five

Supplement 1. R script files to perform the simulations of Figs. 1, 2, and 3.

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File List methods.R (MD5: a6dbce8775f7e95f915c257b09df8eb9) Figure1.R (MD5: 771bfccf830ed45207ad7f42e1dc3b89) Figure2and3.R (MD5: 6030b26a7b56c6a4a1a87afdef477e33) Description The fiel methods.R contains implementations of five methods for fitting logistic models using presence-only data: Expectation-Maximization (EM), Lancaster-Imbens (LI), Lele-Keim (LK), Scaled binomial loss (SB), and Steinberg-Cardell (SC). All methods take as input a matrix of presence data and a matrix of background data, with columns corresponding to environmental predictors. The EM, SB and SC methods also take a third argument: an estimate of species prevalence. Figure1.R contains code for making Fig. 1 in the paper. Comment lines explain the code, describe how to run it, and describe the arguments to the methods. Figure2and3.R contains code for making plots as shown in Figs. 2 and 3 in the paper. Comment lines explain the code, describe how to run it, and describe the arguments to the methods.
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