============================================================================================================ START readme ============================================================================================================ This file focuses more on the details of the data package. For 'administrative' metadata on this data, please view the metadata file within the parent folder of this data package (where this readme file is also found). ============================================================================================================ ## General ============================================================================================================ + Author(s): Danny de Koning-van Nieuwamerongen; Irene Verhagen + Project: Research data management at WUR Library + Contact: danny.dekoning-vannieuwamerongen@wur.nl; irene1.verhagen@wur.nl; data@wur.nl ============================================================================================================ ## Title ============================================================================================================ Readme example for data underlying the publication "DMP_example_FictitiousProject_v01" ============================================================================================================ ## Methods ============================================================================================================ # Introduction This project aims to study the effects of several housing (barren housing vs various types of enriched housing) and dietary conditions (feeding levels, and dietary protein and sugar contents) on the health and welfare of growing pigs (assessed by behaviour, lesions, antibody titers, hormones, body weight). Additionally, the project aims to assess the perception of farmers on pig health and welfare, what they consider poor health and welfare, and what they would take away from the results of these studies (through recorded interviews and online surveys). Please view https: //somejournal.com/withthementionedpublication for added information on materials and methods. # Measurements + Lesion scores Visual live observations made by 2 human observers counting the number of lesions on a pig's body on a grading scale (see section codebook for the scale). The observations were made on paper and transcribed digitally in Excel in csv format. The data also contains lesion score observation previously performed by Utrecht University and published at https: //doi.org/123456/fakedoi. Both newly scored lesions and reused data were merged in R for further processing and statistical analyses (see scripts for further explanation on the exact steps taken). + Behavioral video recordings Video recordings consist of 12 hour video recordings of pigs twice a week for 20 weeks. These recordings were assessed using scan sampling (15 minute intervals) on tail biting behaviour, aggressive behaviours, play behaviours, and resting behaviours. The ethogram used can be found in the publication https: //somejournal.com/withthementionedpublication. Scan sampling were performed in Noldus Observer software and frequencies of the behaviours were exported to csv format. Processing and analysis of the data was done in R (view the scripts for detailed comments on the steps taken). + Behavioural live recordings Live recordings were performed 2 days a week for 20 weeks. Scan sampling performed using 5 minute intervals on detailed behaviours nuzzling and location of nuzzling, defecating and the area, lying position, type of play behaviour, type of aggressive behaviour and body location targeted. Behavioural live scoring was performed on paper and transcribed in Excel in csv format. Processing and analysis of the data was done in R (view the scripts for detailed comments on the steps taken). + Antibody titers Blood sampling was performed at 10, 15, and 20 weeks of age by puncture of the jugular vain and collection of 5 ml of blood. Blood samples were centrifuged, plasma extracted, and stored at -20 degrees Celsius until analysis. Analysis consisted of an ELISA assessment performed as described in https: //somejournal.com/withthementionedpublication . Optical densities values and images resulting from the ELISA reader were exported to csv and jpg respectively. Processing and analysis of the data was done in R (view the scripts for detailed comments on the steps taken). + Serotonin levels Blood sampling was performed at 10, 15, and 20 weeks of age by puncture of the jugular vain and collection of 5 ml of blood. Blood samples were centrifuged, plasma extracted, and stored at -80 degrees Celsius until analysis. Analysis consisted of a fast serotonin assessment performed as described in https: //somejournal.com/withthementionedpublication . Fluorescence levels resulting from the fluorescence reader were exported to csv. Processing and analysis of the data was done in R (view the scripts for detailed comments on the steps taken). + Body weight Body weight of the pigs were measured from 4 weeks of age tot 20 weeks of age with 2 weeks intervals. Body weight was written down on paper and later transcribed in Excel in csv. Processing and analysis of the data was done in R (view the scripts for detailed comments on the steps taken). + Interviews Interviews were performed with farmers on their perception of the results in relation to pig health and welfare. Interviews were performed live with a select few of farmers (10) to handle questions in more depth. interviews were recorded on a voice recorder and later transcribed in Word and saved as pdf. Other