README – Calf growth, health and sensor data Project and Funding: This study was carried out as part of the project “KalbAmmwohl – a concept for promoting animal welfare in foster calf rearing on large farms”, in which the investigated farm was a project partner. The project was funded by the Federal Ministry of Agriculture, Food, and Regional Identity (BMLEH) based on a decision of the Parliament of the Federal Republic of Germany via the Federal Office for Agriculture and Food (BLE) under the innovation support program. This publication was funded by the Open Access Publication Fund of the University of Kassel. Dataset description: This dataset contains longitudinal data on the health, growth, behavior and sensor-based lying activity of dairy calves raised in an organic dairy farming system using foster cows. Data were collected during the rearing period and include repeated health assessments, body weight measurements, sensor (logger) recordings, and information on animal characteristics, housing conditions and management events. Data collection and assessment: Health assessments were conducted repeatedly throughout calf rearing using the ProYoungStock (PYS) health assessment protocol. Parameters included vitality, body condition score (BCS), coat condition, diarrhea, coughing, nasal discharge, ocular discharge, breathing and hair loss. Body weight was recorded using a Meier-Brakenberg livestock scale (1,000 kg capacity). Sensor loggers were attached to the hind legs of selected calves. Logger application, removal and replacement were documented, including the respective logger identification number and leg side. Data files: The dataset consists of three primary .csv files: Calves_Health.csv – Repeated health assessments and body weight measurements of the calves, including housing and life phase information. Calves_MSR.csv – Information on sensor (logger) application, removal and replacement, including logger identification numbers, attachment dates and logger file references. Calves_Overview.csv – General information on the study animals, including animal characteristics, birth data, batch allocation and reasons for removal from the study. Additionally data is providerd in a .tar folder: MSR-Logger-Data.tar – Containing all .msr and .csv files from the logger readings used in the Calves_MSR.R script. Codes are provided in two Primary .R files: Calves_health.R – R Code for analysing the health and growth performance recorded during the study. Calves_MSR.R – R Code for analysing the lying behavior recorded with the msr-accelerometers (sensors/loggers), which are provided in the MSR-Logger-Data.tar Folder. Data structure and variable descriptions: Detailed descriptions of all variables, possible values, units, data formats and references are provided below for each CSV file. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | | | | | CSV file | Column name/ Parameter | Description | Possible Values | Explanation of Values | Reference/Hardware/Software | Format Calves_Health | | | | | | | Date | Date of data collection | | | | DD.MM.YYYY | Pen_Type | Type of pen in which animals where | Small group | Small pen (123 m²) with deep straw bedding, feeding | | text/factor | | housed during assessment | | racks, ad libitum water. Here foster calves, own calves | | | | | | and foster cows where introduced to each other. They | | | | | | were housed here for the first 10 to 14 days of life. | | | | | | Maximum 3 cows, 3 own calves, and 6-9 foster calves | | | | | Large group | Larger pen (477 m²) with deep straw bedding, feeding | | text/factor | | | | racks, ad libitum water. Here several small groups were | | | | | | housed together. They were housed here until weaning. | | | | | | Maximum 14 cows, 14 own calves, and 28-42 foster | | | | | | calves. Over the course of rearing, the large groups | | | | | | in the bigger pens sequentially went through altogether | | | | | | nine similar pens (Pen_Nr) by moving to the next pen in | | | | | | the row about every other week (usually around 10 days) | | | | | | depending on the current herd’s calving rate. | | | | | Weaning pen | For the weaning process, the large group of cows and | | text/factor | | | | calves moved to a different barn. Cows were then housed | | | | | | in a pen between two groups of calves (352 m² each), | | | | | | serving as foster cows for both groups: their own and | | | | | | foster calves plus an older group of unfamiliar calves | | | | | | whose mothers/foster cows had been integrated into the | | | | | | milked herd in another building. Pens had deep straw | | | | | | bedding, feeding racks, and ad libitum water. | | | | | Sick pen | If calves had severely impaired health (according to | | text/factor | | | | the farm staff) they were housed in small boxes for | | | | | | closer and more frequent inspection. Sick pen boxes | | | | | | where straw-bedded, calves had ad libitum water, and | | | | | | heating lamps were available. | | | Pen_Nr | Farm-internal Numbering of pens | 1, 2, 3 , …. | Each pen type appears more frequently and has a unique | | number/factor | | | | number. Therefore, different numbers within the same | | | | | | pen type are duplicates. In the large group/pens a | | | | | | lower number means younger calves, as the animals | | | | | | undergo a rotational system