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On June 2, 2021 at 4:48:19 PM UTC, Administrator:
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in Novel methods to correct for observer and sampling bias in presence-only species distribution models
f | 1 | { | f | 1 | { |
2 | "author": "[{\"affiliation\": \"WSL\", \"affiliation_02\": \"\", | 2 | "author": "[{\"affiliation\": \"WSL\", \"affiliation_02\": \"\", | ||
3 | \"affiliation_03\": \"\", \"email\": \"yohann.chauvier@wsl.ch\", | 3 | \"affiliation_03\": \"\", \"email\": \"yohann.chauvier@wsl.ch\", | ||
4 | \"given_name\": \"Yohann\", \"identifier\": | 4 | \"given_name\": \"Yohann\", \"identifier\": | ||
5 | \"https://orcid.org/0000-0001-9399-3192\", \"name\": \"Chauvier\"}, | 5 | \"https://orcid.org/0000-0001-9399-3192\", \"name\": \"Chauvier\"}, | ||
6 | {\"affiliation\": \"WSL\", \"affiliation_02\": \"ETH\", | 6 | {\"affiliation\": \"WSL\", \"affiliation_02\": \"ETH\", | ||
7 | \"affiliation_03\": \"\", \"email\": \"niklaus.zimmermann@wsl.ch\", | 7 | \"affiliation_03\": \"\", \"email\": \"niklaus.zimmermann@wsl.ch\", | ||
8 | \"given_name\": \"Niklaus\", \"identifier\": | 8 | \"given_name\": \"Niklaus\", \"identifier\": | ||
9 | \"https://orcid.org/0000-0003-3099-9604\", \"name\": \"Zimmermann\"}, | 9 | \"https://orcid.org/0000-0003-3099-9604\", \"name\": \"Zimmermann\"}, | ||
10 | {\"affiliation\": \"LECA\", \"affiliation_02\": \"\", | 10 | {\"affiliation\": \"LECA\", \"affiliation_02\": \"\", | ||
11 | \"affiliation_03\": \"\", \"email\": \"giov.poggiato@gmail.com\", | 11 | \"affiliation_03\": \"\", \"email\": \"giov.poggiato@gmail.com\", | ||
12 | \"given_name\": \"Giovanni\", \"identifier\": \"\", \"name\": | 12 | \"given_name\": \"Giovanni\", \"identifier\": \"\", \"name\": | ||
13 | \"Poggiato\"}, {\"affiliation\": \"LECA\", \"affiliation_02\": | 13 | \"Poggiato\"}, {\"affiliation\": \"LECA\", \"affiliation_02\": | ||
14 | \"INRIA\", \"affiliation_03\": \"\", \"email\": | 14 | \"INRIA\", \"affiliation_03\": \"\", \"email\": | ||
15 | \"daria.bystrova@inria.fr\", \"given_name\": \"Daria\", | 15 | \"daria.bystrova@inria.fr\", \"given_name\": \"Daria\", | ||
16 | \"identifier\": \"\", \"name\": \"Bystrova\"}, {\"affiliation\": | 16 | \"identifier\": \"\", \"name\": \"Bystrova\"}, {\"affiliation\": | ||
17 | \"WSL\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | 17 | \"WSL\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | ||
18 | \"email\": \"philipp.brun@wsl.ch\", \"given_name\": \"Philipp\", | 18 | \"email\": \"philipp.brun@wsl.ch\", \"given_name\": \"Philipp\", | ||
19 | \"identifier\": \"https://orcid.org/0000-0002-2750-9793\", \"name\": | 19 | \"identifier\": \"https://orcid.org/0000-0002-2750-9793\", \"name\": | ||
20 | \"Brun\"}, {\"affiliation\": \"LECA\", \"affiliation_02\": \"CNRS\", | 20 | \"Brun\"}, {\"affiliation\": \"LECA\", \"affiliation_02\": \"CNRS\", | ||
21 | \"affiliation_03\": \"\", \"email\": | 21 | \"affiliation_03\": \"\", \"email\": | ||
22 | \"wilfried.thuiller@univ-grenoble-alpes.fr\", \"given_name\": | 22 | \"wilfried.thuiller@univ-grenoble-alpes.fr\", \"given_name\": | ||
23 | \"Wilfried\", \"identifier\": | 23 | \"Wilfried\", \"identifier\": | ||
24 | \"https://orcid.org/0000-0002-5388-5274\", \"name\": \"Thuiller\"}]", | 24 | \"https://orcid.org/0000-0002-5388-5274\", \"name\": \"Thuiller\"}]", | ||
25 | "author_email": null, | 25 | "author_email": null, | ||
