Changes
On March 4, 2025 at 10:59:33 AM UTC,
-
Changed the version of Repeated detection-nondetection data of corticolous lichens from a standardised monitoring across Switzerland to 1.0
f | 1 | { | f | 1 | { |
2 | "author": "[{\"given_name\": \"Gesa von\", \"name\": | 2 | "author": "[{\"given_name\": \"Gesa von\", \"name\": | ||
3 | \"Hirschheydt\", \"email\": \"gesa.vonhirschheydt@wsl.ch\", | 3 | \"Hirschheydt\", \"email\": \"gesa.vonhirschheydt@wsl.ch\", | ||
4 | \"data_credit\": [\"software\", \"curation\", \"validation\", | 4 | \"data_credit\": [\"software\", \"curation\", \"validation\", | ||
5 | \"publication\"], \"identifier\": \"0000-0001-7930-2527\", | 5 | \"publication\"], \"identifier\": \"0000-0001-7930-2527\", | ||
6 | \"affiliation\": \"Swiss Federal Institute for Forest Snow and | 6 | \"affiliation\": \"Swiss Federal Institute for Forest Snow and | ||
7 | Landscape Research WSL\"}, {\"given_name\": \"Marc\", \"name\": | 7 | Landscape Research WSL\"}, {\"given_name\": \"Marc\", \"name\": | ||
8 | \"K\\u00e9ry\", \"email\": \"marc.kery@vogelwarte.ch\", | 8 | \"K\\u00e9ry\", \"email\": \"marc.kery@vogelwarte.ch\", | ||
9 | \"data_credit\": [\"software\"], \"identifier\": | 9 | \"data_credit\": [\"software\"], \"identifier\": | ||
10 | \"0000-0001-7476-7616\", \"affiliation\": \"Swiss Ornithological | 10 | \"0000-0001-7476-7616\", \"affiliation\": \"Swiss Ornithological | ||
11 | Institute\"}, {\"given_name\": \"Stefan\", \"name\": \"Ekman\", | 11 | Institute\"}, {\"given_name\": \"Stefan\", \"name\": \"Ekman\", | ||
12 | \"email\": \"stefan.ekman@em.uu.se\", \"data_credit\": | 12 | \"email\": \"stefan.ekman@em.uu.se\", \"data_credit\": | ||
13 | [\"supervision\", \"software\"], \"identifier\": | 13 | [\"supervision\", \"software\"], \"identifier\": | ||
14 | \"0000-0003-3021-1821\", \"affiliation\": \"Museum of Evolution, | 14 | \"0000-0003-3021-1821\", \"affiliation\": \"Museum of Evolution, | ||
15 | University of Uppsala\"}, {\"given_name\": \"Silvia\", \"name\": | 15 | University of Uppsala\"}, {\"given_name\": \"Silvia\", \"name\": | ||
16 | \"Stofer\", \"email\": \"silvia.stofer@wsl.ch\", \"data_credit\": | 16 | \"Stofer\", \"email\": \"silvia.stofer@wsl.ch\", \"data_credit\": | ||
17 | [\"supervision\", \"collection\", \"validation\"], \"identifier\": | 17 | [\"supervision\", \"collection\", \"validation\"], \"identifier\": | ||
18 | \"0000-0001-8581-7789\", \"affiliation\": \"Swiss Federal Institute | 18 | \"0000-0001-8581-7789\", \"affiliation\": \"Swiss Federal Institute | ||
19 | for Forest Snow and Landscape Research WSL\"}, {\"given_name\": | 19 | for Forest Snow and Landscape Research WSL\"}, {\"given_name\": | ||
20 | \"Michael\", \"name\": \"Dietrich\", \"email\": | 20 | \"Michael\", \"name\": \"Dietrich\", \"email\": | ||
21 | \"michael.dietrich@wsl.ch\", \"data_credit\": [\"collection\", | 21 | \"michael.dietrich@wsl.ch\", \"data_credit\": [\"collection\", | ||
22 | \"validation\"], \"identifier\": \"\", \"affiliation\": \"Swiss | 22 | \"validation\"], \"identifier\": \"\", \"affiliation\": \"Swiss | ||
23 | Federal Institute for Forest Snow and Landscape Research WSL\"}, | 23 | Federal Institute for Forest Snow and Landscape Research WSL\"}, | ||
24 | {\"given_name\": \"Christine\", \"name\": \"Keller\", \"email\": | 24 | {\"given_name\": \"Christine\", \"name\": \"Keller\", \"email\": | ||
25 | \"christine.keller@wsl.ch\", \"data_credit\": [\"collection\", | 25 | \"christine.keller@wsl.ch\", \"data_credit\": [\"collection\", | ||
26 | \"validation\"], \"identifier\": \"\", \"affiliation\": \"Swiss | 26 | \"validation\"], \"identifier\": \"\", \"affiliation\": \"Swiss | ||
27 | Federal Institute for Forest Snow and Landscape Research WSL\"}, | 27 | Federal Institute for Forest Snow and Landscape Research WSL\"}, | ||
28 | {\"given_name\": \"Christoph\", \"name\": \"Scheidegger\", \"email\": | 28 | {\"given_name\": \"Christoph\", \"name\": \"Scheidegger\", \"email\": | ||