moving from one pen to the | | | | | | next (see Pen_Type/Large group). | | | CalfID | Identification number of the animal | | Number of the animals' ear tag, numbers starting with | | number/factor | | | | 38XXX were female, numbers starting with 09XXX were | | | | | | male | | | Weight | Weight in kg | | | Meier-Brakenberg livestock scale (1,000 | number/metric | | | | | kg capacity) | | | ProYoungStock Scores (PYS) | | PYS stands for "ProYoungStock", a protocol for health | Ivemeyer, S., Simantke, C., & Knierim, | | | | | assessments in young cattle | U. (2021). ProYoungStock: Förderung | | | | | | von Gesundheit und Wohlbefinden | | | | | | bei Jungtieren und Milchkühen | | | | | | durch natürliche Fütterungssysteme | | | | | | [Final report]. Universität Kassel, | | | | | | Fachgebiet Nutztierethologie und | | | | | | Tierhaltung. OR Ivemeyer, S., J. | | | | | | Preußer, D. Haager, C. Simantke, P. | | | | | | Waldherr, K. Kull, G. Utz, U. Knierim | | | | | | and C. Winckler (2022): Impact of | | | | | | enhanced compared to restricted milk | | | | | | feeding on the behavior and health | | | | | | of organic dairy calves. Applied | | | | | | Animal Behaviour Science (252) 105655. | | | | | | https://doi.org/10.1016/j.applanim.2022.105655 | | Vitality | ProYoungStock (PYS)-Score | 0 | Calf is lively | | number/factor | | | 1 | little responding or downer calf; and/or hunched back | | number/factor | | | | or clearly drooping ears | | | BCS | PYS-Score | 0 | good to very good: ribs and spinous processes not | | number/factor | | | | visible, prominent bones well rounded | | | | | 1 | moderate: ribs and spinous processes visible and edgy | | number/factor | | | | hip bones | | | | | 2 | runt: sharp ribs and striking spinous processes, weak | | number/factor | | | | musculature: long back muscle behind shoulder weakly | | | | | | developed, additionally clearly visible tail base | | | | | | without fat cover, weakly developed muscles at the | | | | | | hindquarter | | | Coat_Condition | PYS-Score | 0 | Coat is even, glossy | | number/factor | | | 1 | Coat is scrubby and dull - at least half of the thorax | | number/factor | Diarrhea | PYS-Score | 0 | clean or only slightly dirty around tail | | number/factor | | | 1 | manure plaques around tail amounting to at least the | | number/factor | | | | size of the palm of a hand (fresh or dry soiling) | | | Coughing | PYS-Score | 0 | no coughing | | number/factor | | | 1 | single or repeated cough during assessment | | number/factor | Nasal_Discharge | PYS-Score | 0 | no nasal discharge | | number/factor | | | 1 | clear effluent dripping from nose or any opaque or | | number/factor | | | | purulent discharge | | | Ocular_Discharge | PYS-Score | 0 | no ocular discharge | | number/factor | | | 1 | clearly visible wet or dry flow from the eye of at | | number/factor | | | | least fingers’ breadth and/or any crust (at least 0.5 | | | | | | cm maximal length = ½ finger’s breadth) | | | Breathing | PYS-Score | 0 | normal | | number/factor | | | 1 | hampered, forced breathing | | number/factor | Hairloss | Score | 0 | A full coat or only minor hair loss around tail | | number/factor | | | 1 | The fur around the tail has fallen out in patches at | | number/factor | | | | least the size of the palm of a hand | | | Phase | Assigning the health assessments | small group | in pen "small group" | | text/factor | | to a phase of life according to | | | | | | Housing/Events/Age | | | | | | | large group (beginning) | in pens "large group 2" und "large group 3" | | text/factor | | | large group (mid) | in pens "large group 4" und "large group 5" und "large | | text/factor | | | | group 6" | | | | | large group (end) | in pens "large group 7" und "large group 8" | | text/factor | | | weaning (1) | first week of weaning (with own/familiar foster | | text/factor | | | | cows/dams) in "weaning pen" 6 | | | | | weaning (2) | in "weaning pen "4, dams left into milking routine and | | text/factor | | | | calves could now suckle on alien foster cows | | | | | weaned | in "weaning pens" 1-3 | | text/factor | Comment | | CowManager chip | Any unusual findings, irregularities or noteworthy | | text | | | in ear, purulent | events recorded during data collection. | | | | | ocular discharge, | | | | | | weighing/noting mistake, | | | | | | … | | | | Comment2 | | housed in wrong pen, | Additional notes or relevant information about the | | text | | | weighing/noting mistake, | observation. | | | | | … | | | | | Comment post R Skript | | During the analysis, it became apparent that the manual | | | | | | phase assignment was sometimes incorrect because the | | | | | | operational rotation procedure was suspended or skipped | | | | | | due to herd movement. It has now been determined that | | | | | | the subdivision within the large group will be based on | | | | | | the duration of that phase: the first 3 weeks are the | | | | | | beginning, and the last 3 weeks are the end. | | Calves_MSR.csv | Date | Date of data collection | | When logger applied/attached newly: start date of new | | DD.MM.YYYY | | | | logger; when logger changed: start date of new logger | | | | | | and end date of old logger; when only Logger (old) | | | | | | removed: end date of old logger | | | CalfID | Identification number of the animal | | Number of the animals' ear