26 | "creator_user_id": "e2620cc0-c9ef-4773-889b-4c39c0bbb3c8", | 26 | "creator_user_id": "e2620cc0-c9ef-4773-889b-4c39c0bbb3c8", | ||
27 | "date": "[{\"date\": \"2021-06-02\", \"date_type\": \"created\", | 27 | "date": "[{\"date\": \"2021-06-02\", \"date_type\": \"created\", | ||
28 | \"end_date\": \"2021-06-02\"}]", | 28 | \"end_date\": \"2021-06-02\"}]", | ||
29 | "doi": "10.16904/envidat.226", | 29 | "doi": "10.16904/envidat.226", | ||
30 | "funding": "[{\"grant_number\": \"ANR-10-LAB-56, ANR-16-CE93-004\", | 30 | "funding": "[{\"grant_number\": \"ANR-10-LAB-56, ANR-16-CE93-004\", | ||
31 | \"institution\": \"Agence Nationale de la Recherche\", | 31 | \"institution\": \"Agence Nationale de la Recherche\", | ||
32 | \"institution_url\": \"https://anr.fr/Project-ANR-16-CE93-0004\"}, | 32 | \"institution_url\": \"https://anr.fr/Project-ANR-16-CE93-0004\"}, | ||
33 | {\"grant_number\": \"310030L_170059\", \"institution\": | 33 | {\"grant_number\": \"310030L_170059\", \"institution\": | ||
34 | \"Schweizerischer Nationalfonds zur F\u00f6rderung der | 34 | \"Schweizerischer Nationalfonds zur F\u00f6rderung der | ||
35 | Wissenschaftlichen Forschung\", \"institution_url\": | 35 | Wissenschaftlichen Forschung\", \"institution_url\": | ||
36 | \"http://p3.snf.ch/Project-170059\"}]", | 36 | \"http://p3.snf.ch/Project-170059\"}]", | ||
37 | "groups": [], | 37 | "groups": [], | ||
38 | "id": "a09eb932-e181-47a3-945a-7f7cde5d2393", | 38 | "id": "a09eb932-e181-47a3-945a-7f7cde5d2393", | ||
39 | "isopen": false, | 39 | "isopen": false, | ||
40 | "language": "en", | 40 | "language": "en", | ||
41 | "license_id": "wsl-data", | 41 | "license_id": "wsl-data", | ||
42 | "license_title": "WSL Data Policy", | 42 | "license_title": "WSL Data Policy", | ||
43 | "license_url": | 43 | "license_url": | ||
44 | ps://www.wsl.ch/en/about-wsl/programmes-and-initiatives/envidat.html", | 44 | ps://www.wsl.ch/en/about-wsl/programmes-and-initiatives/envidat.html", | ||
45 | "maintainer": "{\"affiliation\": \"WSL\", \"email\": | 45 | "maintainer": "{\"affiliation\": \"WSL\", \"email\": | ||
46 | \"yohann.chauvier@wsl.ch\", \"given_name\": \"Yohann\", | 46 | \"yohann.chauvier@wsl.ch\", \"given_name\": \"Yohann\", | ||
47 | \"identifier\": \"https://orcid.org/0000-0001-9399-3192\", \"name\": | 47 | \"identifier\": \"https://orcid.org/0000-0001-9399-3192\", \"name\": | ||
48 | \"Chauvier\"}", | 48 | \"Chauvier\"}", | ||
49 | "maintainer_email": null, | 49 | "maintainer_email": null, | ||
50 | "metadata_created": "2021-06-02T13:35:35.900157", | 50 | "metadata_created": "2021-06-02T13:35:35.900157", | ||
n | 51 | "metadata_modified": "2021-06-02T15:47:10.034957", | n | 51 | "metadata_modified": "2021-06-02T16:48:19.023569", |
52 | "name": "correct-observer-bias-only-sdms", | 52 | "name": "correct-observer-bias-only-sdms", | ||
53 | "notes": "Aim: While species distribution models (SDMs) are standard | 53 | "notes": "Aim: While species distribution models (SDMs) are standard | ||
54 | tools to predict species distributions, they can suffer from | 54 | tools to predict species distributions, they can suffer from | ||
55 | observation and sampling biases, particularly presence-only SDMs that | 55 | observation and sampling biases, particularly presence-only SDMs that | ||
56 | often rely on species observations from non-standardized sampling | 56 | often rely on species observations from non-standardized sampling | ||
