Myanmar mammal occupancy baseline assessment dataset
Data files
Oct 03, 2024 version files 405.49 KB
-
MyanmarMammalOccupancyData.rar
396.49 KB
-
README.md
9 KB
Abstract
The dataset consists of detection histories extracted from camera trap dataset which is collected throughout Myanmar during 2014-2020 period. Also, the camera trapping effort matrix and covariates dataset are also included. This data comprise of a total of 47 mammal species detected during our camera trap surveys. The detection histories are extracted at 10 days per occasion in each survey site for each species. The covariate data consists of water density, elevation, terrain roughness, population density, gross primary productivity and NDVI (Normalized difference vegetation index) at five different scales (500 meters, 1000 meters, 1500 meters, 2000 meters and 4000 meters).
Dataset title:
Myanmar mammal Occupancy Baseline Assessment Dataset
https://doi.org/10.5061/dryad.0gb5mkm6w
Dataset contributors:
Kyaw, Pyae. Phyoe., Cushman, Samuel. A., Kaszta, ¸Żaneta., Burnham, Dawn., Zaw, Than. ,Naing, Hla. , Htun, Saw., Moe, Kyaw., Tun, Aung. Ye., Myo, Okka., Aung Zarni., Myo, Khin. Myo., Aung, Htet. Arkar., Po, Saw. Htoo. Tha., Po, Saw, Ehkhu., Nay, Saw. Hay., Tun, Saw. William. L., and Macdonald, David. W.
Dataset citation:
Kyaw et al (2023). Data for: Myanmar mammal occupancy baseline assessment dataset
Corresponding publication:
Kyaw et.al 2023. Seeing the big to fine-grained picture: Exploring the baseline status of mammal occupancy across Myanmar using scale optimized modelling. Diversity and Distributions. Accepted
Contact Information
- Name: Pyae Phyoe Kyaw
- Affiliations: Wildlife Conservation Research Unit, Department of Biology, University of Oxford, The Recanati-Kaplan Centre, Tubney House, Tubney, OX13 5QL
- ORCID ID: https://orcid.org/0000-0002-2763-5706
- Email: pyaephyoekyawwcs@gmail.com
- Contributor ORCID IDs:
- Pyae Phyoe Kyaw: https://orcid.org/0000-0002-2763-5706
File Contents and Structure
The dataset contains 14 Folders and 1 code file.
The folders are organized by to run multiple iterations of univariate and multivariate occupancy analyses for multiple species at multiple sites. Each folder contains multiple csv files.
The folders and their description are as below
1. AKNP_o10 : The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in AKNP site (Alaungdaw Kathapa National Park).
2. Covariates: The folder containing variables recorded or extracted for each camera trap stations.
3. EffortMatrix: The folder containing the number of days each camera trap being active per occasions for all individual survey sites.
4. HKNP17_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in HKNP survey site (Hkakaborazi National Park) in 2017.
5. HMT_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in HMT site (Htamanthi Wildlife Sanctuary).
6. MMLK_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in MMLK site (Myintmolatkhat Key Biodiversity Area).
7. MMLK16_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in a subset of MMLK site surveyed during 2016.
8. MMLK17_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in a subset of MMLK site surveyed during 2017.
9. MMLK1415_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in a subset of MMLK site surveyed during 2014-15.
10. MMLKBC1718_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in a subset of MMLK site surveyed during 2017-18.
11. MMLKPW20_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in a subset of MMLK site surveyed during 2020.
12. Myan_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in all survey sites.
13. RYER_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in RYER survey site (Rakhine Yoma Elephant Range).
14. ST_o10: The folder containing occasion matrixes (extracted at 10 days per occasion) csv files for different species detected in ST survey site (Say Taung Key Biodiversity Area).
15. Example R code to run for Asiatic golden cat in AKNP survey dataset
Description of Occasion Metrix CSVs
The occasion matrix files are named as followed. The occasion matrix is also known as detection history.
File Naming Scheme: SITE + Year(optional) + Shortened Species Name + _Each of Extracted Occasion Length for detection History (e.g. “AKNP17_Agcat_o10.csv” is the detection history file for Asiatic golden cat in Alaung Kathapa National Park in 2017).
The shortened species name codes in file names are listed below.
