This readme.txt file was generated on 20240826 by Drew Swartz Recommended citation for the data: https://doi.org/10.3168/jds.2024-24851 ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Descriptive evaluation of a camera-based dairy cattle lameness detection technology 2. Author Information Principal Investigator Contact Information Name:Gerard Cramer Institution: University of Minnesota Address: 1365 Gortner Ave, St Paul, MN 55108 Email: gcramer@umn.edu ORCID: 0000-0003-2691-3417 Associate or Co-investigator Contact Information Name: Drew Swartz Institution: University of Minnesota Address: 1365 Gortner Ave, St Paul, MN 55108 Email: swart205@umn.edu ORCID: 0000-0003-3619-7055 Associate or Co-investigator Contact Information Name: Elise Shepley Institution: University of Minnesota Address: 1365 Gortner Ave, St Paul, MN 55108 Email: eshepley1@gmail.com ORCID: 0000-0002-9663-7385 Associate or Co-investigator Contact Information Name: Javier Burchard Institution: Council on Dairy Cattle Breeding Address: Bowie, MD, US Email: javier.burchard@uscdcb.com ORCID: 0000-0002-6412-7647 Associate or Co-investigator Contact Information Name: Kristen Gaddis Institution: Council on Dairy Cattle Breeding Address: Bowie, MD, US Email: kristen.gaddis@uscdcb.com ORCID: 0000-0003-1234-1075 3. Date published or finalized for release:July 19, 2024 4. Date of data collection (single date, range, approximate date) 20160307 - 2023-03-06 M 5. Geographic location of data collection (where was data collected?): Minnesota and Iowa 6. Information about funding sources that supported the collection of the data: This research was supported by the Council of Dairy Cattle Breeding, the University of Minnesota College of Veterinary Medicine and Agricultural Experiment Station funding program (Signature Program Funding, accession number 1026927). Drew Swartz was partially funded by the USDA NIFA Food and Agricultural Science National Needs Graduate Fellowship in Dairy Production Systems, proposal number 2020-08149 and accession number 1025222. The funding partners had no input into the study design. 7. Overview of the data (abstract): Lameness in dairy cattle is a clinical sign of impaired locomotion, mainly caused by painful foot lesions, compromising the US dairy industry's economic, environmental, and social sustainability goals. Combining technology and on farm data may be a more precise and less labor-intensive lameness detection tool, particularly for early detection. The objective of this observational study was to describe the association between average weekly autonomous camera-based (AUTO) locomotion scores and hoof trimming (HT) data. The AUTO data were collected from 3 farms from April 2022 to March 2023. Historical farm HT data were collected from March 2016 to March 2023 and used to determine cow lesion history and date of HT event. The HT events were categorized as a regular HT (TRIM; n = 2290) or a HT with a lesion recorded (LESION; n = 670). Events with LESION were sub-categorized based on lesion category: digital dermatitis (DD; n = 276), sole ulcer (SU; n = 79), white line disease (WLD; n = 141), and other (n = 174). The data also contained the leg of the LESION, classified as front left (FL; n = 54), front right (FR; n = 146), rear left (RL; n = 281), or rear right (RR; n = 183) leg with 6 events missing the leg. Cows' HT histories were classified as follows: cows with no previous recorded instance of any lesion were classified as TRIM0 (n = 1554). The first instance of any hoof lesion was classified as LESION1 (n = 238). This classification was retained until a subsequent TRIM occurred - recorded as TRIM1 (n = 632). The next unique instance of any lesion following a TRIM1 was classified as LESION2 (n = 86). Any LESION events occurring after LESION1 or LESION2 without a subsequent TRIM were considered a hoof lesion recurrence and classified as LESIONRE1 (n = 164) and LESIONRE2 (n = 22), respectively. TRIM events after LESION2 or LESION2RE (n = 104) or LESION events after LESIONRE1 or LESIONRE2 were classified as LESION_OTHER (n = 160). The AUTO scores from −28 to −1 days prior to the HT event were summarized into weekly scores and included if cows had at least 1 observation per week in the 4 weeks before the event. For all weeks, LESION cows had a higher median AUTO score than TRIM cows. Cows with TRIM0 had the lowest and most consistent median weekly score compared to LESION and other TRIM classifications. Before HT cows with TRIM0 and TRIM1, both had median score increases of 1 across the 4 weeks, while the LESION categories had an increase of 4 to 8. Scores increased with each subsequent LESION event compared to the previous LESION event. Cows with SU lesions had the highest median score across the 4 weeks, WLD had the largest score increase, and DD had the lowest median score and score increase. When grouping a LESION event by leg the hoof lesion was found on, the AUTO scores for four groups displayed comparable median values. Due to the difference between TRIM and LESION events, this technology shows potential for the early detection of hoof lesions. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). 