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These materials are intended to serve as a resource for researchers who want to score calf disbudding wound healing during future research projects. We have developed a photo test, gold standard scoring, and analysis for calculating inter observer reliability of disbudding wounds, which are all presented here. This code can be modified to calculate intra observer reliability as well.

Description of the data and file structure

• DisbuddingWounds241014.pdf; This file presents the wound tissues scored after hot-iron and caustic paste disbudding in dairy calves. A total of 9 wound tissues are presented along with examples and their definitions. The reliability for identifying the presence and absence of each tissue type is evaluated in the RMD.
• DisbuddingWoundTest.zip; 110 photos presenting examples of wounds after hot-iron and caustic paste disbudding, which should be scored to calculate inter observer reliability. The photos included in this test come from Holstein and Jersey calves that were disbudded using caustic paste at 3 d of age or a hot iron before 8 wk of age. Photos were collected throughout the entire healing process when wounds were scored as “fully healed” which takes an average of 10 wk for hot iron disbudding and 15.9 to 19.4 wk for caustic paste. At the time of disbudding, all calves received a local block and an NSAID.
• DisbuddingWoundScoringReliability_KEY_250227.xlsx; This file presents the gold standard used to calculate inter observer reliability for each of the wound tissues scored. “Photo” corresponds to the numbering of the photos in the test, while 1 indicates a tissue type is present and 0 indicates absence. The tissue definitions presented in Disbudding Wounds 241014.pdf were used to score these photos. Within Excel, the top row has been frozen and filtered to order the rows by photo number to assist with reviewing data in this sheet. We find it is easiest to maintain a frozen top row to allow users to see the tissue types listed as they review the photo scoring.
• DisbuddingWoundScoringReliability_BLANK_250227.xlsx; This file is a blank sheet which can be used to download and score the presence and absence (1/0) by observers for each of the 9 tissue types. Inter observer reliability can then be evaluated by comparing the observers scoring to the gold standard/key provided. The photo column corresponds to the photo number in the “Disbudding Wound Test” folder. For every photo and tissue type, a 0 or a 1 should be entered based on the absence or presence, respectively. If 0’s are not entered when tissues do not appear, the reliability will not be calculated properly. Within Excel, the top row has been frozen and filtered to order the rows by photo number to assist with filling data into this sheet. We find it is easiest to maintain a frozen top row to allow users to see the tissue types listed as they fill in 0/1.
• DisbuddingWoundScoringReliability_ScorerIntern1_250309.xlsx; This file includes the presence and absence (1/0) scored by an intern labeled as Intern1 for anonymity, for each of the 9 tissue types where reliability is being evaluated. Within Excel, the top row has been frozen and filtered to order the rows by photo number to assist with filling data into this sheet. We find it is easiest to maintain a frozen top row to allow users to see the tissue types listed as they fill in 0/1.
• ReliabilityFor_DisbuddingWounds_Analysis.Rmd; This RMarkdown file uses the Disbudding Wound Scoring Reliability KEY 250227.xlsx listed above to calculate the inter observer reliability for 9 wound tissues presented in Disbudding Wounds 241014.pdf. In this example, the Disbudding Wound Scoring Reliability ScorerIntern1 250309.xlsx is used to calculate reliability for Intern1. The file Disbudding Wound Scoring Reliability BLANK 250227.xlsx can be downloaded, filled in, and used to create reliability for other observers against our gold standard. Rmd files can be downloaded and run in R. This file is annotated.
• ReliabilityFor_DisbuddingWounds_Analysis.pdf; This file is the PDF output of the corresponding RMarkdown file, and includes the code and output previews. This file is annotated.
• DisbuddingWoundReliabilityDiscrepancies_Intern1_250312.xlsx; This file was created in the ReliabilityFor_DisbuddingWounds_Analysis.Rmd and exported to review disagreement in scoring between the gold standard and Intern1. The photo column shows the number of the photo scored where interns and the gold standard either “match” or have a “discrepancy”. We are most interested in reviewing the disagreement, so this Excel file specifically focuses on creating a visual representation of tissue types where there is disagreement between the observer and gold standard. If a photo had matches for each of the tissue types, it was excluded from this data frame before being exported. This file is exported from R with any of the discrepancies highlighted in bold red text to support ease of identification when reviewing in Excel.
• WoundReliabilityComparison_GoldandScorerIntern1_250312.xlsx; This file was created in the ReliabilityFor_DisbuddingWounds_Analysis.Rmd and exported to check for disagreement in scoring between the gold standard and Intern 1. It shows the “Photo” number and the 0/1 score for both the Gold standard and Scorer Intern1 in separate columns for each tissue type presented in Disbudding Wounds 241014.pdf.

Code/Software

All analyses were run in R using RStudio. Software versions, including those for all packages used, are included in ReliabilityFor_DisbuddingWounds_Analysis.Rmd, and the associated PDF export.