﻿This R.tunneyi.FireExperiment_READ_ME.txt file was generated on 2021-02-10 by Robyn Shaw


GENERAL INFORMATION

1. Title of Dataset: Unburnt habitat patches are critical for survival and in situ population recovery in a small mammal after fire

2. Author Information
	A. Principal Investigator Contact Information
		Name: Robyn E Shaw
		Institution: Current: Murdoch University
		Address: 90 South Street, Murdoch, Perth, Western Australia
		Email: robyn.shaw@murdoch.edu.au

	B. Associate or Co-investigator Contact Information
		Name: Sam C Banks
		Institution: Charles Darwin University
		Address: Ellengowan Drive, Casuarina, Darwin, Northern Territory
		Email: sam.banks@cdu.edu.au

	C. Alternate Contact Information
		Name: Robyn E Shaw
		Institution: Department of Biodiversity, Conservation and Attractions
		Address: 17 Dick Perry drive, Kensington, Perth, Western Australia
		Email: robyn.shaw@dbca.wa.gov.au

3. Date of data collection (single date, range, approximate date): 
Session 1: 2015-03-10 to 2015-05-11
Session 2: 2015-05-03 to 2015-06-26
Session 3: 2016-04-03 to 2016-06-17

4. Geographic location of data collection:
Mornington Wildlife Sanctuary, Central Kimberley, Western Australia (Lat: -17.54923, Lon: 126.10792)

5. Information about funding sources that supported the collection of the data: 
The Australian Wildlife Conservancy provided equipment, facilities, guidance and field support.
Funding for this project was provided by an Australian Research Council Future Fellowship awarded to Same C Banks (FT130100043).
Robyn E Shaw was awarded the Holsworth Wildlife Research Endowment, 
the Australian Academy of Science Margaret Middleton Fund and
the Royal Zoological Society of NSW Paddy Pallin Science Grant in support of this project. 
Robyn E Shaw was also supported by an Australian Postgraduate Award.

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: 
N/A

2. Links to publications that cite or use the data: 
Shaw, R. E et al. (2021), Unburnt habitat patches are critical for survival and in situ population recovery in a small mammal after fire. Journal of Applied Ecology, https://doi.org/10.1111/1365-2664.13846
Shaw, R. E. (2018) The genetic consequences of demography and disturbance in small mammal populations. The Australian National University, https://doi.org/10.25911/5d612054710c2

3. Links to other publicly accessible locations of the data: 
N/A

4. Links/relationships to ancillary data sets: 
N/A

5. Was data derived from another source? 
No

6. Recommended citation for this dataset: 
Shaw, Robyn E et al. (2021), Unburnt habitat patches are critical for survival and in situ population recovery in a small mammal after fire , Dryad, Dataset, https://doi.org/10.5061/dryad.tmpg4f4xs


DATA & FILE OVERVIEW

1. File List: 
Prelim_Supp_R_code.docx
- Full R code and documentation for preliminary analyses.

Full_R_code.docx
- Full R code and documentation for all analyses in manuscript.

SECR
- Zipped folder containing recapture data used for supplementary spatially explicit capture recapture analysis, to determine if capture rate approximates abundance.

Patchiness_Index.xlsx
- Data/calculation of patchiness index.

Recaptures_per_Site.csv
- Capture-mark-recapture data.

Trap_Autocorrelation.csv
- Data for preliminary trap spatial autocorrelation analysis.

Trap_Data.csv
- Capture data and trap/site meta-data over three trapping sessions.

Trap_Data_Sex_Age.csv
- Capture data and trap/site meta-data over three trapping sessions, split into sex and age.

Veg_Point_Intercept_Data.csv
- Vegetation survey data.


2. Relationship between files, if important: 
"Prelim_Supp_R_code.docx" and "Full_R_code.docx" document the complete R code required to replicate analyses published in the Shaw et al. 2021 (https://doi.org/10.1111/1365-2664.13846), using the data provided.

3. Additional related data collected that was not included in the current data package: 
N/A

4. Are there multiple versions of the dataset? 
No 


METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 
See Shaw et al. 2021 (https://doi.org/10.1111/1365-2664.13846) for full methods and "Prelim_Supp_R_code.docx" and "Full_R_code.docx" for full documentation of analyses.

2. Methods for processing the data: 
See "Prelim_Supp_R_code.docx" and "Full_R_code.docx" for full documentation of processing and analyses.

3. Instrument- or software-specific information needed to interpret the data: 
See "Prelim_Supp_R_code.docx" and "Full_R_code.docx" for full documentation of processing and analyses.

