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@article{Schaeffer2004,
abstract = {Random regression models (RRM) have become common for the analysis of longitudinal data or repeated records on individuals over time. Applications in animal breeding research are emphasized while recognizing that RRM are used in many biological situations including human health. The best known application of RRM has been to genetic evaluation of dairy cattle using test day production records. The basic structure of a RRM is given. Other applications include growth traits in all species, genotype by environment interactions, and ad hoc proposals for the analysis of survival data and fertility data. RRM allow the researcher to study changes in genetic variability with time and allow selection of individuals to alter the general patterns of response over time. {\textcopyright} 2003 Elsevier B.V. All rights reserved.},
author = {Schaeffer, L. R.},
journal = {Livestock Production Science},
keywords = {Fertility,Growth,Random regressions,Survival,Test day models},
number = {1-3},
pages = {35--45},
publisher = {Elsevier},
title = {{Application of random regression models in animal breeding}},
volume = {86},
year = {2004}
}
@article{Kirkeby2021,
author = {Kirkeby, C. and Schwarz, D. and Denwood, M. and Farre, M. and Nielsen, S. S. and Gussmann, M. and Toft, N. and Halasa, T.},
doi = {10.3168/JDS.2020-19378},
issn = {0022-0302},
journal = {Journal of Dairy Science},
keywords = {cattle,differential somatic cell count,mastitis},
month = {mar},
number = {3},
pages = {3427--3438},
pmid = {33455778},
publisher = {Elsevier},
title = {{Dynamics of somatic cell count (SCC) and differential SCC during and following intramammary infections}},
volume = {104},
year = {2021}
}
@article{Nasri2008,
author = {Nasri, M. H.Fathi and France, J. and Odongo, N. E. and Lopez, S. and Bannink, A. and Kebreab, E.},
doi = {10.1017/S0021859608008101},
issn = {00218596},
journal = {Journal of Agricultural Science},
month = {dec},
number = {6},
pages = {633--641},
publisher = {Cambridge University Press},
title = {{Modelling the lactation curve of dairy cows using the differentials of growth functions}},
url = {https://doi.org/10.1017/S0021859608008101},
volume = {146},
year = {2008}
}
@article{Nyman2016,
author = {Nyman, A. K. and {Persson Waller}, K. and Emanuelson, U. and Fr{\"{o}}ssling, J.},
doi = {10.1016/J.PREVETMED.2016.11.009},
issn = {0167-5877},
journal = {Preventive Veterinary Medicine},
keywords = {Bacteriological culturing,Bayesian latent class analysis,Dairy cow,Diagnostic test,Mastitis,PCR analysis,Quarter milk samples,Sensitivity,Specificity,Test milking (DHI) samples},
month = {dec},
pages = {123--131},
pmid = {27931924},
publisher = {Elsevier},
title = {{Sensitivity and specificity of PCR analysis and bacteriological culture of milk samples for identification of intramammary infections in dairy cows using latent class analysis}},
volume = {135},
year = {2016}
}
@article{Tenhagen2006,
author = {Tenhagen, B. A. and K{\"{o}}ster, G. and Wallmann, J. and Heuwieser, W.},
doi = {10.3168/JDS.S0022-0302(06)72330-X},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Tenhagen et al. - 2006 - Prevalence of Mastitis Pathogens and Their Resistance Against Antimicrobial Agents in Dairy Cows in Brandenburg.pdf:pdf},
issn = {0022-0302},
journal = {Journal of Dairy Science},
keywords = {Antimicrobial resistance,Dairy cow,Mastitis},
month = {jul},
number = {7},
pages = {2542--2551},
pmid = {16772573},
publisher = {Elsevier},
title = {{Prevalence of Mastitis Pathogens and Their Resistance Against Antimicrobial Agents in Dairy Cows in Brandenburg, Germany}},
volume = {89},
year = {2006}
}
@misc{Bates1991,
author = {Bates, D.M. and Chambers, J.M.},
publisher = {Wadsworth & Brooks/Cole, Pacific Grove, CA},
title = {{Nonlinear models. Chapter 10}},
year = {1991}
}
@article{Grossman1988,
author = {Grossman, M. and Koops, W. J.},
journal = {Journal of Dairy Science},
number = {6},
pages = {1598--1608},
title = {{Multiphasic Analysis of Lactation Curves in Dairy Cattle}},
volume = {71},
year = {1988}
}
@article{VandenBorne2010,
author = {van den Borne, BHP and Halasa, T and van Schaik, G and Hogeveen, H and Nielen, M},