29 | \"christoph.scheidegger@wsl.ch\", \"data_credit\": [\"supervision\", | 29 | \"christoph.scheidegger@wsl.ch\", \"data_credit\": [\"supervision\", | ||
30 | \"collection\", \"validation\"], \"identifier\": | 30 | \"collection\", \"validation\"], \"identifier\": | ||
31 | \"0000-0003-3713-5331\", \"affiliation\": \"Swiss Federal Institute | 31 | \"0000-0003-3713-5331\", \"affiliation\": \"Swiss Federal Institute | ||
32 | for Forest Snow and Landscape Research WSL\"}]", | 32 | for Forest Snow and Landscape Research WSL\"}]", | ||
33 | "author_email": null, | 33 | "author_email": null, | ||
34 | "creator_user_id": "f4f3f53b-fbce-4399-9834-f1826917dd25", | 34 | "creator_user_id": "f4f3f53b-fbce-4399-9834-f1826917dd25", | ||
35 | "date": | 35 | "date": | ||
36 | \":\"created\",\"date\":\"1995-01-01\",\"end_date\":\"2000-12-31\"}]", | 36 | \":\"created\",\"date\":\"1995-01-01\",\"end_date\":\"2000-12-31\"}]", | ||
37 | "doi": "10.16904/envidat.491", | 37 | "doi": "10.16904/envidat.491", | ||
38 | "funding": "[{\"institution\":\"Swiss Federal Office for the | 38 | "funding": "[{\"institution\":\"Swiss Federal Office for the | ||
39 | Environment | 39 | Environment | ||
40 | \"grant_number\":\"00.5147.PZ/0DF268D21\",\"institution_url\":\"\"}]", | 40 | \"grant_number\":\"00.5147.PZ/0DF268D21\",\"institution_url\":\"\"}]", | ||
41 | "groups": [], | 41 | "groups": [], | ||
42 | "id": "c3307528-44fd-4f64-931d-c28d46ca6920", | 42 | "id": "c3307528-44fd-4f64-931d-c28d46ca6920", | ||
43 | "isopen": true, | 43 | "isopen": true, | ||
44 | "license_id": "cc-by-sa", | 44 | "license_id": "cc-by-sa", | ||
45 | "license_title": "Creative Commons Attribution Share-Alike | 45 | "license_title": "Creative Commons Attribution Share-Alike | ||
46 | (CC-BY-SA)", | 46 | (CC-BY-SA)", | ||
47 | "license_url": "https://creativecommons.org/licenses/by-sa/4.0/", | 47 | "license_url": "https://creativecommons.org/licenses/by-sa/4.0/", | ||
48 | "maintainer": | 48 | "maintainer": | ||
49 | :\"gesa.vonhirschheydt@wsl.ch\",\"given_name\":\"Gesa\",\"name\":\"von | 49 | :\"gesa.vonhirschheydt@wsl.ch\",\"given_name\":\"Gesa\",\"name\":\"von | ||
50 | Hirschheydt\"}", | 50 | Hirschheydt\"}", | ||
51 | "maintainer_email": null, | 51 | "maintainer_email": null, | ||
52 | "metadata_created": "2024-03-04T16:14:45.100215", | 52 | "metadata_created": "2024-03-04T16:14:45.100215", | ||
n | 53 | "metadata_modified": "2024-03-07T15:27:30.746675", | n | 53 | "metadata_modified": "2025-03-04T10:59:32.990128", |
54 | "name": | 54 | "name": | ||
55 | "repeated-detection-nondetection-data-of-corticolous-lichens", | 55 | "repeated-detection-nondetection-data-of-corticolous-lichens", | ||
56 | "notes": "The available lichen data consists of | 56 | "notes": "The available lichen data consists of | ||
57 | detection/nondetection data (1/0) of 373 tree-inhabiting | 57 | detection/nondetection data (1/0) of 373 tree-inhabiting | ||
58 | (*corticolous*) lichen species from 416 plots surveyed 1-2 times. The | 58 | (*corticolous*) lichen species from 416 plots surveyed 1-2 times. The | ||
59 | lichen data were originally collected for the purpose of the Red List | 59 | lichen data were originally collected for the purpose of the Red List | ||
60 | of epiphytic lichen species in Switzerland ([Scheidegger *et al.* | 60 | of epiphytic lichen species in Switzerland ([Scheidegger *et al.* | ||
61 | ionen/rote-liste-gefaehrdete-arten-baum-erdbewohnende-flechten.html)), | 61 | ionen/rote-liste-gefaehrdete-arten-baum-erdbewohnende-flechten.html)), | ||
62 | but updated to recent nomenclature for the purpose of this | 62 | but updated to recent nomenclature for the purpose of this | ||
63 | study.\n\nThis repository contains all the supporting data and R code | 63 | study.\n\nThis repository contains all the supporting data and R code | ||
64 | for the paper:\nvon Hirschheydt, G., K\u00e9ry, M., Ekman, S., Stofer, | 64 | for the paper:\nvon Hirschheydt, G., K\u00e9ry, M., Ekman, S., Stofer, | ||
