DOI: 10.5061/dryad.brv15dvf4
title: Database Bd modelling for South Africa, Lesotho and eSwatini

description: This dataset was used to create a predictive distribution map
 of Batrachochytrium dendrobatidis in South Africa, based on
 lineage. It contains records obtained from published resources, as well as
 records from fieldwork done. Lineage was identified using published
 lineage-specific primers, in conjunction with confirmed lineage typing by
 whole genome sequencing from O'Hanlon et al. 2018.
description: We modelled lineage distributions using Maxent (version
 3.4.4;(Phillips<em> et al.</em>, 2006) and algorithms
 described by Elith <em>et al</em>. (2011) to correlate
 environmental parameters with the presence of either <em>Bd
 </em>lineage. A database for all known <em>Bd</em>
 records  for South Africa, Lesotho and Eswatini was created with the
 following information: locality and coordinates of sample origin, sample
 size, prevalence of <em>Bd</em>, lineage found (if available),
 date of sampling, and host genus and species name. Bioclimatic variables
 used for modelling were obtained from WorldClim (https://www.worldclim.org/data/bioclim.html) and the contribution of the different variables are given in Table 1. Maxent used 80 % of the positive records for training of the model and the remaining 20 % to test for accuracy of predictions. Model replications were set to 100 using subsample, with the regularisation multiplier set to 1. Random seed was set to true with all other settings left at default. Model performances were evaluated using the area under curve (AUC) of the receiving operating characteristic (ROC) curve and by using jack-knife tests. The jack-knife tests examined the importance of each variable, firstly by removing one variable at a time and secondly by testing each variable in isolation (Figure S1 and S2). AUC values of 1 indicates perfect models, while values of 0.5 indicates that the model has no predictive ability. The lineage‑specific prediction models had a “10 percentile training presence logistic threshold” using the average results from the 100 model replications to convert the results to a binary output for display purposes.
description: Maxent v3.4.4 WorldClim (https://www.worldclim.org/data/bioclim.html) ArcGIS
description: # Database Bd modelling South Africa Lesotho eSwatini This dataset
 contains records from *Bd* surveillance and isolation work. The records
 originate from publicly available, peer reviewed articles, along with our
 own fieldwork records. Isolates from our fieldwork has also been entered
 into the database for whole genome sequencing that has been published with
 O'Hanlon *et al.* 2018. Within the dataset the country, common name
 for site, total number of samples taken, the number of samples positive
 and negative, the lineage (if available from the evidence) coordinates,
 and the date of collection is provided. The family, genus and species
 names of the sampled individuals is also given. Please note that any site
 was categorised as POSTIVE, if even a single individual tested positive.
 "None" indicates where no positives were found. "Not
 Available" refers to historical samples included for which the
 lineage was not available.