Abbear: Asiatic black bear
Abtporcupine: Asiatic brush-tailed porcupine
Aelephant: Asian elephant
Agcat: Asiatic golden cat
Amacaque: Assam macaque
Apcivet: Asian-palm civet
Ascotter: Asiatic small-clawed otter
banteng: Banteng
Bfbadger: Burmese ferret badger
binturong: Binturong
blinsang: Banded linsang
Bmonitor: Bengal monitor
cemongoose: Crab-eating mongoose
Cfbadger: Chinese ferret badger
cleopard: Clouded leopard
dhole: Dhole
Ewpig: Eurasian wildpig
Fmuntjac: Fea’s muntjac
gaur: Gaur
Gmuntjac: Gaungshan muntjac
hbadger: Hog badger
lcat: Leopard cat
leopard: Leopard
licivet: Large Indian civet
lmdeer: Lesser mouse-deer
lscivet: Large-spotted civet
mcat: Marbled cat
mpcivet: Masked-palm civet
Mporcupine: Malayan porcupine
Msbear: Malayan sun bear
Mserow: Mainland serow
Mtapir: Malayan tapir
Nptmacaque: Northern pig-tailed macaque
pangolin: Pangolin species
rmacaque: Rhesus macaque
rmuntjac: Red muntjac
rpanda: Red panda
rserow: Red serow
sambar: Sambar deer
sIcivet: Small Indian civet
slangur: Shortridge’s langur
slinsnag: Spotted linsang
stmacaque: Stump-tailed macaque
takin: Takin
tiger: Tiger
ytmarten: Yellow throated marten
The occasion matrix files contains the following columns
Station: The column listing the unique name of each camera trap stations,
VXX: The columns showing whether the species is detected or not for corresponding camera trap stations. (E.g. 1= detected, 0= not detected). “NA” means no data. The number of columns for differ greatly depending on survey site. Thus V1 means first occasion, V2 means second occasion, etc.
Description of variable in “Covariates” folder
The covariates folder contain multiple variable data for each survey site.
File naming schemes: SITE + Year(Optional) + Covs for the predictor variables (e.g. “AKNP17Covs.csv” means the predictor variables extracted for each camera stations in Alaungdaw Kathapa National Park survey site in 2017).
The column names are explained below.
Station: The unique name for each camera trap station
dwater: Water density index extracted for each camera trap station. (% coverage, the higher the water density is higher)
ele: Elevation in meter extracted for each camera trap station. (Meters)
rough: Terrain roughness index extracted for each camera trap station. (The higher the rougher the terrain is)
popu: Population density extracted for each camera trap station. (population per area, the higher the denser population)
gpp: Gross Primary Productivity index extracted for each camera trap station. (carbon weight per area, the higher the better GPP)
ndvi: Normalized Difference Vegetation Index extracted for each camera trap station. (the higher the better NDVI index)
the numbers after underscore “_”, 500, 1000, 1500, 2000, 4000, denotes the scales (in meters) at which the variables are extracted.
For example, “dwater_1500” column means the water density index extracted at 1500 meter circular buffer area around each camera station.
Description of variables in “EffortMatrix” folder
The EffortMatrix folder contains multiple detection effort data for each camera trap station in each survey sites.
File Naming Scheme: SITE + Year(optional) + _Effort_NoScaled for camera trapping effort per each occasion corresponding to the detection history (e.g. “AKNP17_Effort_NoScaled.csv” means the detection effort extracted for each camera trap stations in Alaungdaw Kathapa Nationanl Park survey site in 2017).
The column names are explained below.
Station: The unique name for each camera trap station
oXX: The columns for occasion number. The number of columns for occasions vary for different sites. For example, o1 means first occasion, o2 means second occasion, o3 means third occasion, etc.
The numbers in each cell denote the number of days each camera station is active at certain occasion number. “NA” means no data.
Description of Example R codes.
The example code is provided for working with Asiatic golden cat in AKNP dataset.
The general steps, explanations and descriptions are included in the provided code.
To run other species or for other survey sites dataset, the code need to be modified accordingly.
Notes
“Myan_o10” is the combination of all site data.
“MMLK_o10” is the combination of separate sites from “MMLK….” sites data as a regional level dataset.
The dataset was collected using camera traps during 2014-2020 period. It comprise of surveys targeting differnet focal species. Thus cameras are set up at 1000-1500 meters apart, 2000-3000 meters apart and in some survey, camera trap stations were set up at 2 square kilometers per grid and 16 square kilometers per grid. The six covariates data was obtained using google earth engine.