add references

source/bookdown/mas_uitrol_vlaanderen/index.Rmd

@@ -43,7 +43,7 @@ community: "inbo"
 publication_type: report
 funder: Instituut voor Natuur- en Bosonderzoek (INBO)
 rightsholder: Instituut voor Natuur- en Bosonderzoek (INBO)
-bibliography: references.bib
+bibliography: [software.bib, references.bib, layers.bib]
 link-citations: TRUE
 site: bookdown::bookdown_site
 output:

source/bookdown/mas_uitrol_vlaanderen/layers.bib

@@ -0,0 +1,61 @@
+@misc{landbouwgebruikspercelen,
+  author       = {{Agentschap Landbouw & Zeevisserij}},
+  year         = {2023},
+  title        = {{Open geodata: landbouwgebruikspercelen}},
+  url 	       = {https://landbouwcijfers.vlaanderen.be/open-geodata-landbouwgebruikspercelen}
+}
+
+@misc{landschapselementen,
+  author       = {{Agentschap Landbouw & Zeevisserij}},
+  year         = {2022},
+  title        = {{Open geodata: kaart landschapselementen}},
+  url 	       = {https://landbouwcijfers.vlaanderen.be/open-geodata-kaart-landschapselementen}
+}
+
+@misc{DSM,
+  author       = {{Agentschap Digitaal Vlaanderen}},
+  year         = {2014},
+  title        = {{Digitaal Hoogtemodel Vlaanderen II, DSM, raster, 5 m}},
+  url 	       = {https://download.vlaanderen.be/product/936-digitaal_hoogtemodel_vlaanderen_ii_dsm_raster_5_m}
+}
+
+@misc{DTM,
+  author       = {{Agentschap Digitaal Vlaanderen}},
+  year         = {2014},
+  title        = {{Digitaal Hoogtemodel Vlaanderen II, DTM, raster, 5 m}},
+  url 	       = {https://download.vlaanderen.be/product/938-digitaal_hoogtemodel_vlaanderen_ii_dtm_raster_5_m}
+}
+
+@misc{natuurbeheerplannen,
+  author       = {{Agentschap voor Natuur en Bos}},
+  year         = {2021},
+  title        = {{Natuurbeheerplannen}},
+  url 	       = {https://www.vlaanderen.be/datavindplaats/catalogus/natuurbeheerplannen}
+}
+
+@misc{natuurnetwerk,
+  author       = {{Interprovinciaal Overleg}},
+  year         = {2023},
+  title        = {{Dataset: Natuurnetwerk Nederland (NNN) - Provincies (INSPIRE geharmoniseerd)}},
+  url 	       = {https://www.pdok.nl/introductie/-/article/natuurnetwerk-nederland-nnn-}
+}
+
+@misc{ZNIEFF1,
+  year         = {2023},
+  title        = {{ZNIEFF de type 1 - Métropole}},
+  url 	       = {https://inpn-inspire.mnhn.fr/catalogue/srv/api/records/f30dd410-9c72-47f5-a384-96603ddc703e}
+}
+
+@misc{reseau-natura,
+  author       = {{Service public de Wallonie (SPW)}},
+  year         = {2017},
+  title        = {{Réseau Natura 2000 en vigueur - Série}},
+  url 	       = {https://geoportail.wallonie.be/catalogue/80a837d8-2c0b-4f77-b5d5-824e9780a4ae.html}
+}
+
+@misc{consnat,
+  author       = {{Service public de Wallonie (SPW)}},
+  year         = {2020},
+  title        = {{Conservation de la nature - Série}},
+  url 	       = {https://geoportail.wallonie.be/catalogue/435c454c-0d4b-41cf-a136-a1aba134d9ac.html}
+}

source/bookdown/mas_uitrol_vlaanderen/references.bib

@@ -1,8 +1,318 @@
-@Manual{R,
-  title = {R: A Language and Environment for Statistical Computing},
-  author = {{R Core Team}},
-  organization = {R Foundation for Statistical Computing},
-  address = {Vienna, Austria},
-  year = {2023},
-  url = {https://www.R-project.org/},
+@book{buckland2015,
+  title={Distance sampling: methods and applications},
+  author={Buckland, Stephen T and Rexstad, Eric A and Marques, Tiago Andr{\'e} and Oedekoven, Cornelia Sabrina},
+  volume={431},
+  year={2015},
+  publisher={Springer}
+}
+