57 | efforts. To address this issue, sampling background points with a | 57 | efforts. To address this issue, sampling background points with a | ||
58 | target-group strategy is commonly used, although more robust | 58 | target-group strategy is commonly used, although more robust | ||
59 | strategies and refinements could be implemented. Here, we exploited a | 59 | strategies and refinements could be implemented. Here, we exploited a | ||
60 | dataset of plant species from the European Alps to propose and | 60 | dataset of plant species from the European Alps to propose and | ||
61 | demonstrate efficient ways to correct for observer and sampling bias | 61 | demonstrate efficient ways to correct for observer and sampling bias | ||
62 | in presence-only models. \r\n\r\nInnovation: Recent methods correct | 62 | in presence-only models. \r\n\r\nInnovation: Recent methods correct | ||
63 | for observer bias by using covariates related to accessibility in | 63 | for observer bias by using covariates related to accessibility in | ||
64 | model calibrations (classic bias covariate correction, Classic-BCC). | 64 | model calibrations (classic bias covariate correction, Classic-BCC). | ||
65 | However, depending on how species are sampled, accessibility | 65 | However, depending on how species are sampled, accessibility | ||
66 | covariates may not sufficiently capture observer bias. Here, we | 66 | covariates may not sufficiently capture observer bias. Here, we | ||
67 | introduced BCCs more directly related to sampling effort, as well as a | 67 | introduced BCCs more directly related to sampling effort, as well as a | ||
68 | novel corrective method based on stratified resampling of the | 68 | novel corrective method based on stratified resampling of the | ||
69 | observational dataset before model calibration (environmental bias | 69 | observational dataset before model calibration (environmental bias | ||
70 | correction, EBC). We compared, individually and jointly, the effect of | 70 | correction, EBC). We compared, individually and jointly, the effect of | ||
71 | EBC and different BCC strategies, when modelling the distributions of | 71 | EBC and different BCC strategies, when modelling the distributions of | ||
72 | 1\u2019900 plant species. We evaluated model performance with spatial | 72 | 1\u2019900 plant species. We evaluated model performance with spatial | ||
73 | block split-sampling and independent test data, and assessed the | 73 | block split-sampling and independent test data, and assessed the | ||
74 | accuracy of plant diversity predictions across the European | 74 | accuracy of plant diversity predictions across the European | ||
75 | Alps.\r\n\r\nMain conclusions: Implementing EBC with BCC showed best | 75 | Alps.\r\n\r\nMain conclusions: Implementing EBC with BCC showed best | ||
76 | results for every evaluation method. Particularly, adding the | 76 | results for every evaluation method. Particularly, adding the | ||
77 | observation density of a target group as bias covariate (Target-BCC) | 77 | observation density of a target group as bias covariate (Target-BCC) | ||
78 | displayed most realistic modelled species distributions, with a clear | 78 | displayed most realistic modelled species distributions, with a clear | ||
79 | positive correlation (r\u22430.5) found between predicted and | 79 | positive correlation (r\u22430.5) found between predicted and | ||
