DOI: 10.5061/dryad.wwpzgmsqx
title: Severity outweighs pyrodiversity in shaping avian and bat species distributions following an oak woodland mega-fire

description: Anthropogenic pressures have altered fire regimes across the western
 United States. These altered fire regimes, and the megafires they often
 produce, threaten ecologically and economically critical ecosystems and
 biodiversity across this region. Oak woodland savannas may be particularly
 sensitive to altered fire regimes, but there remains a significant gap in
 our understanding of how different characteristics of wildfire impact
 these ecosystems and the wildlife species that reside within them. In this
 study, we used an occupancy modeling framework to investigate how fire
 severity and pyrodiversity, the diversity of severity patches, impact the
 distributions of bird and bat species assemblages following a major
 wildfire in northern California. We used acoustic monitors deployed across
 the Hopland Research and Extension Center following the 2018 Mendocino
 Complex Fire and compared how patterns of fire severity and pyrodiversity
 influence habitat preferences across a diverse community of woodland bird
 and bat species. We found that fire enhances habitat use and increased
 occupancy for several species and species-groups across both taxonomic
 groups. Specifically, low to moderate severity fire increased occupancy
 for several species and species-groups. Pyrodiversity had smaller,
 negligible effects on species distributions relative to fire severity.
 Fires that reproduce the natural heterogeneity of oak woodland landscapes
 are likely key in sustaining high biodiversity across oak woodland
 ecosystems.  
description: # Severity outweighs pyrodiversity in shaping avian and bat species
 distributions following an oak woodland mega fire This code explores the
 impacts of wildfire on the distributions of bird and bat species following
 a megafire in Mendocino County, CA, USA. Megafire dramatically alter
 landscapes and habitat that may impact the long-term distributions of
 native wildlife species. Though these effects have been described in
 forested systems in the Western US, little work has examined the impacts
 of these types of fires in biodiverse oak woodlands. Alternatively,
 certain characteristics of wildfire (i.e. severity and pyrodiversity) may
 also enhance habtiat for certain species by creating new habitat types and
 niches for certain species groups. In this study, we use a combination of
 biodivesity monitoring techniques, namely Acoustic Recording Units (ARUs),
 and occupancy modeling techniques to describe the variable effects of
 wildfire on a community of bird and bat species to inform future
 management and conservation of these populations. ## Data Collection This
 code explores the impacts of wildfire on the distributions of bird and bat
 species following a mega-fire in Mendocino County, CA, USA. Megafire
 dramatically alters landscapes and habitats that may impact the long-term
 distributions of native wildlife species. Though these effects have been
 described in forested systems in the Western US, little work has examined
 the impacts of these types of fires in biodiverse oak woodlands.
 Alternatively, certain characteristics of wildfire (i.e. severity and
 pyrodiversity) may also enhance habitat for certain species by creating
 new habitat types and niches for certain species groups. In this study, we
 use a combination of biodivesity monitoring techniques, namely Acoustic
 Recording Units (ARUs), and occupancy modeling techniques to describe the
 variable effects of wildfire on a community of bird and bat species to
 inform future management and conservation of these populations. ##
 Analysis Methods We use four primary analysis methods to examine how
 characteristics of wildfire influences the distributions of bird and bat
 communities: 1. Bird Community Occupancy Model - Multi-species occupancy
 model that examines the influence of fire severity and pyrodiversity on
 individual bird species and the bird community as a whole. 2. Bird Nesting
 Group Occupancy Model - Multi-species occupancy model that examines the
 influence of fire severity and pyropdiversity across bird nesting guild
 groups. 3. Bird Diet Group Occupoancy Model - Multi-species occupancy
 model that examines the influence of fire severity and pyrodiversity
 across bird diet guild groups. 4. Bat Cmmunity Occupancy Model -
 Multi-species occupancy model that examines the influence of fire severity
 and pyrodiversity on individual bat species and the bat community as a
 whole. ## Data 1. "bird_record_table.csv" - Table with all raw
 detections of bird species used to create detection history matrices for
 occupancy models Species: Common name of detected animal species
 scientific_name: Scientific name of detected animal species filepath:
 Location of .wav file run through BirNet to obtain species classifcations
 start: Time (in seconds) when the BirdNet 3-second detection clip of a
 species begins in the .wav file end: Time (in seconds) when the BirdNet
 3-second deteection clip of a species ends in the .wav file confidence:
 BirdNet confidence score of species classification used for creating
 species-specific confidence thresholds of false postives filenmae: Name of
 BirdNet output file of classified .wav file Site: Name of unique sampling
 site at the Hopland Research and Extension Center Sunrise: Categorical
 variable, denotes when the ARU was recording (before, during, or after
 sunrise) Date: Calendar date when the detection was recorded detectionID:
 Unique identifier of species detections (Site, Date, Sunrise, Start, End)
 Year: Year that the species was detected Site_ID: Unique Site identifer
 used for modeling, site-year Max False Positive Score: Highest
 species-specific confidence score at which a false positive was detected
 Score Threshold: Species-specific confidnece threshold used to filter
 probable false positives based on "Max False Postive Score".