65 | S., Dietrich, M., Keller, C., Scheidegger, C. (2024) **Occupancy model | 65 | S., Dietrich, M., Keller, C., Scheidegger, C. (2024) **Occupancy model | ||
66 | reveals limited detectability of lichens in a standardised large-scale | 66 | reveals limited detectability of lichens in a standardised large-scale | ||
67 | monitoring**. *Journal of Vegetation Science*.\n\nResults and figures | 67 | monitoring**. *Journal of Vegetation Science*.\n\nResults and figures | ||
68 | presented in the manuscript should be reproducible (with small | 68 | presented in the manuscript should be reproducible (with small | ||
69 | differences in the latter digits due to stochasticity of the MCMC | 69 | differences in the latter digits due to stochasticity of the MCMC | ||
70 | sampler) with the provided data and code.\n\nThe downloadable `.zip` | 70 | sampler) with the provided data and code.\n\nThe downloadable `.zip` | ||
71 | folder has the following structure:\n* `0_data/`\n* `1_code/`\n* | 71 | folder has the following structure:\n* `0_data/`\n* `1_code/`\n* | ||
72 | `2_output/`\n* `lichen_detectability.Rproj`\n* `README.txt`\n* | 72 | `2_output/`\n* `lichen_detectability.Rproj`\n* `README.txt`\n* | ||
73 | `workflow.html`\n- `workflow.Rmd` \n\n \nThe main folder and the | 73 | `workflow.html`\n- `workflow.Rmd` \n\n \nThe main folder and the | ||
74 | three subordinate folders each have their own `README*.txt` file. | 74 | three subordinate folders each have their own `README*.txt` file. | ||
75 | These describe each available file in detail and should be consulted | 75 | These describe each available file in detail and should be consulted | ||
76 | prior to using the data or running any code. The file | 76 | prior to using the data or running any code. The file | ||
77 | `lichen_detectability.Rproj` stores the information about the R | 77 | `lichen_detectability.Rproj` stores the information about the R | ||
78 | project. The user can open the project by clicking/double-clicking on | 78 | project. The user can open the project by clicking/double-clicking on | ||
79 | this file which will automatically define the repository as working | 79 | this file which will automatically define the repository as working | ||
80 | directory for the R session. If the user does not use RStudio/Posit, | 80 | directory for the R session. If the user does not use RStudio/Posit, | ||
81 | they may have to set the working directory manually to the stored | 81 | they may have to set the working directory manually to the stored | ||
82 | location in the R files. The files `workflow.*` guide the user through | 82 | location in the R files. The files `workflow.*` guide the user through | ||
83 | the analysis (`1_code/*.R`) in the correct order so that they can:\n- | 83 | the analysis (`1_code/*.R`) in the correct order so that they can:\n- | ||
84 | bundle the cleaned data into a data list readable for JAGS\n- fit the | 84 | bundle the cleaned data into a data list readable for JAGS\n- fit the | ||
85 | multi-species occupancy model to the data and store the output\n- | 85 | multi-species occupancy model to the data and store the output\n- | ||
86 | assess the goodness-of-fit of the model to the data\n- conduct a prior | 86 | assess the goodness-of-fit of the model to the data\n- conduct a prior | ||
87 | sensitivity analysis with 2 additional sets of priors\n- extract the | 87 | sensitivity analysis with 2 additional sets of priors\n- extract the | ||
88 | summary statistics reported in the manuscript and supplementary | 88 | summary statistics reported in the manuscript and supplementary | ||
89 | materials\n- generate the figures shown in the manuscript and | 89 | materials\n- generate the figures shown in the manuscript and | ||
90 | supplementary materials", | 90 | supplementary materials", | ||
91 | "num_resources": 1, | 91 | "num_resources": 1, | ||
92 | "num_tags": 12, | 92 | "num_tags": 12, | ||
