DOI: 10.25338/b8tk5p
title: Data and analysis code for "Forest recovery following extreme drought in California, USA: natural patterns and effects of pre-drought management"

description: This repository contains data and code for the paper "Forest recovery
 following extreme drought in California, USA: natural patterns and effects
 of pre-drought management" by Young et al., published in Ecological
 Applications. The abstract of the paper is as follows. Rising temperatures
 and more frequent and severe droughts are driving increases in tree
 mortality in forests around the globe. However, in many cases, the likely
 trajectories of forest recovery following drought-related mortality are
 poorly understood. In many fire-suppressed western U.S. forests,
 management is applied to reverse densification and restore natural forest
 structure and composition, but it is unclear how such management affects
 post-mortality recovery. We addressed these uncertainties by examining
 forest stands that experienced mortality during the severe drought of
 2012-2016 in California, USA. We surveyed post-drought vegetation along a
 gradient of overstory mortality severity in paired treated (mechanically
 thinned or prescribed-burned) and untreated areas in the Sierra Nevada.
 Treatment substantially reduced tree density, particularly in smaller tree
 size classes, and these effects persisted through severe drought-related
 overstory mortality. However, even in treated areas with severe mortality
 (&gt; 67% basal area mortality), the combined density of residual
 (surviving) trees (mean 44 trees ha-1) and saplings (mean 189 saplings
 ha-1) frequently (86% of plots) fell within or exceeded the natural range
 of variation (NRV) of tree density, suggesting little need for
 reforestation intervention to increase density. Residual tree densities in
 untreated high-mortality plots were significantly higher (mean 192 trees
 ha-1 and 506 saplings ha-1), and 96% of these plots met or exceeded the
 NRV. Treatment disproportionately removed shade-tolerant conifer species,
 while mortality in the drought event was concentrated in pines (Pinus
 ponderosa and P. lambertiana); as a consequence, the residual trees,
 saplings, and seedlings in treated areas, particularly those that had
 experienced moderate or high drought-related mortality, were more heavily
 dominated by broadleaf (“hardwood”) trees (particularly Quercus kelloggii
 and Q. chrysolepis). In contrast, residual trees and regeneration in
 untreated stands were heavily dominated by shade-tolerant conifer species
 (Abies concolor and Calocedrus decurrens), suggesting a need for future
 treatment. Because increased dominance of hardwoods brings benefits for
 plant and animal diversity and stand resilience, the ecological advantages
 of mechanical thinning and prescribed-fire treatments may, depending on
 the management perspective, extend even to stands that ultimately
 experience high drought-related mortality following treatment.
description: See the associated paper for a detailed description of data
 colleciton methods. Some raw plot data have been processed to a certain
 degree, following the methods described in the paper. For example,
 field-based counts of dead, down woody fuels have been converted to toal
 fuel density estimates.
description: Description of code and data files
 accompanying Young et al. (2019) "Forest recovery following extreme
 drought in California, USA: natural patterns and effects of pre-drought
 management" published in <i>Ecological
 Applications</i>  
 <b>Analysis code</b>
 <b>File:</b> Young_etal_analysis.R
 R code for fitting the Bayesian models and extracting 95%
 credible intervals for the effect of treatment on each response variable
 for each mortality severity level.  
 <b>Plot-level biotic and abiotic
 data</b> <b>File:</b>
 Young_etal_plot_data.csv Each row of this table
 provides values of various biotic and abiotic attributes of a given study
 plot. There is one row per study plot. The meaning of each column is as
 follows. <b>PlotName:</b> The unique
 identifier of the plot. <b>Forest:</b> The
 National Forest or National Park (or “BLM” for Bureau of Land Management
 land) within which the plot was located.
 <b>Treated:</b> The status of the plot as treated
 (“Y”) or not treated (“N”).
 <b>MortClass:</b> The identity of the plot category
 with respect to its drought-associated mortality severity. Options are
 “low” (0-33% basal area mortality), “moderate” (33-67% basal area
 mortality), and “high” (67-100% basal area mortality).