+@article{thomas2012,
+	title = {Distance Sampling},
+	author = {Thomas, Len and Buckland, Stephen T. and Burnham, Kenneth P. and Anderson, David R. and Laake, Jeffrey L. and Borchers, David L. and Strindberg, Samantha},
+	year = {2012},
+	month = {08},
+	date = {2012-08-31},
+	journal = {Encyclopedia of Environmetrics},
+	doi = {10.1002/9780470057339.vad033.pub2},
+	url = {http://dx.doi.org/10.1002/9780470057339.vad033.pub2}
+}
+
+@techreport{wiersma2021,
+	title = {Trends van vogels van het agrarisch gebied van Flevoland in 2011-2021},
+	author = {Wiersma, Popko and Hakkert, Jitty},
+	year = {2021},
+	date = {2021},
+	publisher = {Grauwe Kiekendief - Kenniscentrum Akkervogels},
+	number = {GKA-Rapport (2021-17)},
+	address = {Scheemda}
+}
+
+@incollection{kéry2016,
+	title = {Modeling Abundance Using Hierarchical Distance Sampling},
+	author = {{Kéry}, Marc and Royle, J. Andrew},
+	year = {2016},
+	editor = {{Kéry}, Marc and Royle, J. Andrew},
+  booktitle = {{Applied Hierarchical Modeling in Ecology}},
+	publisher = {Elsevier},
+	pages = {393--461},
+	doi = {10.1016/b978-0-12-801378-6.00008-4}
+}
+
+@book{buckland2001,
+  title={Introduction to distance sampling: estimating abundance of biological populations},
+  author={Buckland, Stephen T and Anderson, David R and Burnham, Kenneth Paul and Laake, Jeffrey Lee and Borchers, David Louis and Thomas, Leonard},
+  year={2001},
+  publisher={Oxford university press}
+}
+
+@article{rosenstock2002,
+	title = {Landbird Counting Techniques: Current Practices and an Alternative},
+	author = {Rosenstock, Steven S. and Anderson, David R. and Giesen, Kenneth M. and Leukering, Tony and Carter, Michael F.},
+	editor = {Thompson III, F.},
+	year = {2002},
+	month = {01},
+	date = {2002-01-01},
+	journal = {The Auk},
+	pages = {46--53},
+	volume = {119},
+	number = {1},
+	doi = {10.1093/auk/119.1.46},
+	url = {http://dx.doi.org/10.1093/auk/119.1.46},
+	langid = {en}
+}
+
+@techreport{roodbergen2011,
+	title = {Achtergronddocument Meetnet Agrarische Soorten (MAS)},
+	author = {Roodbergen, Maja and van Scharenburg, Kees and Soldaat, Leo and Teunissen, Wolf and Koks, Ben and van Leeuwen, Merijn},
+	year = {2011},
+	publisher = {SOVON Vogelonderzoek Nederland},
+	number = {SOVON Onderzoeksrapport (2011/08)},
+	address = {Nijmegen},
+	langid = {nl}
+}
+
+@article{marques2007,
+	title = {Improving Estimates of Bird Density Using Multiple- Covariate Distance Sampling},
+	author = {Marques, Tiago A. and Thomas, Len and Fancy, Steven G. and Buckland, Stephen T.},
+	editor = {Handel, C. M.},
+	year = {2007},
+	month = {10},
+	date = {2007-10-01},
+	journal = {The Auk},
+	pages = {1229--1243},
+	volume = {124},
+	number = {4},
+	doi = {10.1093/auk/124.4.1229},
+	url = {http://dx.doi.org/10.1093/auk/124.4.1229},
+	langid = {en}
+}
+
+@article{gelman1992,
+  title={{Inference from iterative simulation using multiple sequences}},
+  author={Gelman, Andrew and Rubin, Donald B},
+  journal={Statistical Science},
+  volume={7},
+  number={4},
+  pages={457-472},
+  year={1992},
+  doi={10.1214/ss/1177011136}
+}
+
+@book{gelman2013,
+  title={{Bayesian data analysis}},
+  author={Gelman, A. and Carlin, J.B. and Stern, H.S. and Dunson, D.B. and Vehtari, A. and Rubin, D.B.},
+  year={2013},
+  edition = {3},
+  publisher={Chapman {and} Hall/CRC},
+  doi={10.1201/b16018}
+}
+
+@article{moilanen2002,
+	title = {Simple connectivity measures in spatial ecology},