80 | expert-based species richness. Although EBC must be carefully | 80 | expert-based species richness. Although EBC must be carefully | ||
81 | implemented in a species-specific manner, such limitations may be | 81 | implemented in a species-specific manner, such limitations may be | ||
82 | addressed via automated diagnostics included in a provided R function. | 82 | addressed via automated diagnostics included in a provided R function. | ||
83 | Implementing EBC and bias covariate correction together may allow | 83 | Implementing EBC and bias covariate correction together may allow | ||
84 | future studies to address efficiently observer bias in presence-only | 84 | future studies to address efficiently observer bias in presence-only | ||
85 | models, and overcome the standard need of an independent test dataset | 85 | models, and overcome the standard need of an independent test dataset | ||
86 | for model evaluation.", | 86 | for model evaluation.", | ||
87 | "num_resources": 1, | 87 | "num_resources": 1, | ||
88 | "num_tags": 10, | 88 | "num_tags": 10, | ||
89 | "organization": { | 89 | "organization": { | ||
90 | "approval_status": "approved", | 90 | "approval_status": "approved", | ||
91 | "created": "2018-05-31T14:24:18.890912", | 91 | "created": "2018-05-31T14:24:18.890912", | ||
92 | "description": "The dynamic macroecology group studies different | 92 | "description": "The dynamic macroecology group studies different | ||
93 | aspects of ecology on large spatial and temporal scales, from the | 93 | aspects of ecology on large spatial and temporal scales, from the | ||
94 | Pleistocene to the Anthropocene, related to the question: \u201cHow do | 94 | Pleistocene to the Anthropocene, related to the question: \u201cHow do | ||
95 | species and their traits change in space and time, particularly with | 95 | species and their traits change in space and time, particularly with | ||
96 | global change?\u201d", | 96 | global change?\u201d", | ||
97 | "id": "8bdea9a0-ea8c-424f-8c27-a4a1f0c55f02", | 97 | "id": "8bdea9a0-ea8c-424f-8c27-a4a1f0c55f02", | ||
98 | "image_url": "2018-07-10-102727.341687LogoWSL.svg", | 98 | "image_url": "2018-07-10-102727.341687LogoWSL.svg", | ||
99 | "is_organization": true, | 99 | "is_organization": true, | ||
100 | "name": "dynamic-macroecology", | 100 | "name": "dynamic-macroecology", | ||
101 | "state": "active", | 101 | "state": "active", | ||
102 | "title": "Dynamic Macroecology", | 102 | "title": "Dynamic Macroecology", | ||
103 | "type": "organization" | 103 | "type": "organization" | ||
104 | }, | 104 | }, | ||
105 | "owner_org": "8bdea9a0-ea8c-424f-8c27-a4a1f0c55f02", | 105 | "owner_org": "8bdea9a0-ea8c-424f-8c27-a4a1f0c55f02", | ||
106 | "private": false, | 106 | "private": false, | ||
107 | "publication": "{\"publication_year\": \"2021\", \"publisher\": | 107 | "publication": "{\"publication_year\": \"2021\", \"publisher\": | ||
108 | \"EnviDat\"}", | 108 | \"EnviDat\"}", | ||
t | 109 | "publication_state": "approved", | t | 109 | "publication_state": "published", |
110 | "related_datasets": "KARGER, Dirk Nikolaus, CONRAD, Olaf, | 110 | "related_datasets": "KARGER, Dirk Nikolaus, CONRAD, Olaf, | ||
111 | B\u00d6HNER, J\u00fcrgen, et al. Climatologies at high resolution for | 111 | B\u00d6HNER, J\u00fcrgen, et al. Climatologies at high resolution for | ||
112 | the earth\u2019s land surface areas. Scientific data, 2017, vol. 4, no | 112 | the earth\u2019s land surface areas. Scientific data, 2017, vol. 4, no | ||
