Publications by Sam Rowe
case control preliminary analysis
Table of contents Acknowledgements Import data and start packages Dataframe summary Reasons for exclusion Show duplicates Cases Controls Incomplete pairs Remove exclusions from dataset Dataframe summary of new dataset Compare cases and controls Models Univariable conditional logistic regression. No covariates. Multivariable conditional logist...
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cow movement experiment
library(tidyverse) We assume that in a herd of 1000 cows, each cow spends 200 days in Pen X. This means that the average cow has 200 cow-days (rows) and 1 of those rows will be move==1 I’m guessing that someone would observe this in the data then calculate that the probability of movement on an average day is 1 / 200 = 0.005. Below is my attempt ...
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Prelim results - prediction for John House
Table of contents Conclusions Import data and run packages Identify 80th percentile for each outcome probability Objectives Show overview of predictions Show ROC curves Show predictions (probability) by true status for each outcome Performance using different thresholds Show distribution of model Se/Sp by herd More tables shown in a different ...
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Bovine digital dermatitis in Australian Dairy Herds: Sampling
Development of sampling strategy to identify bovine digital dermatitis in Australian dairy cows Table of contents Prevalence of cow-level DD by farm Plot of DD vs milking stage stratified by farm (loess smoother) GLM and GLMM to investigate association between milking stage and odds of DD Conclusion Sample size table Step 1 is to estimate true p...
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Preliminary data
Table of contents Acknowledgements Import data and run packages Pathogen profiles Frequency of mastitis pathogens for intensive and non-intensive herds Treatment targets by system Proportion of pathogen groups identified by point of care tests as a treatment target. Treatment target = Gram positive bacteria only Treatment target = Gram positiv...
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Epidemiology of bovine digital dermatitis in Australian dairy cows
Epidemiology of bovine digital dermatitis in Australian dairy cows Acknowledgements Authors and affiliations Sam Rowe1 Bill Tranter,2,3 Ash Phipps,4 Andrew McPherson,1 Richard Laven,5 John House,1 Ruth Zadoks,1 1Sydney School of Veterinary Science, The University of Sydney, Camden, New South Wales 2570, Australia 2College of Public Health, Medica...
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Clinical mastitis decision support tool: Sample size calculation
Treatments Positive control = Standard treatment on the farm Treatment = Decision support tool Outcomes The primary outcome will be absence of recurrence of clinical mastitis Sample size assumptions Expected absence of recurrence for control group = 70% (Based on large dataset of Australian dairy herds, unpublished) Expected absence of recurre...
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Bovine digital dermatitis in Australian Dairy Herds
# About this document This is an interim analysis report for an epidemologic study of digital dermatitis in dairy herds in Australia # Acknowledgements Sam Rowe1 Bill Tranter,2,3 Ash Phipps,4 Andrew McPherson,1 Richard Laven,5 John House,1 Ruth Zadoks,1 1Sydney School of Veterinary Science, The University of Sydney, Camden, New South Wales 25...
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Identification of an immunoassay for investigating previous exposure to Coxiella burnetii in Australian alpacas
Acknowledgements Author list for this study: Anastasia N. Tellis1, Sam M. Rowe2, Ronald Coilparampil3, Cheryl Jenkins3, Andrew Dart2, Ruth N. Zadoks2 and Katrina L. Bosward2, 4 Author affiliations: 1The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Camperdown, NSW, 2006 Australia 2The University of Sydney, S...
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Herd Udder Hygiene and Clinical mastitis in Pasture-based dairy cows
Acknowledgements Co-authors Bill Tranter Richard Laven Others Richard Maclehose Dennis Byrnes and the staff at Lakeside dairy Anonymous peer reviewers Download all datasets HERE library(knitr) ## Warning: package 'knitr' was built under R version 4.0.2 library(readr) knitr::opts_chunk$set(echo=TRUE, warning=FALSE, message=FALSE) load(file="...
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