doi = {10.3168/jds.2009-3030},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/P van den Borne et al. - Unknown - Bioeconomic modeling of lactational antimicrobial treatment of new bovine subclinical intramammary in.pdf:pdf},
journal = {Journal of Dairy Science},
keywords = {antimicrobial treatment,stochastic economic model,subclinical mastitis,transmission},
pages = {4034--4044},
title = {{Bioeconomic modeling of lactational antimicrobial treatment of new bovine subclinical intramammary infections caused by contagious pathogens}},
volume = {93},
year = {2010}
}
@misc{VonElm2007,
author = {{Von Elm}, Erik and Altman, Douglas G. and Egger, Matthias and Pocock, Stuart J. and G{\o}tzsche, Peter C. and Vandenbroucke, Jan P.},
booktitle = {Annals of Internal Medicine},
doi = {10.7326/0003-4819-147-8-200710160-00010},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Von Elm et al. - 2007 - The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement Guidelines for repor.pdf:pdf},
issn = {00034819},
month = {oct},
number = {8},
pages = {573--577},
pmid = {17938396},
publisher = {American College of Physicians},
title = {{The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: Guidelines for reporting observational studies}},
urldate = {2020-11-02},
volume = {147},
year = {2007}
}
@article{Pantoja2009,
author = {Pantoja, J. C.F. and Hulland, C. and Ruegg, P. L.},
doi = {10.3168/JDS.2008-1477},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Pantoja, Hulland, Ruegg - 2009 - Somatic cell count status across the dry period as a risk factor for the development of clinical mastit.pdf:pdf},
issn = {1525-3198},
journal = {Journal of dairy science},
number = {1},
pages = {139--148},
pmid = {19109272},
publisher = {J Dairy Sci},
title = {{Somatic cell count status across the dry period as a risk factor for the development of clinical mastitis in the subsequent lactation}},
url = {https://pubmed.ncbi.nlm.nih.gov/19109272/},
volume = {92},
year = {2009}
}
@article{Peters2015,
author = {Peters, M D P and Silveira, I D B and Fischer, V},
doi = {10.1017/S1751731115001391},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Peters, Silveira, Fischer - 2015 - Impact of subclinical and clinical mastitis on sensitivity to pain of dairy cows.pdf:pdf},
keywords = {clinical mastitis,lactating cows,nociceptive threshold,subclinical mastitis,thermal threshold meter},
title = {{Impact of subclinical and clinical mastitis on sensitivity to pain of dairy cows}},
year = {2015}
}
@misc{SEGES2020,
author = {SEGES},
title = {{Cattle breeds in Danish Dairy production}},
url = {https://www.seges.dk/da-dk/fagomraader/kvaeg/tal-og-fakta-om-kvaegproduktion/maelkeproduktion},
urldate = {2020-09-11},
year = {2020}
}
@article{Skjølstrup2021,
author = {Skj{\o}lstrup, Nanna K. and Nielsen, Liza R. and Jensen, Carsten S. and Lastein, Dorte B.},
doi = {10.3389/FVETS.2020.547975/FULL},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Skj{\o}lstrup et al. - 2021 - Veterinary Herd Health Consultancy and Antimicrobial Use in Dairy Herds.pdf:pdf},
issn = {22971769},
journal = {Frontiers in Veterinary Science},
keywords = {antimicrobial resistance,antimicrobial use,dairy cattle,decision-making,farmers,social factors,veterinarians,veterinary herd health consultancy},
month = {feb},
publisher = {Frontiers Media S.A.},
title = {{Veterinary Herd Health Consultancy and Antimicrobial Use in Dairy Herds}},
volume = {7},
year = {2021}
}
@article{Gustavsson2014,
author = {Gustavsson, F. and Buitenhuis, A. J. and Johansson, M. and Bertelsen, H. P. and Glantz, M. and Poulsen, N. A. and {Lindmark M{\aa}nsson}, H. and St{\aa}lhammar, H. and Larsen, L. B. and Bendixen, C. and Paulsson, M. and Andr{\'{e}}n, A.},
doi = {10.3168/jds.2013-7312},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Gustavsson et al. - 2014 - Effects of breed and casein genetic variants on protein profile in milk from Swedish Red, Danish Holstein, an.pdf:pdf},
issn = {15253198},
journal = {Journal of Dairy Science},
keywords = {Casein,Composite genotype,Genetic polymorphism,Milk protein composition},
month = {jun},
number = {6},
pages = {3866--3877},
pmid = {24704225},
publisher = {Elsevier Ltd},
title = {{Effects of breed and casein genetic variants on protein profile in milk from Swedish Red, Danish Holstein, and Danish Jersey cows}},
volume = {97},
year = {2014}
}
@misc{Vehtari,