113 | 1, p. 1-20.\r\n\r\nAeschimann, D., Lauber, K., Moser, D.M. & | 113 | 1, p. 1-20.\r\n\r\nAeschimann, D., Lauber, K., Moser, D.M. & | ||
114 | Theurillat, J.P. (2004) Flora alpina: ein Atlas s\u00e4mtlicher 4500 | 114 | Theurillat, J.P. (2004) Flora alpina: ein Atlas s\u00e4mtlicher 4500 | ||
115 | Gef\u00e4sspflanzen der Alpen., (ed. by Haupt).", | 115 | Gef\u00e4sspflanzen der Alpen., (ed. by Haupt).", | ||
116 | "related_publications": "", | 116 | "related_publications": "", | ||
117 | "relationships_as_object": [], | 117 | "relationships_as_object": [], | ||
118 | "relationships_as_subject": [], | 118 | "relationships_as_subject": [], | ||
119 | "resource_type": "dataset", | 119 | "resource_type": "dataset", | ||
120 | "resource_type_general": "dataset", | 120 | "resource_type_general": "dataset", | ||
121 | "resources": [ | 121 | "resources": [ | ||
122 | { | 122 | { | ||
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125 | "created": "2021-06-02T14:00:52.109758", | 125 | "created": "2021-06-02T14:00:52.109758", | ||
126 | "description": "Non-copyright data, scripts, diversity outputs", | 126 | "description": "Non-copyright data, scripts, diversity outputs", | ||
127 | "doi": "", | 127 | "doi": "", | ||
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135 | "name": "PPM_bias_correction", | 135 | "name": "PPM_bias_correction", | ||
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143 | "size": 93698243, | 143 | "size": 93698243, | ||
144 | "state": "active", | 144 | "state": "active", | ||
145 | "url": | 145 | "url": | ||
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147 | "url_type": "upload" | 147 | "url_type": "upload" | ||
148 | } | 148 | } | ||
149 | ], | 149 | ], | ||
150 | "spatial": | 150 | "spatial": | ||
151 | ,[17.5341796875,42.7416346551412],[4.9658203125,42.7416346551412]]]}", | 151 | ,[17.5341796875,42.7416346551412],[4.9658203125,42.7416346551412]]]}", | ||
152 | "spatial_info": "European Alps", | 152 | "spatial_info": "European Alps", | ||
153 | "state": "active", | 153 | "state": "active", | ||
154 | "subtitle": "", | 154 | "subtitle": "", | ||
155 | "tags": [ | 155 | "tags": [ | ||
156 | { | 156 | { | ||
157 | "display_name": "BACKGROUND DATA", | 157 | "display_name": "BACKGROUND DATA", | ||
158 | "id": "1e27ed57-ffec-4efd-b062-7f2a5c468276", | 158 | "id": "1e27ed57-ffec-4efd-b062-7f2a5c468276", | ||
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160 | "state": "active", | 160 | "state": "active", | ||
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163 | { | 163 | { | ||
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167 | "state": "active", | 167 | "state": "active", | ||
168 | "vocabulary_id": null | 168 | "vocabulary_id": null | ||
169 | }, | 169 | }, | ||
170 | { | 170 | { | ||
171 | "display_name": "COVARIATE CORRECTION", | 171 | "display_name": "COVARIATE CORRECTION", | ||
172 | "id": "05fb2a81-0db9-4c1e-8606-bad1d5205f14", | 172 | "id": "05fb2a81-0db9-4c1e-8606-bad1d5205f14", | ||
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174 | "state": "active", | 174 | "state": "active", | ||
175 | "vocabulary_id": null | 175 | "vocabulary_id": null | ||
176 | }, | 176 | }, | ||
177 | { | 177 | { | ||
178 | "display_name": "ENVIRONMENTAL STRATIFICATION", | 178 | "display_name": "ENVIRONMENTAL STRATIFICATION", | ||
