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