farmers (30) received question through a survey designed in Qualtrics. Responses were exported as csv. Processing and analysis of the data was done in R (view the scripts for detailed comments on the steps taken). + Processing and analysis scripts All processing of data (modifications, calculations, etx) and analysis of data was performed in R. All scripts are elaborately commented, describing each different step taken and the reason for the step. + Figures and tables All figures and tables were created through R. Refer to the R scripts for detailed information within the script. ============================================================================================================ ## FolderStructure ============================================================================================================ - HeWa_prj123456 --- HeWa_raw_data ----- HeWa_raw_video_observations ------- HeWa_video_obs_week1 --------- HeWa_video_obs_week1_pen1 --------- HeWa_video_obs_week1_pen2 ------- HeWa_video_obs_week2 ...[similar subfolders for video obs; 10 pens 20 weeks]... ----- HeWa_raw_scansampling ----- HeWa_raw_interview_recordings ----- HeWA_raw_interview_transcriptions ----- HeWa_raw_bodyweight ----- HeWa_raw_surveys ----- HeWa_raw_antibodies ----- HeWa_raw_serotonin ----- HeWa_raw_lesions --- HeWA_reused_data_lesions --- HeWa_scripts ----- HeWa_processing_scripts ----- HeWa_analysis_scripts --- HeWa_processed_data ----- HeWa_processed_behavioural ----- HeWa_processed_laboratory ----- HeWa_processed_interviews ----- HeWA_processed_surveys ----- HeWa_processed_bodyweight ----- HeWa_processed_lesions --- HeWa_results ----- HeWa_stat_output ----- HeWa_figures ----- HeWa_tables --- Protocols --- Administrative_documents ============================================================================================================ ## FolderContents ============================================================================================================ --- HeWa_raw_data/ Contains the raw collected data from observations or laboratory analyses and are the original form of the digital data. ----- HeWa_raw_video_observations/ Contains video observations of pigs within their housing system. Video observations are collected in .avi format. Subfolders are created for each week that video observations took place (20 weeks = 20 folders) and within those subfolders 32 .avi per folder is found (1 .avi for each pen recorded and indicated in the filename with the word 'pen' followed by a number). ----- HeWa_raw_scansampling/ Contains the exported scan sampling results from Noldus Observer in 1 .csv format and the transcribed live scan sampling observations in 1 csv format. This folder contains 2 csv's. ----- HeWa_raw_interview_recordings/ Contains .mp4 files from audio recordings made with a handheld audiorecorder. There are 10 .mp4 files, 1 for each interview performed with each farmer (farmer subject is indicated in the filename by the word 'farmer' followed by a number; there are no names or identifying information retained). ----- HeWA_raw_interview_transcriptions/ Contains the transcriptions of the live interview .mp4 recordings. There are 10 .txt files present, 1 for each interviewed farmer (farmer subject is indicated in the filename by the word 'farmer' followed by a number; there are no names or identifying information retained). ----- HeWa_raw_bodyweight/ Contains the body weights of the pigs. There is 1 csv file present containing all body weight measurements. ----- HeWa_raw_surveys/ Contains the Qualtrics exported responses of the survey send to 20 farmers. There is 1 csv file present containing all responses. ----- HeWa_raw_antibodies/ Contains the exported antibody titer results of the ELISA reader. There are 3 csv files containing the optical density values corresponding to the three blood sampling moment (blood sampling moments are indicated with the word 'wk' followed by a number (10, 15, or 20)). There are 20 .tiff files containing the optical density images from which the optical density values where calculated. These .tiff files where created with a high resolution camera without flash with a standard white background before each plate would enter the ELISA reader. Each .tiff file contains various plates that were analysed (correspondence to blood sampling moment is indicated with the word 'wk' followed by a number (10, 15, or 20) and and correspondence to sample is indicated with the word 'sample' followed by a number that corresponds to the sample well specified in the csv). ----- HeWa_raw_serotonin/ Contains the exported serotonin fluorescence values from of the fluorescence reader used. There is 1 .txt file containing all values. ----- HeWa_raw_lesions/ Contains the transcribed body lesions scores. There is 1 csv present containing the lesions scored. --- HeWA_reused_data_lesions/ Contains the reused data from the University of Utrecht publication https://doi.org/123456/fakedoi. The data is a direct copy of the mentioned publication. There is 1 csv file containing body lesion scores. --- HeWa_scripts/ Contains the processing and analysis scripts performed in R. ----- HeWa_processing_scripts/ Contains processing scripts in R. Each processing script corresponds to the aforementioned measurements / data collected and are indicated within the filename to which of the measurements the scripts corresponds. There is 1 processing script that merges required data together for analyses. There are 10 .R files. ----- HeWa_analysis_scripts/ Contains analysis scripts in R. Each analysis script corresponds to the aforementioned