4. Environmental/experimental conditions: 
See Shaw et al. 2021 (https://doi.org/10.1111/1365-2664.13846)


DATA-SPECIFIC INFORMATION FOR: Prelim_Supp_R_code.docx
This is a word document of the Rmarkdown file for all preliminary and supplementary analyses performed in Shaw et al. 2021 (https://doi.org/10.1111/1365-2664.13846). Code chunks are provided in the grey boxes and details are provided for the relevant datasets, R packages and specific functions/analyses used.


DATA-SPECIFIC INFORMATION FOR: Full_R_code.docx
This is a word document of the Rmarkdown file for all analyses performed in the main manuscript Shaw et al. 2021 (https://doi.org/10.1111/1365-2664.13846). Code chunks are provided in the grey boxes and details are provided for the relevant datasets, R packages and specific functions/analyses used.


DATA-SPECIFIC INFORMATION FOR: SECR
This is a zipped folder containing 21 capture history text files and 21 trap history text files for secr analysis.
There is 1 capture history and 1 trap history text file for each site and session.
There is one total capture history and trap history file for the whole study.
There is one capture history and trap history file for between session recaptures.
All analyses these files were used in are described in "Prelim_Supp_R_code.docx"

Capture history variables:
Session: Trapping session
ID: R. tunneyi IDs - individually identified using microchips
Occasion: Trap night individual was recorded
Detector: Trap recorded at

Trap history variables:
Detector: trap code
X: UTMX (Zone 52K)
Y: UTMY (Zone 52K)


DATA-SPECIFIC INFORMATION FOR: Patchiness_Index.xlsx

1. Number of variables: 
12

2. Number of cases/rows: 
10

3. Variable List: 
Site: Study site/location codes.
Burnt: Number of trap points where vegetation fully burnt
Patchy: Number of trap points where vegetation patchily burnt
Unconnected burn points_2: Number of trap points where burn scar is not connected to burns at other trap points
Edge: Number of trap points at the edge of burn
Unburnt: Number of unburnt trap points
Grand Total: Total trap points
Burnt points/total points: Calculation
Unburnt points/total points: Calculation
Unconnected burn points/total points: Calculation
Unburnt.weighted: Calculation
Index: Patchiness Index

4. Missing data codes: 
None

5. Specialized formats or other abbreviations used: 
N/A


DATA-SPECIFIC INFORMATION FOR: Recaptures_per_Site.csv

1. Number of variables: 
13

2. Number of cases/rows: 
10

3. Variable List: 
Group: Group codes (two paired sites, a priori assigned as experimental and control)
Site: Study site/location codes.
S1_S2: Individuals marked in session 1, recaptured in session 2
S2_S3: Individuals marked in session 2, recaptured in session 3
S1_S3: Individuals marked in session 1, recaptured in session 3
Total_Chipped_S1: Total number of individuals marked with a microchip in session 1
Total_Chipped_S2: Total number of individuals marked with a microchip in session 2
Total_Chipped: Total number of individuals marked with a microchip in session 1 + 2
S1_S2_Recap_Rate: S1_S2/Total_Chipped_S1
S1_S3_Recap_Rate: S1_S3/Total_Chipped_S3
S2_S3_Recap_Rate: S2_S3/Total_Chipped
Burn_status_at_site: Fire experiment treatment
Prop_Site_Burnt: Proportion of the site that was burnt

4. Missing data codes: 
None

5. Specialized formats or other abbreviations used: 
N/A


DATA-SPECIFIC INFORMATION FOR: Trap_Autocorrelation.csv

1. Number of variables: 
5

2. Number of cases/rows: 
20

3. Variable List: 
DC: Distance class (metres)
Session: Trapping session 
r: The multilocus genetic spatial autocorrelation r value, as calculated by GenAlEx
Uerr: Upper error
Lerr: Lower error

