk, in square cm. This area is removed from each of the area measurements before calculating decay_prop.
• decay_prop: Proportion of the cross-sectional area of the trunk showing decay, calculated as (decay_area - outline_area)/(full_area - outline_area).
• pitjpgfile: Name of file showing the Picus3 tomogram image for that tree.

Sharing/Access information

Data are published under the CCO license waiver; we encourage interested parties to contact us to discuss collaboration.

Data was derived from the following sources:

Most data were collected for this study.

FDP data from the 2010 census were derived from Condit R., Perez, R., Aguilar, S., Lao, S., Foster, R., Hubbell, S.P. 2019. Complete data from the Barro Colorado 50-ha plot: 423617 trees, 35 years, 2019 version. https://doi.org/10.15146/5xcp-0d46.
Those variables include the following: tag, code6, Qx, Qy, lx, ly, dbh2010, gx, gy, abund1cm, abund20cm, BA_m2, meanDBHmm, medianDBHmm, maxDBHmm.

Code/Software

The data may be viewed in Microsoft Excel or R.

We used R version 4.4.2 and RStudio v. 2024.12 to analyze the data along with packages tidyverse, reshape2, picante, metR, mgcv, VGAM, and RColorBrewer.