Back

The effects of data adequacy and calibration size on the accuracy of presence-only species distribution models

Santika, T.; Hutchinson, M. F.; Wilson, K. A.

2019-09-19 ecology
10.1101/775700 bioRxiv
Show abstract

O_LIPresence-only data used to develop species distribution models are often biased towards areas that are frequently surveyed. Furthermore, the size of calibration area with respect to the area covered by the species occurrences has been shown to affect model accuracy. However, existing assessments of the effect of data inadequacy and calibration size on model accuracy have predominately been conducted using empirical studies. These studies can give ambiguous results, since the data used to train and test the model can both be biased.\nC_LIO_LIThese limitations were addressed by applying simulated data to assess how inadequate data coverage and the size of calibration area affect the accuracy of species distribution models generated by MaxEnt and BIOCLIM. The validity of four presence-only performance measures, Contrast Validation Index (CVI), Boyce index, AUC and AUCratio, was also assessed.\nC_LIO_LICVI, AUC and AUCratio ranked the accuracy of univariate models correctly according to the true importance of their defining environmental variable, a desirable property of an accuracy measure. Contrastingly, Boyce index failed to rank the accuracy of univariate models correctly and a high percentage of irrelevant variables produced models with a high Boyce index.\nC_LIO_LIInadequate data coverage and increased calibration area reduced model accuracy by reducing the correct identification of the dominant environmental determinant. BIOCLIM outperformed MaxEnt models in predicting the true distribution of simulated species with a symmetric dominant response. However, MaxEnt outperformed BIOCLIM in predicting the true distribution of simulated species with skew and linear dominant responses. Despite this, the standard performance measures consistently overestimated the performance of MaxEnt models and showed them as always having higher model accuracy than the BIOCLIM models.\nC_LIO_LIIt has been acknowledged that research should be directed towards testing and improving species distribution modelling tools, particularly how to handle the inevitable bias and scarcity of species occurrence data. Simulated data, as demonstrated here, provides a powerful approach to comprehensively test the performance of modelling tools and to disentangle the effects of data properties and modelling options on model accuracy. This may be impossible to achieve using real-world data.\nC_LI

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
Ecography
54 papers in training set
Top 0.1%
26.0%
2
Ecological Informatics
33 papers in training set
Top 0.1%
11.7%
3
Ecology and Evolution
267 papers in training set
Top 0.8%
6.6%
4
Diversity and Distributions
28 papers in training set
Top 0.1%
4.2%
5
Methods in Ecology and Evolution
176 papers in training set
Top 0.6%
4.2%
50% of probability mass above
6
Journal of Biogeography
46 papers in training set
Top 0.3%
3.4%
7
Ecosphere
57 papers in training set
Top 0.5%
2.7%
8
PeerJ
308 papers in training set
Top 3%
2.7%
9
Global Ecology and Biogeography
47 papers in training set
Top 0.4%
2.6%
10
Peer Community Journal
281 papers in training set
Top 2%
2.4%
11
Frontiers in Ecology and Evolution
69 papers in training set
Top 0.9%
2.3%
12
Ecological Modelling
28 papers in training set
Top 0.2%
2.3%
13
Landscape Ecology
13 papers in training set
Top 0.1%
2.1%
14
PLOS ONE
5266 papers in training set
Top 49%
1.7%
15
Environmental DNA
56 papers in training set
Top 0.4%
1.7%
16
Oikos
84 papers in training set
Top 0.9%
1.6%
17
Global Ecology and Conservation
25 papers in training set
Top 0.6%
1.5%
18
Biological Conservation
46 papers in training set
Top 0.6%
1.4%
19
Ecology
85 papers in training set
Top 1%
1.3%
20
Ecological Indicators
21 papers in training set
Top 0.4%
1.3%
21
Ecological Applications
34 papers in training set
Top 0.7%
1.1%
22
Science of The Total Environment
186 papers in training set
Top 3%
1.0%
23
Population Ecology
10 papers in training set
Top 0.2%
1.0%
24
Molecular Ecology Resources
171 papers in training set
Top 2%
0.8%
25
Journal of Animal Ecology
75 papers in training set
Top 2%
0.8%
26
Conservation Science and Practice
15 papers in training set
Top 0.5%
0.6%
27
Journal of Applied Ecology
39 papers in training set
Top 1%
0.6%