93 | "organization": { | 93 | "organization": { | ||
94 | "approval_status": "approved", | 94 | "approval_status": "approved", | ||
95 | "created": "2018-05-18T09:12:30.577470", | 95 | "created": "2018-05-18T09:12:30.577470", | ||
96 | "description": "We study the relationship between threatened | 96 | "description": "We study the relationship between threatened | ||
97 | species and their habitat with the objective to develop evidence-based | 97 | species and their habitat with the objective to develop evidence-based | ||
98 | instruments for conservation. The viability of populations of habitat | 98 | instruments for conservation. The viability of populations of habitat | ||
99 | specialists is often limited due to restricted availability of | 99 | specialists is often limited due to restricted availability of | ||
100 | suitable habitat or discontinuous distribution. We focus on selected | 100 | suitable habitat or discontinuous distribution. We focus on selected | ||
101 | animal species of conservation concern (forest birds, bats, forest | 101 | animal species of conservation concern (forest birds, bats, forest | ||
102 | insects) and analyse species-habitat relationships at a scale ranging | 102 | insects) and analyse species-habitat relationships at a scale ranging | ||
103 | from single subpopulations to entire metapopulations. We strive | 103 | from single subpopulations to entire metapopulations. We strive | ||
104 | towards standardised recording of elusive species with novel | 104 | towards standardised recording of elusive species with novel | ||
105 | techniques, assessing environmental variables and combining these | 105 | techniques, assessing environmental variables and combining these | ||
106 | field data with data from remote sensing. We determine limiting | 106 | field data with data from remote sensing. We determine limiting | ||
107 | factors (habitat, climate, resources) and predict species occurrence | 107 | factors (habitat, climate, resources) and predict species occurrence | ||
108 | and habitat suitability with modelling techniques.\r\n\r\nThese models | 108 | and habitat suitability with modelling techniques.\r\n\r\nThese models | ||
109 | allow to predict species occurrence patterns and to delineate | 109 | allow to predict species occurrence patterns and to delineate | ||
110 | evidence-based priority areas for conservation. Our long-term | 110 | evidence-based priority areas for conservation. Our long-term | ||
111 | collaboration with federal and cantonal stakeholders of forest and | 111 | collaboration with federal and cantonal stakeholders of forest and | ||
112 | nature conservation enables the combination of research results with | 112 | nature conservation enables the combination of research results with | ||
113 | conservation requirements (e.g. species action plans, forest | 113 | conservation requirements (e.g. species action plans, forest | ||
114 | biodiversity expert panel, scientific counsel for bat protection). | 114 | biodiversity expert panel, scientific counsel for bat protection). | ||
115 | While we investigate complete distribution ranges in bats, we focus on | 115 | While we investigate complete distribution ranges in bats, we focus on | ||
116 | forest habitats in birds and insects given the large extent and high | 116 | forest habitats in birds and insects given the large extent and high | ||
117 | importance of forests for biodiversity conservation in Switzerland.", | 117 | importance of forests for biodiversity conservation in Switzerland.", | ||
118 | "id": "32672ec5-c180-471e-92f7-ef58e00eb1fb", | 118 | "id": "32672ec5-c180-471e-92f7-ef58e00eb1fb", | ||
119 | "image_url": "2018-07-10-090115.162284LogoWSL.svg", | 119 | "image_url": "2018-07-10-090115.162284LogoWSL.svg", | ||
120 | "is_organization": true, | 120 | "is_organization": true, | ||
121 | "name": "conservation-biology", | 121 | "name": "conservation-biology", | ||