author = {Vehtari, Aki},
booktitle = {Github},
title = {{BDA_R_demos}},
url = {https://github.com/avehtari/BDA_R_demos}
}
@article{Toft2019,
author = {Toft, N. and Halasa, T. and Nielsen, S. S. and Hechinger, S. and Zervens, L. M. and Schwarz, D. and Kirkeby, C.},
doi = {10.1016/j.prevetmed.2019.05.002},
issn = {01675877},
journal = {Preventive Veterinary Medicine},
keywords = {Bacterial culture,Latent class analysis,Mastitis,Staph. aureus,qPCR},
month = {nov},
pages = {104689},
pmid = {31097205},
publisher = {Elsevier B.V.},
title = {{Composite or aseptic quarter milk samples: Sensitivity and specificity of PCR and bacterial culture of Staphylococcus aureus based on Bayesian latent class evaluation}},
volume = {171},
year = {2019}
}
@article{Shook2017,
author = {Shook, G. E. and Kirk, R. L.Bamber and Welcome, F. L. and Schukken, Y. H. and Ruegg, P. L.},
doi = {10.3168/JDS.2017-12810},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Shook et al. - 2017 - Relationship between intramammary infection prevalence and somatic cell score in commercial dairy herds.pdf:pdf},
issn = {0022-0302},
journal = {Journal of Dairy Science},
keywords = {intramammary infection,mastitis pathogens,somatic cell score,udder health},
month = {dec},
number = {12},
pages = {9691--9701},
pmid = {28987587},
publisher = {Elsevier},
title = {{Relationship between intramammary infection prevalence and somatic cell score in commercial dairy herds}},
volume = {100},
year = {2017}
}
@article{Verdugo2015,
author = {Verdugo, Cristobal and Toft, Nils and Nielsen, S{\o}ren Saxmose},
doi = {10.1016/j.prevetmed.2015.07.012},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Verdugo, Toft, Nielsen - 2015 - Within- and between-herd prevalence variation of Mycobacterium avium subsp. paratuberculosis infection a.pdf:pdf},
issn = {01675877},
journal = {Preventive Veterinary Medicine},
keywords = {Bayesian inference,Control programme,Mycobacterium avium subsp. paratuberculosis,Prevalence},
month = {oct},
number = {3-4},
pages = {282--287},
publisher = {Elsevier},
title = {{Within- and between-herd prevalence variation of Mycobacterium avium subsp. paratuberculosis infection among control programme herds in Denmark (2011-2013)}},
volume = {121},
year = {2015}
}
@misc{Maechler,
author = {Maechler, Martin},
title = {{R: Empirical Cumulative Distribution Function}},
url = {https://stat.ethz.ch/R-manual/R-devel/library/stats/html/ecdf.html},
urldate = {2021-12-17}
}
@article{Halasa2007,
author = {Halasa, T. and Huijps, K. and {\O}ster{\aa}s, O. and Hogeveen, H.},
doi = {10.1080/01652176.2007.9695224},
issn = {18755941},
journal = {Veterinary Quarterly},
keywords = {Cattle diseases,Dairy cattle,Economics,Mammary gland diseases,Management,Mastitis},
number = {1},
pages = {18--31},
title = {{Economic effects of bovine mastitis and mastitis management: A review}},
volume = {29},
year = {2007}
}
@article{VanderWeele2012,
author = {VanderWeele, Tyler J.},
doi = {10.1515/2161-962X.1004},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/VanderWeele - 2012 - Confounding and effect modification Distribution and measure.pdf:pdf},
issn = {2161962X},
journal = {Epidemiologic Methods},
keywords = {Causal inference,confounding,effect heterogeneity,effect modification},
number = {1},
pages = {54--82},
publisher = {Walter de Gruyter GmbH},
title = {{Confounding and effect modification: Distribution and measure}},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249691/},
volume = {1},
year = {2012}
}
@article{Harmon1994,
author = {Harmon, R. J.},
doi = {10.3168/jds.S0022-0302(94)77153-8},
issn = {00220302},
journal = {Journal of Dairy Science},
keywords = {BTSCC,GSH-Px,PMN,bulk tank SCC,glutathione peroxidase,mastitis,polymorphonuclear neutrophil leukocyte,somatic cell count},
month = {jul},
number = {7},
pages = {2103--2112},
pmid = {7929968},
publisher = {Elsevier},
title = {{Physiology of Mastitis and Factors Affecting Somatic Cell Counts}},
volume = {77},
year = {1994}
}
@article{Gonda2006,
author = {Gonda, M. G. and Chang, Y. M. and Shook, G. E. and Collins, M. T. and Kirkpatrick, B. W.},
journal = {Journal of Dairy Science},
keywords = {Genetic variation,Heritability,Holstein,Johne's disease},
number = {5},
pages = {1804--1812},
publisher = {American Dairy Science Association},