processing scripts and are indicated within the filename to which of the processing scripts it corresponds. There are 10 .R files. --- HeWa_processed_data/ These folders and its subfolders are empty and are used as containers for the processing scripts outputs. By running the processing scripts, the resulting dataframes are written to the corresponding folders. --- HeWa_results/ Contains the output of the statistical analyses or descriptive statistics. ----- HeWa_stat_output/ Contains the output of statistical analyses performed in r. There are 10 .txt files corresponding to each of the analyses scripts. ----- HeWa_figures/ Contains the output of analysis scripts in which figures where created through R. There are 10 .jpg files corresponding to each of the analyses scripts. ----- HeWa_tables/ Contains the output of analyses scripts in which tables where created through R. There are 10 .jpg files corresponding to each of the analyses scripts. --- Protocols/ Contains: + laboratory protocols (1 pdf file for each assessment). + the interview questions performed live with farmers in 1 pdf file. + the survey questions performed in Qualtrics as 1 pdf file and as a Qualtrics structure file. + protocol for behavioural assessment in 1 pdf file. + protocol for locomotion assessment in 1 pdf file. + protocol for lesion scoring of pigs in 1 pdf file. + protocol for body weight measurements in 1 pdf file. --- Administrative_documents/ Contains the informed consents of participants within the study. ============================================================================================================ ## Software ============================================================================================================ SoftwareRequired: + R 4.20 + Rstudio 2022.07.1 Build 554 + NoldusObserver XT v16 (note that this is not required to reproduce processing and analysis; this program was used for video scoring of behaviour of pigs). OtherSoftwareRequirements: The version of R libraries used is specified within each script at the start of the file. Please note that for full reproducibility, one requires the installation of the correct R version and associated libraries. Noldus software is not open source, but the scoring of behaviours can be reproduced using the open source software BORIS (Behavioral Observation Research Interactive Software) at https://www.boris.unito.it/. ============================================================================================================ ## FileFormats ============================================================================================================ + .R + .csv + .txt + .mp4 + .avi + .jpg + .tiff ============================================================================================================ ## CodeBook ============================================================================================================ Please view the open access article https: //somejournal.com/withthementionedpublication for information, meaning, and abbreviations of the different types of behaviours scored within the ethogram present in that journal article. Please view codebook.csv (where this readme file is also found) for documentation of abbreviations, column names, datapoints, etc. The file codebook.csv uses the columns: + index = a number used to distinguish the different entries. + code = the abbreviation, variable / data / column name used. + used = location where the code is used. (filename, foldername, columnname, datapoint, protocol, etc.). + meaning = the literal meaning of the code. (e.g., fully written out abbreviation) + represents = what the code represents in terms of data or usage. (e.g., units of measurements, coding used, more in depth explanation) Note that this file is ';' delimited. To avoid possible confusion and inconsistencies, sentences within cells do not contain reading symbols as comma's or semicolons. When required, separation within sections of a sentence is made possible using the hashtag symbol (#). Example: The sex of an animal is described as "m = male pig (boar) # f = female pig (sow)" where the hashtag separates the element in a sentence. ============================================================================================================ ## Other ============================================================================================================ Please note that not all parts of this data was published as it contains sensitive data of farmers. This data package represents a full reproducible package that is internally archived. The full data can be requested by contacting the secretariat of our group at email data@wur.nl. We have internally made sure that there will always be someone available that is intimately familiar with this data to decide if it can be shared with the requesting party. When the requesting party is allowed to receive this data, a data sharing agreement is signed by the requesting party. The data sharing agreement stipulates what the requesting party is and is not allowed to do. Other non-sensitive data (pig observation, anonymized surveys and interview transcriptions) have been published within 4TU.ResearchData at https: //doi.org/789465/fakedoi. Please view the associated metadata and codebook file within the parent folder of the data package (where you found this readme file). ============================================================================================================ END readme ============================================================================================================