 Calculated as "Max False Positive Score" + 0.05 2.
 "bat_record_table.csv" - Table with all raw detections of bat
 species used to create detection history matrices for occupancy models
 Filename: Name of recorded .wav file from SongMeter Minibat Species:
 Abbreviated bat speceis code names for detected animal species Site: Name
 of unique sampling site at the Hopland Research and Extension Center
 Monitoring Night: Date of night sampled when animal species was detected
 Year: Year when animal species was detected Site_ID: Unique Site identifer
 used for modeling, site-year 3. "group_info.csv" - Table with
 bird species nesting and diest groupings used in group occupancy models
 Species: Common name of animal species scientific_name: Scientific name of
 animal species Nesting: Categorial; nesting life history of bird (primary
 cavity, secondary cavity, shrub, tree, or ground) Diet: Categoricall; diet
 life history of bird (insectivore, granivore, nectar, or omnivore)
 Include: Categorical; indication whether to include listed speceis in
 occupancy model (Y/N) 4. "audiomoth_metadata.csv" - Site
 metadata used in bird occupancy models Site_ID: Unique Site identifer used
 for modeling, site-year Site: Name of unique sampling site at the Hopland
 Research and Extension Center Year: Year when animal species was detected
 Elevation: Mean Elevational height of sampling site (meters) taken from a
 100-meter buffer Elevation_500: Mean Elevatonal height of sampling site
 (meters) taken from a 500-meter buffer Canopy_2020: Percentage (%) canopy
 cover surrounding sampling site in a 100-meter buffer, measured 2 years
 following the 2018 Mendocino Complex Fire chap: Percent (%) chaparral
 landcover from a 100-meter buffer surrounding the site wood: Percent (%)
 woodland landcover from a 100-meter buffer surrounding the site chap_500:
 Percent (%) chaparral landcover from a 500-meter buffer surrounding the
 site wood_500: Percent (%) chaparral landcover from a 500-meter buffer
 surrounding the site CBI: Composite Burn Index; continuous measure of fire
 severity; average across a 100-meter buffer surroudning the sampling site
 CBI_500: Composite Burn Index; continuous measure of fire severity;
 average across a 500-meter buffer surroudning the sampling site
 pyrodiversity_residuals: Continuous measure of pyrodiversity calculated as
 the residual term of the equation: Severity_StandardDeviationi =
 Severity_meani + Severity2i; severity (CBI) taken at a 500-meter buffer
 surrounding sampling sites pyrodiversity_residuals100: Continuous measure
 of pyrodiversity calculated as the residual term of the equation:
 Severity_StandardDeviationi = Severity_meani + Severity2i; severity (CBI)
 taken at a 100-meter buffer surrounding sampling sites CBI_isidi: Inverse
 Simpson's Diversity Index of categorical severity patches within a
 500-meter buffer of the sampling site. 5. "minibat_metadata.csv"
 - Site metadata used in bat occupancy models Site_ID: Unique Site
 identifer used for modeling, site-year Site: Name of unique sampling site
 at the Hopland Research and Extension Center Year: Year when animal
 species was detected Elevation: Mean Elevational height of sampling site
 (meters) taken from a 100-meter buffer Elevation_500: Mean Elevatonal
 height of sampling site (meters) taken from a 500-meter buffer
 Canopy_2020: Percentage (%) canopy cover surrounding sampling site in a
 100-meter buffer, measured 2 years following the 2018 Mendocino Complex
 Fire chap: Percent (%) chaparral landcover from a 100-meter buffer
 surrounding the site wood: Percent (%) woodland landcover from a 100-meter
 buffer surrounding the site chap_500: Percent (%) chaparral landcover from
 a 500-meter buffer surrounding the site wood_500: Percent (%) chaparral
 landcover from a 500-meter buffer surrounding the site CBI: Composite Burn
 Index; continuous measure of fire severity; average across a 100-meter
 buffer surroudning the sampling site CBI_500: Composite Burn Index;
 continuous measure of fire severity; average across a 500-meter buffer
 surroudning the sampling site pyrodiversity_residuals: Continuous measure
 of pyrodiversity calculated as the residual term of the equation:
 Severity_StandardDeviationi = Severity_meani + Severity2i; severity (CBI)
 taken at a 500-meter buffer surrounding sampling sites
 pyrodiversity_residuals100: Continuous measure of pyrodiversity calculated
 as the residual term of the equation: Severity_StandardDeviationi =
 Severity_meani + Severity2i; severity (CBI) taken at a 100-meter buffer
 surrounding sampling sites CBI_isidi: Inverse Simpson's Diversity
 Index of categorical severity patches within a 500-meter buffer of the
 sampling site. 6. "am_temp_log.csv" - log of temperature data
 recorded on dates when audiomoths were active Date: Calendar date of
 temperature recording Time: Time that temperature recording twas logged
 Temp_Avg: Average temperature of sampled date (F) Temp_Max: Maximum
 recorded temperature of sampled date (F) Temp_Min: Minimum recorded
 temperature of sampled date (F) 7. "mb_temp_log.csv" - log of
 temperature data recorded on dates when minibats were active Date:
 Calendar date of temperature recording Time: Time that temperature
 recording twas logged Temp_Avg: Average temperature of sampled date (F)
 Temp_Max: Maximum recorded temperature of sampled date (F) Temp_Min:
 Minimum recorded temperature of sampled date (F) 8.