title = {{Genetic variation of Mycobacterium avium ssp. paratuberculosis infection in US Holsteins}},
volume = {89},
year = {2006}
}
@article{Wood1967,
author = {Wood, P. D.P.},
doi = {10.1038/216164A0},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wood - 1967 - Algebraic model of the lactation curve in cattle.pdf:pdf},
journal = {Nature},
number = {5111},
pages = {164--165},
title = {{Algebraic model of the lactation curve in cattle}},
volume = {216},
year = {1967}
}
@article{Gussmann2018,
author = {Gussmann, Maya and Gr{\ae}sb{\o}ll, Kaare and Toft, Nils and Nielsen, S{\o}ren S. and Farre, Michael and Kirkeby, Carsten and Halasa, Tariq},
doi = {10.3168/JDS.2017-12994},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Gussmann et al. - 2018 - Determinants of antimicrobial treatment for udder health in Danish dairy cattle herds.pdf:pdf},
issn = {0022-0302},
journal = {Journal of Dairy Science},
keywords = {antibiotic treatment,cluster analysis,dairy cattle,mastitis},
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publisher = {Elsevier},
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author = {{Olde Riekerink}, R. G. M. and Barkema, H. W. and Veenstra, W. and Berg, F. E. and Stryhn, H. and Zadoks, R. N.},
doi = {10.3168/JDS.2007-0001},
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journal = {Journal of Dairy Science},
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number = {8},
pages = {3733--3741},
publisher = {Elsevier},
title = {{Somatic Cell Count During and Between Milkings}},
volume = {90},
year = {2007}
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author = {Laevens, H. and Deluyker, H. and Schukken, Y. H. and {De Meulemeester}, L. and Vandermeersch, R. and {De Mu{\^{e}}lenaere}, E. and {De Kruif}, A.},
doi = {10.3168/JDS.S0022-0302(97)76295-7},
issn = {0022-0302},
journal = {Journal of Dairy Science},
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publisher = {Elsevier},
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author = {Bradley, Andrew and Green, Martin},
doi = {10.1136/INPRACT.27.6.310},
issn = {20427689},
journal = {In Practice},
number = {6},
pages = {310--315},
publisher = {BMJ Publishing Group},
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author = {Mahmmod, Y. S. and Klaas, I. C. and Enevoldsen, C.},
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file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Mahmmod, Klaas, Enevoldsen - 2017 - DNA carryover in milk samples from routine milk recording used for PCR-based diagnosis of bovine Sta.pdf:pdf;:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Mahmmod, Klaas, Enevoldsen - 2017 - DNA carryover in milk samples from routine milk recording used for PCR-based diagnosis of bovine (2).pdf:pdf;:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Mahmmod, Klaas, Enevoldsen - 2017 - DNA carryover in milk samples from routine milk recording used for PCR-based diagnosis of bovine (3).pdf:pdf},
issn = {15253198},
journal = {Journal of Dairy Science},
keywords = {DNA carryover,PathoProof PCR assay,Staphylococcus aureus,milking order,test misclassification},
month = {jul},
number = {7},
pages = {5709--5716},
pmid = {28527807},
publisher = {Elsevier Inc.},
title = {{DNA carryover in milk samples from routine milk recording used for PCR-based diagnosis of bovine Staphylococcus aureus mastitis}},
url = {https://doi.org/10.3168/jds.2016-12330},
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author = {{De Haas}, Y. and Barkema, H. W. and Veerkamp, R. F.},
doi = {10.3168/JDS.S0022-0302(02)74196-9},
issn = {0022-0302},
journal = {Journal of dairy science},
keywords = {Animals,Bovine / microbiology*,Bovine / pathology,Bovine / physiopathology,Cattle,Cell Count*,Coagulase / analysis,Escherichia coli / isolation & purification,Escherichia coli Infections / pathology,Escherichia coli Infections / physiopathology,Female,H W Barkema,Lactation*,MEDLINE,Mastitis,Milk / cytology*,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,Non-U.S. Gov't,Parity,PubMed Abstract,R F Veerkamp,Research Support,Staphylococcal Infections / pathology,Staphylococcal Infections / physiopathology,Staphylococcus / enzymology,Staphylococcus / isolation & purification,Staphylococcus aureus / isolation & purification,Streptococcal Infections / pathology,Streptococcal Infections / physiopathology,Streptococcus / isolation & purification,Y de Haas,doi:10.3168/jds.S0022-0302(02)74196-9,pmid:12086069},