 <b>LiveOverstory: </b>Ocularly estimated percent
 cover of the study plot, looking directly down from above, by biomass
 belonging to live trees. <b>ShrubCover:</b>
 Ocularly estimated percent cover of the study plot, looking directly down
 from above, by biomass belonging to shrubs.
 <b>ShrubSp:</b> The USDA PLANTS database code for the
 shrub species with greatest cover within the plot.
 <b>fuel_mass_total:</b> The estimated total density
 (in kg / ha) of dead, down woody fuels, estimated as described in the
 Methods section of the manuscript this data file accompanies.
 <b>Remaining columns:</b> The
 remaining columns have three-part names in the format X_Y_Z (for example,
 "BA_Pines_L”). These columns present specific attributes of forest
 stand structure within each study plot. The meaning of the three
 components (X, Y, and Z) of the column names are as follows.
 <b>X:</b> The structure metric reported. Options are
 “BA” (basal area in sq. m / ha), “Sapling” (the number of saplings in the
 plot), “Seedling” (the number of seedlings in the plot), “Stems” (the
 total number of tree stems in the plot, including seedlings, saplings, and
 trees), “TREES” (the number of adult trees—i.e., trees larger than
 saplings—within the plot), “TREESsmall” (the number of small adult
 trees—i.e., trees smaller than 30 cm DBH), “TREESmed” (the number of
 medium-sized adult trees—i.e., trees above 30 cm DBH but below 70 cm DBH),
 “TREESlarge” (the number of large-sized adult trees—i.e., trees larger
 than 70 cm DBH). <b>Y:</b> The species
 group for which the structure metric is reported. Options are “Hdwds” for
 angiosperm (or “hardwood” or “broadleaf”) trees; “Pines” for
 <i>Pinus</i> spp., “ShadeTols” for <i>Abies
 concolor</i> and <i>Calocedrus decurrens</i>, and
 “Trees” for all tree species. <b>Z:</b> The
 category of trees for which the structure metric is reported. Options are
 “DS” (all dead trees, including recent, drought-associated mortality and
 trees dead prior to the drought), “L” (trees that were alive at the time
 of survey), and “T” (trees that were alive at the time of survey plus
 recent, drought-associated mortality). Dead trees were considered to
 reflect “recent, drought-associated mortality” if they had some dead
 needles and fine branches (see the Methods section of the manuscript this
 data file accompanies).  
 <b>Tree size distribution
 data</b> <b>File:</b>
 Young_etal_tree_size_distribution.csv Each row of this
 table provides mean live tree density for a specfiic combination of time
 period (pre-drought or post-drought), treatment status (treated or
 untreated), mortality severity (low, moderate, or high), tree size class,
 and species group. The meaning of each column is as follows.
 <b>Period:</b> Time period for which trees were
 considered “live”. Options are “Pre-drought” and “Post-drought.”
 Post-drought live trees reflect all trees that were alive at the time of
 survey. Pre-drought live trees reflect all trees that were alive at the
 time of survey plus all trees that were recently-dead at the time of
 survey (i.e., dead trees that still had some needles and fine branches
 intact). <b>Treated: </b>Identity of plot
 category with respect to whether it was treated (“Y”) or not treated
 (“N”). <b>BAmort_class:</b> The identity of
 the plot category with respect to its drought-associated mortality
 severity. Options are “low” (0-33% basal area mortality), “moderate”
 (33-67% basal area mortality), and “high” (67-100% basal area
 mortality). <b>DBH_cat:</b> The diameter at
 breast height (DBH) category for which tree density is reported. Values
 (in cm) reflect the middle of a 10-cm-wide range of DBH values. For
 example, the value 35 reflects trees between 30 and 40 cm in
 DBH. <b>SpeciesCat:</b> The species group
 for which tree density is reported. Options are “Hardwoods” (all
 angiosperm trees), “Pines” (all <i>Pinus</i> spp.), and “Shade
 tolerants” (<i>Abies concolor</i> and <i>Calocedrus
 decurrens</i>). <b>TPH:</b> Tree
 density (in trees per hectare) for the specified plot category (e.g.,
 untreated, low-mortality), time period, diameter category, and species
 group. Values reflect means across all plots representing the specified
 plot category.