tag, numbers starting with | | number/factor | | | | 38XXX were female, numbers starting with 09XXX were | | | | | | male | | | Logger_new | Individual number of the logger | 27,45,108,... | | | number/factor | | attached to the calf | | | | | Leg_new | Side of the hind leg, to which the | right/left | | | text/factor | | logger was attached | | | | | Logger_Time | Time of day, at which the logger | | | | HH:MM | | was either attached, removed or | | | | | | switched for a new one | | | | | Logger_old | Individual number of the logger | 27,45,108,... | | | number/factor | | removed from to the calf | | | | | Leg_old | Side of the hind leg, from which | right/left | | | text/factor | | the logger was removed | | | | | Comment | | Strap loose, Logger lost, | | | text | | | turned inside out, … | | | | | | Side of Leg_new/Leg_old | To record the side of the leg was only introduced after | | text | | | not noted yet (first | the first assessments, hence this info is missing for | | | | | assessments) | the first rows of data | | | Phase | Assigning the health assessments | 1. week, 2. week, 8. week | First, second and eights week of life of the calf | | text/factor | | to a phase of life according to | | | | | | Housing/Events/Age | | | | | | | weaning (1) | first week of weaning (with own/familiar foster | | text/factor | | | | cows/dams) in "weaning pen" 6 | | | | | weaning (2) | in "weaning pen "4, dams left into milking routine and | | text/factor | | | | calves could now suckle on alien foster cows | | | Filename | Name of .csv/.msr file from Logger | | The linked logger file corresponds to the logger that | file exported from software | text | | reading | | was removed on the respective data collection date | msr-reader for msr-145 loggers: | | | | | (i.e., the logger from the previous week). | https://www.msr.ch/de/produkt/datenlogger-temperatur-feuchte-druck-beschleunigung-msr145/ | Calves_Overview | Batch | Assigning the calves to a | A | Added to sample on 29.04.2024 | | text/factor | | group/batch, as a repeating | | | | | | measure. Every week a median of | | | | | | 10 calves (2-12) were added to the | | | | | | sample. | | | | | | | B | Added to sample on 07.05.2024 | | text/factor | | | C | Added to sample on 14.05.2024 | | text/factor | | | D | Added to sample on 22.05.2024 | | text/factor | | | E | Added to sample on 28.05.2024 | | text/factor | | | F | Added to sample on 04.06.2024 | | text/factor | | | G | Added to sample on 11.06.2024 | | text/factor | | | H | Added to sample on 18.06.2024 | | text/factor | | | I | Added to sample on 24.06.2024 | | text/factor | | | J | Added to sample on 02.07.2024 | | text/factor | CalfID | Identification number of the animal | | Number of the animals' ear tag, numbers starting with | | number/factor | | | | 38XXX were female, numbers starting with 09XXX were | | | | | | male | | | Birthdate | Date of birth of the animal | | | | DD.MM.YYYY | Birthweight | Weight measures on date of birth | | measured/weighed by farm staff, usually by rolling onto | | number/metric | | | | a cow scale with the calf in a wheelbarrow | | | Status | The relationship or status the calf | foster calf | a calf assigned to a foster cow, own dam was | | text/factor | | has to their assigned foster cow | | reintroduced to normal milking routine and housed in a | | | | | | different barn | | | | | own calf | the biological calf birthed by the foster cow | | text/factor | Sex | | male/female | | | text/factor | Breed | | hf | Holstein Frisian | | text/factor | | | fv | Fleckvieh (-crossbred), usually the dam was HF, and the | | text/factor | | | | bull was Fleckvieh | | | Logger_YesNo | Animals that were collected to be | yes/no | | | text/factor | | equipped with loggers/sensors | | | | | Comment | Notable features in health or | e.g. Tendon disorder, | | | text | | behavior | Trichophytie, jumping | | | | | | over weighing scale | | | | FocalAnimal | Information about whether the calf | removed/complete | | | text/factor | | stayed within the sample until the | | | | | | end of data collection | | | | | Date_Removal | The date on which the animal was | | | | DD.MM.YYYY | | removed from the sample | | | | | Reason_Removal | The reason why the animal was | died | died/euthanized | | text | | removed from the sample during data | | | | | | collection | | | | | | | foster cow (dam) diseased | This resulted in a "change of status" of the own calf, | | text | | | | as it had no longer its own dam | | | | | foster cow (dam) | This resulted in a "change of status" of the own calf, | | text | | | slaughtered | as it had no longer its own dam | | | Comment_Removal | The reason why the animal was | Sex of calf pair mixed | This made comparison within pairs impossible, only if | | text | | removed from the sample during | | sex/breed were added as fixed factors in the models | | | | analyses and data clearence | | | | | | | Breed of calf pair mixed | This made comparison within pairs impossible, only if | | text | | | | sex/breed were added as fixed factors in the models | | | | | Only calf of foster cow | This made comparison within pairs impossible | | text | | | Third/excess focal calf | This made comparison within pairs impossible | | text | | | to foster cow | | | | | | twins | This made comparison within pairs impossible | | text