number = {5},
pages = {1314--1323},
pmid = {12086069},
publisher = {J Dairy Sci},
title = {{The effect of pathogen-specific clinical mastitis on the lactation curve for somatic cell count}},
url = {https://pubmed.ncbi.nlm.nih.gov/12086069/},
volume = {85},
year = {2002}
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author = {Neal, C. and Thornley, J. H.M.},
doi = {10.1017/S0021859600037710},
journal = {The Journal of Agricultural Science},
number = {2},
pages = {389--400},
title = {{The lactation curve in cattle: A mathematical model of the mammary gland}},
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author = {Silvestre, A. M. and Petim-Batista, F. and Cola{\c{c}}o, J.},
doi = {10.3168/jds.S0022-0302(06)72250-0},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Silvestre, Petim-Batista, Cola{\c{c}}o - 2006 - The accuracy of seven mathematical functions in modeling dairy cattle lactation curves based o.pdf:pdf},
issn = {00220302},
journal = {Journal of Dairy Science},
keywords = {Dairy cow,Lactation curve},
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number = {5},
pages = {1813--1821},
pmid = {16606753},
publisher = {American Dairy Science Association},
title = {{The accuracy of seven mathematical functions in modeling dairy cattle lactation curves based on test-day records from varying sample schemes}},
url = {http://www.journalofdairyscience.org/article/S0022030206722500/fulltext http://www.journalofdairyscience.org/article/S0022030206722500/abstract https://www.journalofdairyscience.org/article/S0022-0302(06)72250-0/abstract},
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annote = {R package version 3.1-152},
author = {Pinheiro, Jose and Bates, Douglas and DebRoy, Saikat and Sarkar, Deepayan and {R Core Team}},
title = {{nlme: Linear and Nonlinear Mixed Effects Models}},
url = {httpsCRAN.R-project.orgpackage=nlme},
year = {2021}
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author = {Spiegelhalter, D. J. and Myles, J. P. and Jones, D. R. and Abrams, K. R.},
booktitle = {Health Technology Assessment},
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pmid = {11134920},
title = {{Bayesian methods in health technology assessment: A review}},
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year = {2000}
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author = {Jashari, R. and Piepers, S. and {De Vliegher}, S.},
doi = {10.3168/jds.2015-10753},
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issn = {15253198},
journal = {Journal of Dairy Science},
keywords = {dairy cow,infection status,predictive value,somatic cell count,test characteristics},
month = {nov},
number = {11},
pages = {9271--9286},
pmid = {27544856},
publisher = {Elsevier Inc.},
title = {{Evaluation of the composite milk somatic cell count as a predictor of intramammary infection in dairy cattle}},
url = {https://pubmed.ncbi.nlm.nih.gov/27544856/},
volume = {99},
year = {2016}
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author = {Carta, A. and Sanna, S. R. and Casu, S.},
journal = {Livestock Production Science},
keywords = {Dairy sheep,Lactation curve,Seasonal effect,TD model},
number = {1},
pages = {37--44},
title = {{Estimating lactation curves and seasonal effects for milk, fat and protein in Sarda dairy sheep with a test day model}},
volume = {44},
year = {1995}
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@article{Hagnestam-Nielsen2009,
author = {Hagnestam-Nielsen, C. and Emanuelson, U. and Berglund, B. and Strandberg, E.},
doi = {10.3168/jds.2008-1719},
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issn = {15253198},
journal = {Journal of Dairy Science},
keywords = {Dairy cow,Production loss,Somatic cell count,Subclinical mastitis},
month = {jul},
number = {7},
pages = {3124--3133},
pmid = {19528590},
publisher = {American Dairy Science Association},
title = {{Relationship between somatic cell count and milk yield in different stages of lactation}},
volume = {92},
year = {2009}
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@misc{Dunn2011,
author = {Dunn, Alan M. and Hofmann, Owen S. and Waters, Brent and Witchel, Emmett},