4. Missing data codes: 
None

5. Specialized formats or other abbreviations used: 
Session: S = session, T_S2 = treatment sites in session 2


DATA-SPECIFIC INFORMATION FOR: Trap_Data.csv

1. Number of variables: 
47

2. Number of cases/rows: 
3050

3. Variable List: 
Group: Group codes (two paired sites, a priori assigned as experimental and control)
Site: Study site/location codes
Trap: Trap location code
Session: Trapping session 
Session_Trap: Combined site/session identifier
Longitude: Location in decimal degrees
Latitude: Location in decimal degrees
Easting: Location in UTMs (zone 52K)
Northing: Location in UTMs (zone 52K)
Site_TreatmentControl: Control (unburnt) or treatment (burnt)
Site_BurntTreatment: Burn treatment (thorough or patchy burn)
Burnt_at_Trap: Patchy burn, thorough burn or unburnt at trap point
Patchiness_Index: Site-level index decribing degree of patchiness
Prop_Site_Burnt: The proportion of area burnt within a 50 m buffer of the transect lines
Perc_Site_Burnt: The percentage (proportion * 100) of area burnt within a 50 m buffer of the transect lines
Perc_Site_Crk: The percentage of area covered by creek habitat within 50 m buffer of the transect lines
Perc_Site_Rip: The percentage of area covered by riparian vegetation within 50 m buffer of the transect lines
Perc_Site_Tuss: The percentage of area covered by tussock grass vegetation within 50 m buffer of the transect lines
Perc_Site_AG: The percentage of area covered by annual grassland vegetation within 50 m buffer of the transect lines
Perc_Site_MG: The percentage of area covered by mixed grassland vegetation within 50 m buffer of the transect lines
Perc_Site_Oth: The percentage of area covered by other (scalds and roads, i.e. bare ground) within 50 m buffer of the transect lines
PreVeg_at_Trap: Pre-fire dominant vegetation type at trap point
PreProp20m_Crk: The pre-fire proportion of area covered by creek habitat within a 20 m radius of the trap point
PreProp20m_Rip: The pre-fire proportion of area covered by riparian vegetation within a 20 m radius of the trap point
PreProp20m_Tuss: The pre-fire proportion of area covered by tussock grass vegetation within a 20 m radius of the trap point
PreProp20m_AG: The pre-fire proportion of area covered by annual grassland vegetation within a 20 m radius of the trap point
PreProp20m_MG: The pre-fire proportion of area covered by mixed grass vegetation within a 20 m radius of the trap point
PreProp20m_Oth: The pre-fire proportion of area covered by other (scalds and roads, i.e. bare ground) within a 20 m radius of the trap point
AFProp20m_Unburnt: The immediate post-fire proportion of area unburnt within a 20 m radius of the trap point
AFProp20m_Burnt: The immediate post-fire proportion of area burnt within a 20 m radius of the trap point
AFProp20m_Crk: The immediate post-fire proportion of area covered by creek habitat within a 20 m radius of the trap point
AFProp20m_Rip: The immediate post-fire proportion of area covered by riparian vegetation within a 20 m radius of the trap point
AFProp20m_Tuss: The immediate post-fire proportion of area covered by tussock grass vegetation within a 20 m radius of the trap point
AFProp20m_AG: The immediate post-fire proportion of area covered by annual grassland vegetation within a 20 m radius of the trap point
AFProp20m_MG: The immediate post-fire proportion of area covered by mixed grass vegetation within a 20 m radius of the trap point
AFProp20m_Oth: The immediate post-fire proportion of area covered by other (scalds and roads, i.e. bare ground) within a 20 m radius of the trap point
Total_Trap_Nights: Total nights trap open in session
Corrected_Potential_Capture_Events: Trap nights - (within session recaptures + non-target species). i.e. If the trap was occupied by an animal that had already been captured or another species, it was essentially closed for that night
Rtun_WSRecap: Within session R. tunneyi recaptures
Non_Target_Captures: Non-target species
Rtun_Total: Total number of R. tunneyi captures for trap in specified session
Rtun_F: Number of female R. tunneyi captures for trap in specified session
Rtun_M: Number of male R. tunneyi captures for trap in specified session
Rtun_Sex_NA: Number of R. tunneyi captures with unknown sex for trap in specified session
Rtun_Adult: Number of adult R. tunneyi captures for trap in specified session
Rtun_Juv_Sub: Number of juvenile and sub-adult R. tunneyi captures for trap in specified session
Rtun_Age_NA: Number of R. tunneyi captures with unknown age for trap in specified session

4. Missing data codes: 
NA

5. Specialized formats or other abbreviations used: 
Descriptive variables are detailed in Shaw et al. 2021 (https://doi.org/10.1111/1365-2664.13846).


DATA-SPECIFIC INFORMATION FOR: Trap_Data_Sex_Age.csv
Note: This dataset is identical to Trap_Data.csv, but has been reformatted to provide separate records for males/females/adults/juveniles for certain analyses.

