DOI: 10.5061/dryad.0gb5mkm6w
title: Myanmar mammal occupancy baseline assessment dataset

description: 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).
description: 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.
description: # Dataset Information # Dataset title: --- Myanmar mammal Occupancy
 Baseline Assessment Dataset
 [https://doi.org/10.5061/dryad.0gb5mkm6w](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](https://orcid.org/0000-0002-2763-5706) * Email: [pyaephyoekyawwcs@gmail.com](mailto:pyaephyoekyawwcs@gmail.com) * Contributor ORCID IDs: * Pyae Phyoe Kyaw: [https://orcid.org/0000-0002-2763-5706](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.