booktitle = {Proceedings of the 20th USENIX Security Symposium},
isbn = {9781931971874},
pages = {395--410},
title = {{Cloaking malware with the trusted platform module}},
year = {2011}
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author = {Bolker, Benjamin M. and Gardner, Beth and Maunder, Mark and Berg, Casper W. and Brooks, Mollie and Comita, Liza and Crone, Elizabeth and Cubaynes, Sarah and Davies, Trevor and de Valpine, Perry and Ford, Jessica and Gimenez, Olivier and K{\'{e}}ry, Marc and Kim, Eun Jung and Lennert-Cody, Cleridy and Magnusson, Arni and Martell, Steve and Nash, John and Nielsen, Anders and Regetz, Jim and Skaug, Hans and Zipkin, Elise},
doi = {10.1111/2041-210X.12044},
editor = {Ramula, Satu},
issn = {2041210X},
journal = {Methods in Ecology and Evolution},
keywords = {AD Model Builder,JAGS,Optimization,Parameter estimation,R,WinBUGS},
month = {jun},
number = {6},
pages = {501--512},
publisher = {John Wiley & Sons, Ltd},
title = {{Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS}},
url = {http://doi.wiley.com/10.1111/2041-210X.12044},
volume = {4},
year = {2013}
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@misc{SEGES2021a,
author = {SEGES},
title = {{Nye regler for gold- og yverbehandlinger af malkekv{\ae}g}},
url = {https://www.landbrugsinfo.dk/public/0/a/0/sundhed_velfard_nye_-regler_gold_-yverbehandlinger},
urldate = {2021-10-14},
year = {2021}
}
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author = {Milner, P. and Page, K. L. and Hillerton, J. E.},
doi = {10.3168/JDS.S0022-0302(97)76008-9},
issn = {00220302},
journal = {Journal of Dairy Science},
keywords = {Intramammary treatment,Somatic cell count,Staphylococcus aureus,Streptococcus uberis},
number = {5},
pages = {859--863},
pmid = {9178126},
publisher = {American Dairy Science Association},
title = {{The Effects of Early Antibiotic Treatment Following Diagnosis of Mastitis Detected by a Change in the Electrical Conductivity of Milk}},
volume = {80},
year = {1997}
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@misc{SEGESBovisoft2020,
author = {{SEGES Bovisoft}},
title = {{BoviSoft | Software til landbruget | SEGES}},
url = {https://www.seges.dk/da-dk/software/kvaeg/bovisoft},
urldate = {2020-09-07},
year = {2020}
}
@misc{SEGES2021,
author = {SEGES},
title = {{Fakta om m{\ae}lkeproduktion | Kv{\ae}g | SEGES}},
url = {https://www.seges.dk/fagomraader/kvaeg/tal-og-fakta-om-kvaegproduktion/maelkeproduktion#Danske malkekv{\ae}gsracer},
urldate = {2021-12-29},
year = {2021}
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author = {Pedersen, M. W. and Berg, C. W. and Thygesen, U. H. and Nielsen, A. and Madsen, H.},
doi = {10.1016/j.ecolmodel.2011.01.007},
issn = {03043800},
journal = {Ecological Modelling},
keywords = {AD Model Builder,Hidden Markov model,Mixed model,Monte Carlo,Theta logistic population model,WinBUGS},
month = {apr},
number = {8},
pages = {1394--1400},
publisher = {Elsevier},
title = {{Estimation methods for nonlinear state-space models in ecology}},
volume = {222},
year = {2011}
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@misc{RYKfonden2012,
author = {RYK fonden},
title = {{RYK fonden, milk recording scheme}},
url = {https://www.landbrugsinfo.dk/public/9/6/5/malkeproduktion_ryk_ydelseskontrol},
year = {2012}
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author = {Niemi, R.E. and Hovinen, M. and Rajala-Schultz, P.J.},
doi = {10.3168/JDS.2021-20918},
issn = {0022-0302},
journal = {Journal of Dairy Science},
keywords = {composite somatic cell count,drying off,milk production,time series analysis},
month = {feb},
number = {2},
pages = {1387--1401},
pmid = {34955269},
publisher = {Elsevier},
title = {{Selective dry cow therapy effect on milk yield and somatic cell count: A retrospective cohort study}},
url = {http://www.journalofdairyscience.org/article/S0022030221010651/fulltext http://www.journalofdairyscience.org/article/S0022030221010651/abstract https://www.journalofdairyscience.org/article/S0022-0302(21)01065-1/abstract},
volume = {105},
year = {2022}
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author = {EU},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Unknown - Unknown - Animal Health Law 2016.pdf:pdf},
title = {{Animal Health Law 2016}},
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year = {2016}