+	author = {Moilanen, Atte and Nieminen, Marko},
+	year = {2002},
+	month = {04},
+	date = {2002-04},
+	journal = {Ecology},
+	pages = {1131--1145},
+	volume = {83},
+	number = {4},
+	doi = {10.1890/0012-9658(2002)083[1131:scmise]2.0.co;2},
+	url = {http://dx.doi.org/10.1890/0012-9658(2002)083[1131:SCMISE]2.0.CO;2},
+	langid = {en}
+}
+
+@techreport{klaassen2022,
+	title = {Evaluatie van de effecten van het agrarisch natuurbeheer op voorkomen en trends van akkervogels in de provincie Groningen 2015 - 2020},
+	author = {Klaassen, Raymond and Schultinga, Marjon and Sirks, {Aniëla} and Kleyheeg, Erik and Wiersma, Popko},
+	year = {2022},
+	publisher = {Grauwe Kiekendief - Kenniscentrum Akkervogels},
+	number = {GKA-rapport (2022-01)},
+	address = {Scheemda},
+	langid = {nl}
+}
+
+@article{zhang2016,
+	title = {Bayesian Regression Using a Prior on the Model Fit: The R2-D2 Shrinkage Prior},
+	author = {Zhang, Yan Dora and Naughton, Brian P. and Bondell, Howard D. and Reich, Brian J.},
+	year = {2016},
+	journal = {{arXiv}},
+	doi = {10.48550/ARXIV.1609.00046},
+	url = {https://arxiv.org/abs/1609.00046}
+}
+
+@article{yanchenko2021,
+	title = {The R2D2 Prior for Generalized Linear Mixed Models},
+	author = {Yanchenko, Eric and Bondell, Howard D. and Reich, Brian J.},
+	year = {2021},
+	date = {2021},
+	journal = {{arXiv}},
+	doi = {10.48550/ARXIV.2111.10718},
+	url = {https://arxiv.org/abs/2111.10718}
+}
+
+@article{sharps2023,
+	title = {Reversing declines in farmland birds: How much agri{-}environment provision is needed at farm and landscape scales?},
+	author = {Sharps, Elwyn and Hawkes, Robert W. and Bladon, Andrew J. and Buckingham, David L. and Border, Jennifer and Morris, Antony J. and Grice, Philip V. and Peach, Will J.},
+	year = {2023},
+	month = {01},
+	date = {2023-01-04},
+	journal = {Journal of Applied Ecology},
+	pages = {568--580},
+	volume = {60},
+	number = {4},
+	doi = {10.1111/1365-2664.14338},
+	url = {http://dx.doi.org/10.1111/1365-2664.14338},
+	langid = {en}
+}
+
+@misc{openstreetmapcontributors2022,
+  title = {Belgium dump retrieved from https://download.geofabrik.de/europe/belgium.html on 2022-02-22},
+  url = {https://www.openstreetmap.org},
+  author = {{OpenStreetMap contributors}},
+  year = 2022
+}
+
+@techreport{poelmans2021,
+	title = {Landgebruik en ruimtebeslag in Vlaanderen, toestand 2019},
+	author = {Poelmans, Lien and Janssen, Liliane and Hambsch, Lorenz},
+	year = {2021},
+	publisher = {Uitgevoerd in opdracht van het Vlaams Planbureau voor Omgeving},
+	number = {VITO-rapport (2021/RMA/R/2458)},
+	address = {Brussel},
+	url = {https://archief.algemeen.omgeving.vlaanderen.be/xmlui/handle/acd/449392}
+}
+
+@article{cochran1950,
+  title={The comparison of percentages in matched samples},
+  author={Cochran, William G},
+  journal={Biometrika},
+  volume={37},
+  number={3/4},
+  pages={256--266},
+  year={1950},
+  publisher={JSTOR}
+}
+
+@article{grafström2011,
+	title = {Spatially Balanced Sampling through the Pivotal Method},
+	author = {{Grafström}, Anton and {Lundström}, Niklas L. P. and Schelin, Lina},
+	year = {2011},
+	month = {10},
+	date = {2011-10-31},
+	journal = {Biometrics},
+	pages = {514--520},
+	volume = {68},
+	number = {2},
+	doi = {10.1111/j.1541-0420.2011.01699.x},
+	url = {http://dx.doi.org/10.1111/j.1541-0420.2011.01699.x},
+	langid = {en}
+}
+
+@techreport{onkelinx2023a,