 "am_wind_log.csv" - log of wind speed data recorded when
 audiomoths were active Date: Calendar date of wind speed recording Time:
 Time that wind speed recording was logged Wind_Avg: Average wind speed of
 sampled date (mph) Wind_Max: MAximum wind speed of sampled date (mph) 9.
 "mb_wind_log.csv" - log of wind speed data recorded when minbat
 were active Date: Calendar date of wind speed recording Time: Time that
 wind speed recording was logged Wind_Avg: Average wind speed of sampled
 date (mph) Wind_Max: MAximum wind speed of sampled date (mph) 10.
 "audiomoth_oplopg_phase123.csv" - Full operational log of dates
 when audiomoths were actively sampling Site: Unique Site identifer used
 for modeling, site-year Start: Calendar date when site was first sampled
 End: Calendar date when site was last sampled Problem1_from: Calendar date
 when an audiomoth was non-operational at a site before the "End"
 date of a site Problem1_to: Calendar date when an audiomoth became
 operational again at a site following "Problem1_from"
 Problem2_from: Calendar date when an audiomoth was non-operational at a
 site before the "End" date of a site; following
 "Problem1_to" Problem2_to: Calendar date when an audiomoth
 became operational again at a site following "Problem2_from"
 no_days: Summed number of days the site was sampled by an audimoth 11.
 "audiomoth_oplopg_phase123AprJul.csv" - Operational log of dates
 when audiomoths were actively sampling, limited to season of interest for
 study (April - July) Site: Unique Site identifer used for modeling,
 site-year Start: Calendar date when site was first sampled End: Calendar
 date when site was last sampled Problem1_from: Calendar date when an
 audiomoth was non-operational at a site before the "End" date of
 a site Problem1_to: Calendar date when an audiomoth became operational
 again at a site following "Problem1_from" Problem2_from:
 Calendar date when an audiomoth was non-operational at a site before the
 "End" date of a site; following "Problem1_to"
 Problem2_to: Calendar date when an audiomoth became operational again at a
 site following "Problem2_from" no_days: Summed number of days
 the site was sampled by an audimoth 12. "MiniBat Log.csv" -
 Operational log of dates when minibats were actively sampling at sites
 Site_ID: Unique Site identifer used for modeling, site-year Start:
 Calendar date when site was first sampled End: Calendar date when site was
 last sampled Nights Sampled: Number of nights the site was sampled by a
 minibat 13 - 63) - Species-specific detection history CSVs. For each
 modeled species (12 bats, 39 birds) we created species-specific detection
 histories denoting whether or not a species was detected on a certain
 date. In each [Species]_detection_history.csv, the rows of the matrix
 correspond to sampled site years (A03_2020) and columns correspond to date
 ranges of detection sampling ("2020-04-23_2020-04-23"). A zero
 (0) indicates a a species was not detected at the corresponding site and
 date range, a one (1) indicates at least on individual of that species was
 detected at the corresponding site and date range, and an NA indicates
 that sampling at that site was non-operational during that period. List of
 speies detection tables: **Bats**: 13\)
 "Anpa_detection_history.csv" (Pallid Bat) 14\)
 "Epfu_detection_history.csv" (Big Brown Bat) 15\)
 "Labl_detection_history.csv" (Western Red Bat) 16\)
 "Laci_detection_history.csv" (Hoary Bat) 17\)
 "Lano_detection_history.csv" (Silver-haired Bat) 18\)
 "Myca_detection_history.csv" (California Myotis) 19\)
 "Myev_detection_history.csv" (Long-eared Myotis) 20\)
 "Mylu_detection_history.csv" (Little Brown Bat) 21\)
 "Myth_detection_history.csv" (Fringed Myotis) 22\)
 "Myyu_detection_history.csv" (Yuma Myotis) 23\)