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author = {Johnson, Michael L.},
doi = {10.1016/S0091-679X(07)84024-6},
isbn = {0123725208},
issn = {0091679X},
journal = {Methods in Cell Biology},
pages = {781--805},
pmid = {17964949},
title = {{Nonlinear Least-Squares Fitting Methods}},
volume = {84},
year = {2008}
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author = {Denwood, M. J. and Kleen, J. L. and Jensen, D. B. and Jonsson, N. N.},
doi = {10.3168/jds.2017-12828},
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issn = {15253198},
journal = {Journal of Dairy Science},
keywords = {acidosis,remote sensing data,reticuloruminal pH,statistical model},
month = {jan},
number = {1},
pages = {233--245},
pmid = {29055552},
publisher = {Elsevier Inc.},
title = {{Describing temporal variation in reticuloruminal pH using continuous monitoring data}},
volume = {101},
year = {2018}
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@misc{SEGES,
author = {SEGES},
booktitle = {Landbrug og f{\o}devarer},
title = {{Danish Cattle Database}},
url = {https://www.seges.dk/fagomraader/kvaeg/raadgivning/kvaeg-it}
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author = {Cox, D. R. and Kartsonaki, Christiana and Keogh, Ruth H.},
doi = {10.1016/J.SPL.2018.02.015},
issn = {0167-7152},
journal = {Statistics & Probability Letters},
keywords = {Big data,Electronic health records,Epidemiology,Metrology,Precision},
month = {may},
pages = {111--115},
publisher = {North-Holland},
title = {{Big data: Some statistical issues}},
volume = {136},
year = {2018}
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author = {Madouasse, A. and Huxley, J. N. and Browne, W. J. and Bradley, A. J. and Green, M. J.},
doi = {10.1016/J.PREVETMED.2010.05.005},
issn = {0167-5877},
journal = {Preventive Veterinary Medicine},
keywords = {Herd,Mastitis,Somatic cell count},
month = {aug},
number = {1-2},
pages = {56--64},
pmid = {20627342},
publisher = {Elsevier},
title = {{Somatic cell count dynamics in a large sample of dairy herds in England and Wales}},
volume = {96},
year = {2010}
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author = {Mahmmod, Y. S. and Klaas, I. C. and Nielsen, S. S. and Katholm, J. and Toft, N.},
doi = {10.3168/jds.2012-6059},
issn = {00220302},
journal = {Journal of Dairy Science},
keywords = {Dairy cow,Presampling procedure,Staphylococcus aureus,Teat disinfection},
month = {apr},
number = {4},
pages = {2226--2233},
pmid = {23403201},
publisher = {J Dairy Sci},
title = {{Effect of presampling procedures on real-time PCR used for diagnosis of intramammary infections with Staphylococcus aureus in dairy cows at routine milk recordings}},
url = {https://pubmed.ncbi.nlm.nih.gov/23403201/},
volume = {96},
year = {2013}
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author = {Paul, S. and Agger, J. F. and Agerholm, J. S. and Markussen, B.},
doi = {10.1016/j.prevetmed.2014.01.018},
issn = {01675877},
journal = {Preventive Veterinary Medicine},
keywords = {Bayesian analysis,Cattle,Coxiella burnetii,Seroprevalence,Test uncertainty,True prevalence},
month = {mar},
number = {4},
pages = {504--511},
title = {{Prevalence and risk factors of Coxiella burnetii seropositivity in Danish beef and dairy cattle at slaughter adjusted for test uncertainty}},
volume = {113},
year = {2014}
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author = {Dufour, Simon and Labrie, Jos{\'{e}}e and Jacques, Mario},
doi = {10.1128/mra.00133-19},
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issn = {2576-098X},
journal = {Microbiology Resource Announcements},
month = {apr},
number = {15},
publisher = {American Society for Microbiology},
title = {{The Mastitis Pathogens Culture Collection}},
url = {/pmc/articles/PMC6460030/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460030/},
volume = {8},
year = {2019}
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@article{Kargo2007,
author = {Kargo, Morten},
title = {{Crossbreeding - An Important Part of Sustainable Breeding in Dairy Cattle and Possibilities for Implementation}},
url = {https://www.researchgate.net/publication/242322753_Crossbreeding_-_An_Important_Part_of_Sustainable_Breeding_in_Dairy_Cattle_and_Possibilities_for_Implementation},
year = {2007}