2. Links to publications that cite or use the data: https://www.journalofdairyscience.org/article/S0022-0302(24)01017-8/fulltext#%20 3. Was data derived from another source? If yes, list source(s): 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/policies/#drum-terms-of-use --------------------- DATA & FILE OVERVIEW - See revised version of this section below (revised secction submitted by researcher on 20240827) --------------------- 1. File List A. Filename:0000_SourceData Short description: Contains 3 sub folders CE, LESION, NEW_CE. These contain the raw data used for the projects B. Filename:000_code_files Short description: This contains the .rda files used to save and load in data after processing C. Filename: 00_DataManipulation Short description:These contains the files that are used to create data manipulation for each farm D. Filename: 01_Output Short description:These contain the results R files that are used to craft each output 2. Relationship between files: The order of the files are dependent where it must go A then B then C then D -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Collected data from 3 farms using their farm software, online downloads. 2. Methods for processing the data:Annotated in Materials and methods and annotated in the R file 3. Instrument- or software-specific information needed to interpret the data: Use R studio 4. Standards and calibration information, if appropriate: 5. Environmental/experimental conditions: 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission:Authors --------------------- DATA & FILE OVERVIEW (revised secction submitted by researcher on 20240827) --------------------- 1. File List A. Filename: Descriptive evaluation/Folder/0000_SourceData/CE/Farm_A/B_2022_04_16_2023_03_06.csv Short description: The raw data for Farm A that contains Cow ID, Mobility Score, Body Condition Score, and Time, collected from April 16, 2022, to March 6, 2023. B. Filename: Descriptive evaluation/Folder/0000_SourceData/CE/Farm_B/J_2022_04_16_2023_03_06.csv Short description: The raw data for Farm B that contains Cow ID, Mobility Score, Body Condition Score, and Time, collected from April 16, 2022, to March 6, 2023. C. Filename: Descriptive evaluation/Folder/0000_SourceData/CE/Farm_C/S_2022_04_16_2023_03_06.csv Short description: The raw data for Farm C that contains Cow ID, Mobility Score, Body Condition Score, and Time, collected from April 16, 2022, to March 6, 2023. D. Filename: Descriptive evaluation/Folder/0000_SourceData/Lesion/Farm_A_2016_03_06_2023_03_06.CSV Short description: This file contains lesion data for Farm A, including various metrics such as ID, CBRD, FDAT, LACT, Event, DIM, and Technician, collected from March 6, 2016, to March 6, 2023. E. Filename: Descriptive evaluation/Folder/0000_SourceData/Lesion/Farm_B_2016_03_06_2023_03_06.CSV Short description: This file contains lesion data for Farm B, including various metrics such as ID, CBRD, FDAT, LACT, Event, DIM, and Technician, collected from March 6, 2016, to March 6, 2023. F. Filename: Descriptive evaluation/Folder/0000_SourceData/Lesion/Farm_C_2016_03_06_2023_03_06.CSV Short description: This file contains lesion data for Farm C, including various metrics such as ID, CBRD, FDAT, LACT, Event, DIM, and Technician, collected from March 6, 2016, to March 6, 2023. G. Filename: Descriptive evaluation/Folder/000_code_files/ Short description: This folder contains all the `.rda` files that are created during the execution of the `00_DataManipulation` scripts. H. Filename: Descriptive evaluation/Folder/00_DataManipulation/ Short description: This folder contains all of the R scripts that are run to process each farm's data and then merge the files together. I. Filename: Descriptive evaluation/Folder/01_Output/ Short description: This folder contains all of the R scripts that process the results of the projects. J. Filename: Descriptive evaluation/Folder/02-methods/ Short description: This folder contains the `.qmd` file for the methods section of the research paper. K. Filename: Descriptive evaluation/Folder/03-results/ Short description: This folder contains the `.qmd` file for the results section of the research paper. L. Filename: Descriptive evaluation/Folder/04-discussion/ Short description: This folder contains the `.qmd` file for the discussion section of the research paper. M. Filename: Descriptive evaluation/Folder/05-conclusion/ Short description: This folder contains the `.qmd` file for the conclusion section of the research paper. N. Filename: Descriptive evaluation/Folder/99-references/ Short description: This folder contains the `.qmd` file for the references section of the research paper. O. Filename: Descriptive evaluation/Folder/index/ Short description: This file serves as the index for the research paper, formatted as a Quarto Markdown (`.qmd`) document. P. Filename: Descriptive evaluation/Folder/umn-thesis/ Short description: This is the R project folder for the University of Minnesota thesis. 2. Relationship between files: The files in the `Descriptive evaluation/Folder/0000_SourceData/CE` folder contain raw data for cow evaluations (Mobility Score and Body Condition Score) for three different farms (A, B, C). The files in the `Descriptive evaluation/Folder/0000_SourceData/Lesion` folder contain lesion data for the same three farms over a similar period. The `Descriptive evaluation/Folder/00_DataManipulation/` folder contains scripts that process and merge these raw data files, while the `Descriptive evaluation/Folder/000_code_files/` folder stores intermediate data outputs generated during this process. The `Descriptive evaluation/Folder/01_Output/` folder processes these results further. The `.qmd` files in the `Descriptive evaluation/Folder/02-methods/` to `Descriptive evaluation/Folder/99-references/` folders represent sections of the research paper, and the `Descriptive evaluation/Folder/umn-thesis/` serves as the main R project file for managing and coordinating the entire analysis process.