122 | "state": "active", | 122 | "state": "active", | ||
123 | "title": "Conservation Biology", | 123 | "title": "Conservation Biology", | ||
124 | "type": "organization" | 124 | "type": "organization" | ||
125 | }, | 125 | }, | ||
126 | "owner_org": "32672ec5-c180-471e-92f7-ef58e00eb1fb", | 126 | "owner_org": "32672ec5-c180-471e-92f7-ef58e00eb1fb", | ||
127 | "private": false, | 127 | "private": false, | ||
128 | "publication": | 128 | "publication": | ||
129 | "{\"publisher\":\"EnviDat\",\"publication_year\":\"2024\"}", | 129 | "{\"publisher\":\"EnviDat\",\"publication_year\":\"2024\"}", | ||
130 | "publication_state": "published", | 130 | "publication_state": "published", | ||
131 | "related_datasets": "* **SwissLichens** - Distribution of lichens in | 131 | "related_datasets": "* **SwissLichens** - Distribution of lichens in | ||
132 | Switzerland: | 132 | Switzerland: | ||
133 | /doi.org/10.16904/envidat.118](https://doi.org/10.16904/envidat.118)", | 133 | /doi.org/10.16904/envidat.118](https://doi.org/10.16904/envidat.118)", | ||
134 | "relationships_as_object": [], | 134 | "relationships_as_object": [], | ||
135 | "relationships_as_subject": [], | 135 | "relationships_as_subject": [], | ||
136 | "resource_type": "dataset", | 136 | "resource_type": "dataset", | ||
137 | "resource_type_general": "dataset", | 137 | "resource_type_general": "dataset", | ||
138 | "resources": [ | 138 | "resources": [ | ||
139 | { | 139 | { | ||
140 | "cache_last_updated": null, | 140 | "cache_last_updated": null, | ||
141 | "cache_url": null, | 141 | "cache_url": null, | ||
142 | "created": "2024-03-06T14:46:49.439075", | 142 | "created": "2024-03-06T14:46:49.439075", | ||
143 | "description": "Repository containing the full data, code, | 143 | "description": "Repository containing the full data, code, | ||
144 | README and workflow files.", | 144 | README and workflow files.", | ||
145 | "doi": "", | 145 | "doi": "", | ||
146 | "format": "ZIP", | 146 | "format": "ZIP", | ||
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232 | "state": "active", | 232 | "state": "active", | ||
233 | "vocabulary_id": null | 233 | "vocabulary_id": null | ||
234 | }, | 234 | }, | ||
235 | { | 235 | { | ||
236 | "display_name": "OCCUPANCY MODEL", | 236 | "display_name": "OCCUPANCY MODEL", | ||
237 | "id": "a2c7da70-e34d-44ea-8ef7-01974321d0f8", | 237 | "id": "a2c7da70-e34d-44ea-8ef7-01974321d0f8", | ||
238 | "name": "OCCUPANCY MODEL", | 238 | "name": "OCCUPANCY MODEL", | ||
239 | "state": "active", | 239 | "state": "active", | ||
240 | "vocabulary_id": null | 240 | "vocabulary_id": null | ||
241 | }, | 241 | }, | ||
242 | { | 242 | { | ||
243 | "display_name": "SESSILE SPECIES", | 243 | "display_name": "SESSILE SPECIES", | ||
244 | "id": "4d107ad6-9177-448b-8785-9761e4a161fa", | 244 | "id": "4d107ad6-9177-448b-8785-9761e4a161fa", | ||
245 | "name": "SESSILE SPECIES", | 245 | "name": "SESSILE SPECIES", | ||
246 | "state": "active", | 246 | "state": "active", | ||
247 | "vocabulary_id": null | 247 | "vocabulary_id": null | ||
248 | }, | 248 | }, | ||
249 | { | 249 | { | ||
250 | "display_name": "SWISSLICHENS", | 250 | "display_name": "SWISSLICHENS", | ||
251 | "id": "30010def-ce8c-4a2b-80b8-e9afb39747d3", | 251 | "id": "30010def-ce8c-4a2b-80b8-e9afb39747d3", | ||
252 | "name": "SWISSLICHENS", | 252 | "name": "SWISSLICHENS", | ||
253 | "state": "active", | 253 | "state": "active", | ||
254 | "vocabulary_id": null | 254 | "vocabulary_id": null | ||
255 | } | 255 | } | ||
256 | ], | 256 | ], | ||
257 | "title": "Repeated detection-nondetection data of corticolous | 257 | "title": "Repeated detection-nondetection data of corticolous | ||
258 | lichens from a standardised monitoring across Switzerland", | 258 | lichens from a standardised monitoring across Switzerland", | ||
259 | "type": "dataset", | 259 | "type": "dataset", | ||
t | 260 | "url": null | t | 260 | "url": null, |
261 | "version": "1.0" | ||||
261 | } | 262 | } |