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@misc{SEGESwebdyr2020,
author = {SEGES webdyr},
title = {{Webdyr Plus | Software til landbruget | SEGES}},
url = {https://www.seges.dk/da-dk/software/kvaeg/webdyr-plus},
urldate = {2020-09-07},
year = {2020}
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author = {Taponen, S. and Liski, E. and Heikkil{\"{a}}, A. M. and Py{\"{o}}r{\"{a}}l{\"{a}}, S.},
doi = {10.3168/JDS.2016-11465},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Taponen et al. - 2017 - Factors associated with intramammary infection in dairy cows caused by coagulase-negative staphylococci, Staphyl.pdf:pdf},
issn = {0022-0302},
journal = {Journal of Dairy Science},
keywords = {bovine mastitis,dairy cow,pathogen,polymerase chain reaction assay,risk factor},
month = {jan},
number = {1},
pages = {493--503},
pmid = {28341052},
publisher = {Elsevier},
title = {{Factors associated with intramammary infection in dairy cows caused by coagulase-negative staphylococci, Staphylococcus aureus, Streptococcus uberis, Streptococcus dysgalactiae, Corynebacterium bovis, or Escherichia coli}},
volume = {100},
year = {2017}
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@misc{Padfield2020,
abstract = {Non-linear least squares regression with the Levenberg-Marquardt algorithm using multiiple starting values for increasing the chance that the minimum found is the global minim},
author = {Padfield, Daniel and Matheson, Granville},
file = {:C\:/Users/zjt234/Downloads/nls.multstart.pdf:pdf},
pages = {1--5},
publisher = {CRAN},
title = {{Package ‘nls.multstart'}},
year = {2020}
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@misc{Plummer2021,
author = {Plummer, M. and Stukalov, A. and Denwood, M.},
file = {:C\:/Users/zjt234/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Unknown - 2019 - Package 'rjags'(2).pdf:pdf},
title = {{rjags: Bayesian Graphical Models using MCMC}},
year = {2021}
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@misc{Microsoft2020,
author = {Microsoft},
title = {{Azure}},
url = {https://azure.microsoft.com/en-us/features/storage-explorer/},
urldate = {2020-09-11},
year = {2020}
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author = {Kuipers, A. and Koops, W. J. and Wemmenhove, H.},
doi = {10.3168/JDS.2014-8428},
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issn = {0022-0302},
journal = {Journal of Dairy Science},
keywords = {Antibiotic use,Dairy farmer group,Treatment category,Variation and trend},
month = {feb},
number = {2},
pages = {1632--1648},
pmid = {26709178},
publisher = {Elsevier},
title = {{Antibiotic use in dairy herds in the Netherlands from 2005 to 2012}},
volume = {99},
year = {2016}
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author = {Cederl{\"{o}}f, Sara Ellinor and Toft, Nils and Aalbaek, Bent and Klaas, Ilka Christine},
doi = {10.1186/1751-0147-54-65/TABLES/3},
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issn = {17510147},
journal = {Acta veterinaria Scandinavica},
keywords = {Animal Anatomy / Morphology / Histology,Veterinary Medicine/Veterinary Science},
month = {nov},
number = {1},
pages = {65},
pmid = {23164432},
publisher = {BioMed Central},
title = {{Latent class analysis of the diagnostic characteristics of PCR and conventional bacteriological culture in diagnosing intramammary infections caused by Staphylococcus aureus in dairy cows at dry off.}},
url = {https://actavetscand.biomedcentral.com/articles/10.1186/1751-0147-54-65},
volume = {54},
year = {2012}
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issn = {15253198},
journal = {Journal of Dairy Science},
keywords = {Intramammary infection,Mastitis,Selective dry cow therapy},
month = {jun},
number = {6},
pages = {3606--3614},
pmid = {24746132},
publisher = {Elsevier Ltd},
title = {{Evaluation of the use of dry cow antibiotics in low somatic cell count cows}},
volume = {97},
year = {2014}
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author = {Patel, K. and Godden, S. M. and Royster, E. and Crooker, B. A. and Timmerman, J. and Fox, L.},
doi = {10.3168/JDS.2019-16692},
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issn = {0022-0302},
journal = {Journal of Dairy Science},
keywords = {bacteria count,bedding,mastitis,milk quality},
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