+	title = {Trends op basis van de Algemene Broedvogelmonitoring Vlaanderen (ABV): Technisch achtergrondrapport voor de periode 2007-2022},
+	author = {Onkelinx, Thierry and Vermeersch, Glenn and Devos, Koen},
+	year = {2023},
+	date = {2023},
+	doi = {10.21436/inbor.89419879},
+	publisher = {Instituut voor Natuur- en Bosonderzoek},
+	number = {Rapporten van het Instituut voor Natuur- en Bosonderzoek 2023 (1)},
+	address = {Brussel}
+}
+
+@article{miller2013,
+	title = {Spatial models for distance sampling data: recent developments and future directions},
+	author = {Miller, David L. and Burt, M. Louise and Rexstad, Eric A. and Thomas, Len},
+	editor = {Gimenez, Olivier},
+	year = {2013},
+	month = {08},
+	date = {2013-08-27},
+	journal = {Methods in Ecology and Evolution},
+	pages = {1001--1010},
+	volume = {4},
+	number = {11},
+	doi = {10.1111/2041-210x.12105},
+	url = {http://dx.doi.org/10.1111/2041-210X.12105},
+	langid = {en}
+}
+
+@article{royle2004,
+	title = {Modeling abundance effects in distance sampling},
+	author = {Royle, J. Andrew and Dawson, Deanna K. and Bates, Scott},
+	year = {2004},
+	month = {06},
+	date = {2004-06},
+	journal = {Ecology},
+	pages = {1591--1597},
+	volume = {85},
+	number = {6},
+	doi = {10.1890/03-3127},
+	url = {http://dx.doi.org/10.1890/03-3127},
+	langid = {en}
+}
+
+@article{hedley2004,
+	title = {Spatial models for line transect sampling},
+	author = {Hedley, Sharon L. and Buckland, Stephen T.},
+	year = {2004},
+	month = {06},
+	date = {2004-06},
+	journal = {Journal of Agricultural, Biological, and Environmental Statistics},
+	pages = {181--199},
+	volume = {9},
+	number = {2},
+	doi = {10.1198/1085711043578},
+	url = {http://dx.doi.org/10.1198/1085711043578},
+	langid = {en}
+}
+
+@article{wadoux2023,
+	title = {Uncertainty of spatial averages and totals of natural resource maps},
+	author = {Wadoux, {Alexandre M. J.{-}C.} and Heuvelink, Gerard B. M.},
+	year = {2023},
+	month = {04},
+	date = {2023-04-10},
+	journal = {Methods in Ecology and Evolution},
+	pages = {1320--1332},
+	volume = {14},
+	number = {5},
+	doi = {10.1111/2041-210x.14106},
+	url = {http://dx.doi.org/10.1111/2041-210X.14106},
+	langid = {en}
+}
+
+@techreport{agentschapvoornatuurenbos2021,
+	title = {Achtergrondrapport bij het soortenbeschermingsprogramma voor de akkervogels},
+	author = {{Agentschap voor Natuur en Bos}},
+	year = {2021},
+	number = {MB 20/12/2021},
+	publisher = {Agentschap voor Natuur en Bos},
+	address = {Brussel}
+}
+
+@techreport{dochy2005,
+	title = {Van de stakkers van de akkers naar de helden van de velden. Beschermingsmaatregelen voor akkervogels.},
+	author = {Dochy, Olivier and Hens, Maarten},
+	year = {2005},
+	address = {Brussel, i.s.m. het provinciebestuur West-Vlaanderen, Brugge},
+	number = {Rapport van het Instituut voor Natuurbehoud (IN.R.2005.01)}
+}
+
+@techreport{dochy2021,
+	title = {Resultaten van de Frans-Belgische inventarisatie van plattelandsvogels in 2013 en 2019},
+	author = {Dochy, Olivier},
+	year = {2021},
+	publisher = {Provincie West-Vlaanderen},
+	address = {Brugge},
+	langid = {nl}
+}
+
+@techreport{vermeersch2018,
+	title = {Methodehandleiding bij het project Algemene Broedvogelmonitoring Vlaanderen (ABV)},
+	author = {Vermeersch, Glenn and Ledegen, Hannes and Feys, Simon},
+	year = {2018},
+	doi = {10.21436/inbor.15674942},
+	publisher = {Instituut voor Natuur- en Bosonderzoek},
+	number = {Rapporten van het Instituut voor Natuur- en Bosonderzoek 2018 (93)},
+	address = {Brussel}
 }