DOI: 10.5061/dryad.kprr4xhfx
title: Data for: Hidden decay of live trees in a tropical rain forest

description: These data are associated with a study to assess the scale and patterns of
 internal wood decay in live trees of the tropical forest on Barro Colorado
 Island, Republic of Panama.  We used acoustic tomography to
 measure prevalence and severity of decay in 1744 live trees (&gt; 20
 cm diameter) of 171 species on the 50-ha Forest Dynamics Plot. Most trees
 showed some signs of internal decay, with larger trees suffering more
 decay. Decay prevalence and severity varied among species. The results
 suggest that that hidden wood decay affects a large proportion of living
 tropical forest trees.
description: Internal decay of wood in trunks of live trees was measured using
 sonic tomography (Picus 3, Argus Electronic GmbH) on trees on the 50-ha
 Forest Dynamics Plot on Barro Colorado Island, Republic of
 Panama. 
description: # Data for: Hidden decay of live trees in a tropical rain forest ##
 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](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.