179 | "id": "54036d5a-28d8-46ed-ab48-9a9e556408b9", | 179 | "id": "54036d5a-28d8-46ed-ab48-9a9e556408b9", | ||
180 | "name": "ENVIRONMENTAL STRATIFICATION", | 180 | "name": "ENVIRONMENTAL STRATIFICATION", | ||
181 | "state": "active", | 181 | "state": "active", | ||
182 | "vocabulary_id": null | 182 | "vocabulary_id": null | ||
183 | }, | 183 | }, | ||
184 | { | 184 | { | ||
185 | "display_name": "INDEPENDENT DATASET", | 185 | "display_name": "INDEPENDENT DATASET", | ||
186 | "id": "7d31474e-3f35-499d-89bd-b37b1b9e615a", | 186 | "id": "7d31474e-3f35-499d-89bd-b37b1b9e615a", | ||
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188 | "state": "active", | 188 | "state": "active", | ||
189 | "vocabulary_id": null | 189 | "vocabulary_id": null | ||
190 | }, | 190 | }, | ||
191 | { | 191 | { | ||
192 | "display_name": "PLANT SPECIES", | 192 | "display_name": "PLANT SPECIES", | ||
193 | "id": "269cf433-87f4-4c60-bcd7-52cc7ad22bc2", | 193 | "id": "269cf433-87f4-4c60-bcd7-52cc7ad22bc2", | ||
194 | "name": "PLANT SPECIES", | 194 | "name": "PLANT SPECIES", | ||
195 | "state": "active", | 195 | "state": "active", | ||
196 | "vocabulary_id": null | 196 | "vocabulary_id": null | ||
197 | }, | 197 | }, | ||
198 | { | 198 | { | ||
199 | "display_name": "POINT PROCESS MODEL", | 199 | "display_name": "POINT PROCESS MODEL", | ||
200 | "id": "37903065-b772-45e2-b27b-10ba6204738c", | 200 | "id": "37903065-b772-45e2-b27b-10ba6204738c", | ||
201 | "name": "POINT PROCESS MODEL", | 201 | "name": "POINT PROCESS MODEL", | ||
202 | "state": "active", | 202 | "state": "active", | ||
203 | "vocabulary_id": null | 203 | "vocabulary_id": null | ||
204 | }, | 204 | }, | ||
205 | { | 205 | { | ||
206 | "display_name": "RANDOM STRATIFIED SAMPLING", | 206 | "display_name": "RANDOM STRATIFIED SAMPLING", | ||
207 | "id": "1f1eb4bb-6443-4307-bda5-a0eae20f1afb", | 207 | "id": "1f1eb4bb-6443-4307-bda5-a0eae20f1afb", | ||
208 | "name": "RANDOM STRATIFIED SAMPLING", | 208 | "name": "RANDOM STRATIFIED SAMPLING", | ||
209 | "state": "active", | 209 | "state": "active", | ||
210 | "vocabulary_id": null | 210 | "vocabulary_id": null | ||
211 | }, | 211 | }, | ||
212 | { | 212 | { | ||
213 | "display_name": "SURVEY EFFORT", | 213 | "display_name": "SURVEY EFFORT", | ||
214 | "id": "522315db-d363-4b75-8a17-5960c6f391f0", | 214 | "id": "522315db-d363-4b75-8a17-5960c6f391f0", | ||
215 | "name": "SURVEY EFFORT", | 215 | "name": "SURVEY EFFORT", | ||
216 | "state": "active", | 216 | "state": "active", | ||
217 | "vocabulary_id": null | 217 | "vocabulary_id": null | ||
218 | }, | 218 | }, | ||
219 | { | 219 | { | ||
220 | "display_name": "TARGET GROUP", | 220 | "display_name": "TARGET GROUP", | ||
221 | "id": "b835c741-e505-4fb5-95d3-817d0173a1c0", | 221 | "id": "b835c741-e505-4fb5-95d3-817d0173a1c0", | ||
222 | "name": "TARGET GROUP", | 222 | "name": "TARGET GROUP", | ||
223 | "state": "active", | 223 | "state": "active", | ||
224 | "vocabulary_id": null | 224 | "vocabulary_id": null | ||
225 | } | 225 | } | ||
226 | ], | 226 | ], | ||
227 | "title": "Novel methods to correct for observer and sampling bias in | 227 | "title": "Novel methods to correct for observer and sampling bias in | ||
228 | presence-only species distribution models", | 228 | presence-only species distribution models", | ||
229 | "type": "dataset", | 229 | "type": "dataset", | ||
230 | "url": null, | 230 | "url": null, | ||
231 | "version": "1.0" | 231 | "version": "1.0" | ||
232 | } | 232 | } |