1. Number of variables: 
43

2. Number of cases/rows: 
12200

3. Variable List: 
Group: Group codes (two paired sites, a priori assigned as experimental and control)
Site: Study site/location codes
Trap: Trap location code
Session: Trapping session 
Session_Trap: Combined site/session identifier
Longitude: Location in decimal degrees
Latitude: Location in decimal degrees
Easting: Location in UTMs (zone 52K)
Northing: Location in UTMs (zone 52K)
Site_TreatmentControl: Control (unburnt) or treatment (burnt)
Site_BurntTreatment: Burn treatment (thorough or patchy burn)
Burnt_at_Trap: Patchy burn, thorough burn or unburnt at trap point
Patchiness_Index: Site-level index decribing degree of patchiness
Prop_Site_Burnt: The proportion of area burnt within a 50 m buffer of the transect lines
Perc_Site_Burnt: The percentage (proportion * 100) of area burnt within a 50 m buffer of the transect lines
Perc_Site_Crk: The percentage of area covered by creek habitat within 50 m buffer of the transect lines
Perc_Site_Rip: The percentage of area covered by riparian vegetation within 50 m buffer of the transect lines
Perc_Site_Tuss: The percentage of area covered by tussock grass vegetation within 50 m buffer of the transect lines
Perc_Site_AG: The percentage of area covered by annual grassland vegetation within 50 m buffer of the transect lines
Perc_Site_MG: The percentage of area covered by mixed grassland vegetation within 50 m buffer of the transect lines
Perc_Site_Oth: The percentage of area covered by other (scalds and roads, i.e. bare ground) within 50 m buffer of the transect lines
PreVeg_at_Trap: Pre-fire dominant vegetation type at trap point
PreProp20m_Crk: The pre-fire proportion of area covered by creek habitat within a 20 m radius of the trap point
PreProp20m_Rip: The pre-fire proportion of area covered by riparian vegetation within a 20 m radius of the trap point
PreProp20m_Tuss: The pre-fire proportion of area covered by tussock grass vegetation within a 20 m radius of the trap point
PreProp20m_AG: The pre-fire proportion of area covered by annual grassland vegetation within a 20 m radius of the trap point
PreProp20m_MG: The pre-fire proportion of area covered by mixed grass vegetation within a 20 m radius of the trap point
PreProp20m_Oth: The pre-fire proportion of area covered by other (scalds and roads, i.e. bare ground) within a 20 m radius of the trap point
AFProp20m_Unburnt: The immediate post-fire proportion of area unburnt within a 20 m radius of the trap point
AFProp20m_Burnt: The immediate post-fire proportion of area burnt within a 20 m radius of the trap point
AFProp20m_Crk: The immediate post-fire proportion of area covered by creek habitat within a 20 m radius of the trap point
AFProp20m_Rip: The immediate post-fire proportion of area covered by riparian vegetation within a 20 m radius of the trap point
AFProp20m_Tuss: The immediate post-fire proportion of area covered by tussock grass vegetation within a 20 m radius of the trap point
AFProp20m_AG: The immediate post-fire proportion of area covered by annual grassland vegetation within a 20 m radius of the trap point
AFProp20m_MG: The immediate post-fire proportion of area covered by mixed grass vegetation within a 20 m radius of the trap point
AFProp20m_Oth: The immediate post-fire proportion of area covered by other (scalds and roads, i.e. bare ground) within a 20 m radius of the trap point
Total_Trap_Nights: Total nights trap open in session
Corrected_Potential_Capture_Events: Trap nights - (within session recaptures + non-target species). i.e. If the trap was occupied by an animal that had already been captured or another species, it was essentially closed for that night
Rtun_WSRecap: Within session R. tunneyi recaptures
Non_Target_Captures: Non-target species
Sex: Sex (male or female) of R. tunneyi captures at trap within specified session.
Age: Age (juvenile/sub-adult or adult) of R. tunneyi captures at trap within specified session.
Captures: Number of captures within sex/age category at trap within specified session.

4. Missing data codes: 
NA

5. Specialized formats or other abbreviations used: 
Descriptive variables are detailed in Shaw et al. 2021 (https://doi.org/10.1111/1365-2664.13846).


DATA-SPECIFIC INFORMATION FOR: Veg_Point_Intercept_Data.csv

1. Number of variables: 
14

2. Number of cases/rows: 
12250

3. Variable List: 
Session: Trapping session
Group: Group codes (two paired sites, a priori assigned as experimental and control)
Site: Study site/location codes
Quadrat: Unique code for permanent 10m2 quadrat, revisited throughout study
Point: 50 random points recorded for each quadrat to measure vegetation density
cm10: Point estimate at a height category of 0 - 10cm
cm30: Point estimate at a height category of 10 - 30cm
cm100: Point estimate at a height category of 30 - 100cm
Prop_Site_Burnt: The proportion of area burnt within a 50 m buffer of the transect lines
Survey_Date: DD/MM/YYYY
Veg_type: Descriptive variable for vegetation category
Quadrat_Burn_Type_S2: Burn type at quadrat
Site_Treatment_Control: Control (unburnt) or treatment (burnt), site-level
Site_Burn_Type: Burn treatment (thorough or patchy burn), site-level

4. Missing data codes: 
NA

5. Specialized formats or other abbreviations used: 
Descriptive variables are detailed in Shaw et al. 2021 (https://doi.org/10.1111/1365-2664.13846).