 "Pahe_detection_history.csv" (Canyon Bat) 24\)
 "Tabr_detection_history.csv" (Mexican Free-tailed Bat)
 **Birds**: 25\) "Acorn Woodpecker_detection_history.csv" 26\)
 "American Robin_detection_history.csv" 27\) "Anna's
 Hummingbird_detection_history.csv" 28\) "Ash-throated
 Flycatcher_detection_history.csv" 29\) "Bewick's
 Wren_detection_history.csv" 30\) "Black
 Phoebe_detection_history.csv" 31\) "Black-headed
 Grosebeak_detection_history.csv" 32\) "Black-throated Gray
 Warbler.csv" 33\) "Blue-gray
 Gnatcatcher_detection_history.csv" 34\) "Brown-headed
 Cowbird_detection_history.csv" 35\) "Bullock's
 Oriole_detection_history.csv" 36\)
 "Bushtit_detection_history.csv" 37\) "California
 Quail_detection_history.csv" 38\) "California
 Scrub-Jay_detection_history.csv" 39\) "California
 Towhee_detection_history.csv" 40\) "Common
 Raven_detection_history.csv" 41\) "Dark-eyed
 Junco_detection_history.csv" 42\) "House
 Finch_detection_history.csv" 43\) "Lazuli
 Bunting_detection_history.csv" 44\) "Lesser
 Goldfinch_detection_history.csv" 45\) "Mountain
 Quail_detection_history.csv" 46\) "Mourning
 Dove_detection_history.csv" 47\) "Northern
 Flicker_detection_history.csv" 48\) "Nuttall's
 Woodpecker_detection_history.csv" 49\) "Oak
 Titmouse_detection_history.csv" 50\) "Orange-crowned
 Warbler_detection_history.csv" 51\) "Pacific-slope
 Flycatcher_detection_history.csv" 52\) "Pileated
 Woodpecker_detection_history.csv" 53\) "Rufous-crowned
 Sparrow_detection_history.csv" 54\) "Spotted
 Towhee_detection_history.csv" 55\) "Steller's
 Jay_detection_history.csv" 56\) "Violet-green
 Swallow_detection_history.csv" 57\) "Warbling
 Vireo_detection_history.csv" 58\) "Western
 Bluebird_detection_history.csv" 59\) "Western
 Kingbird_detection_history.csv" 60\) "Western
 Meadowlark_detection_history.csv" 61\) "Wester
 Wood-Peewee_detection_history.csv" 62\) "White-breasted
 Nuthatch_detection_history.csv" 63\)
 "Wrentit_detection_history.csv" ## R Scripts 1. "Bird
 MultiSppOccu Setup Severity.R" - Script for preparing detection
 histories, metadata, and priors for bird multi-species occupancy models
 testing the effects of fire severity. 2. "Bird Community Occ Model
 Severity.R" - Script for running bird multi-species occupancy model
 for bird community model testing the effects of fire severity 3.
 "Bird Group Occ Model Severity.R" - Script for running bird
 nesting group and bird diet group ocucpancy models testing the effects of
 fire severity 4. "Bat MultiSppOccu Setup Severity.R" - Script
 for preparing detection histories, metadata, and priprs for bat
 multi-species occupancy model testing the effects of fire severity 5.
 "Bat Community Occ Model Severity.R" - Script for running bat
 community multi-species occupancy model testing the effects of fire
 severity 6. "visualizations.R" - Script for visualizing results
 of bird and bat multi-species occupancy models 7. "Bird MultiSppOccu
 Setup Pyrodiversity.R" - Script for preparing detection histories,
 metadata, and priors for bird multi-species occupancy models testing the
 effects of pyrodiversity. 8. "Bird Community Occ Model
 Pyrodiversity.R" - Script for running bird multi-species occupancy
 model for bird community model testing the effects of pyrodiversity 9.
 "Bird Group Occ Model Pyrodiversity.R" - Script for running bird
 nesting group and bird diet group ocucpancy models testing the effects of
 pyrodiversity 10. "Bat MultiSppOccu Setup Pyrodiversity.R" -
 Script for preparing detection histories, metadata, and priprs for bat
 multi-species occupancy model testing the effects of pyrodiversity 11.
 "Bat Community Occ Model Pyrodiversity.R" - Script for running
 bat community multi-species occupancy model testing the effects of
 pyrodiversity