DOI: 10.5061/dryad.41ns1rns3
title: Data and code from: Onset of feeding behavior in intensively housed dairy calves

description: Development of early feed and water intake is not well-documented in dairy
 calves, and little is known about how traditional, intensive feeding
 management influences the development of species-specific behaviors, like
 rumination. Our first objective was to describe grain, water, and hay
 intake in calves from birth. Our second objective was to evaluate whether
 early access to hay influenced the likelihood of reaching biologically
 relevant thresholds of grain and water intake (grain: 50, 100, 250, 500,
 900 g; water: 1, 2, 3, 4, 5 L), and rumination (5, 10, 15, 20 % of a 24-h
 d) compared to grain alone. Our third objective was to evaluate whether
 hay provision affected the age at which calves reached these thresholds.
 We enrolled 49 Holstein heifer calves over 2 yr (2018: 22; 2019: 27) that
 were housed individually and fed milk replacer via a bottle (2018: 5.7-8.4
 L/d; 2019: 3.8-5.6 L/d), as is common in the US. Calves received ad
 libitum water and grain (Control: n = 20) with additional access to
 chopped mountaingrass hay (Hay: n = 29) from d 0. Intake was measured
 daily until the start of weaning at 49-51 d. Calves were ear-tagged at 3 ±
 2 d (mean ± SD) of age with an accelerometer (SenseHub, Merck Animal
 Health) that classified rumination by minute continuously through 38 ± 10
 d (mean ± SD) of age. We analyzed age of onset as the first of 3
 consecutive days that a calf met the threshold level with a zero-inflated
 hurdle model. The logistic regression component of this model evaluated
 whether access to hay affected the likelihood of reaching each onset
 threshold. The second, conditional component of the model evaluated, among
 the calves that met a given threshold, if having access to hay affected
 the age they reached it. We found that calves consumed grain, hay, and
 water within 1 d of birth. Calves consumed small quantities of hay
 throughout the milk-fed period, typically &lt; 100 g/d, but this still
 led to differences in feeding development, with hay-fed calves reaching 5
 % rumination at younger ages, and a greater proportion reaching higher
 rumination thresholds compared to controls: specifically, 89 % vs. 53 %
 reached the 15 % threshold, and 61% vs. 5 % reached the 20 % threshold
 (Hay vs. Control, respectively). Hay-fed calves also tended to be more
 likely to reach the 500 g grain threshold. There was no evidence that
 access to hay affected age at reaching higher rumination or grain
 thresholds, possibly because all calves were in similarly restrictive,
 milk-limited environments, where calories from solid food intake were
 particularly important. Calves with hay tended to reach the 3 L water
 threshold at a younger age than controls, but there was no evidence that
 hay affected likelihood of consuming increasing amounts of water. Overall,
 our results demonstrate that calves will consume grain, hay, and water as
 soon as they are provided, highlighting the importance of opportunities to
 perform species-specific feeding behaviors. Withholding hay from very
 young animals, which is common in the US and allowable under the EU 2008
 Directive, limits the development of motivated behaviors like rumination.
description: # Data from: Onset of feeding behavior in intensively housed dairy calves
 B.C. Downey and C.B. Tucker Data were collected from 49 Holstein heifer
 calves across 2 years (2018-2019) from birth until the start of step-down
 weaning (approximately d 50). Calves were fed *ad libitum* grain and water
 from birth (Control, n = 20) or given additional access to *ad libitum*
 hay (Hay, n = 29). All calves were individually housed and fed milk
 replacer via a bottle (2018: 5.7-8.4 L/d; 2019: 3.8-5.6 L/d). We measured
 feed and water intake daily from d 0. Calves were ear-tagged on d 3 ± 2
 (mean ± SD; range: d 0-7) of life with an accelerometer (MSD Animal Health
 Technology) that classified rumination by minute continuously throughout
 the milk-fed period. Due to tag failure, 72 % of all possible calf-days
 for 49 calves from birth through the start of weaning (1770/2451 days)
 were available. We used these data to describe early life feed and water
 intake, and whether access to hay affected the likelihood of reaching
 biologically relevant thresholds of grain and water intake, and
 rumination, as well as whether hay affected the age at which calves
 reached these thresholds. ## Description of the data and file structure
 #### Data * *1_Intake_and_rumination_complete_daily_data.xlsx*; * This
 file has daily intake and rumination values for each calf throughout the
 data collection period. Calves have data from day 0 (birth) until weaning
 began. Weaning began on day 49 to 51 for all calves, so the last day of
 data collection was day 48 to 50. Weaning age varied in one year due to
 another experiment. * Each sheet includes columns for: * "Year"
 (2018 or 2019; the year data collection occurred for each calf) *
 "Calf" (calf ID), "Treatment" (Hay or Control) *
 "Age_days" (the calf's age in days; day 0 = the day the
 calf was born) * "Week" (the calf's age in weeks) * and a
 final column for the data collected that day * NAs represent missing or
 unknown data. * For grain, hay, and water, these NAs typically occurred
 because of issues with drying feed samples or calves spilling or
 defecating in buckets, as these issues made it impossible to generate an
 accurate 24-h representation of what the calf consumed. * NAs for
 rumination occurred due to issues with the accelerometers, either because
 they did not record any data, recorded &lt; 1440 minutes (1 full day) of
 data, recorded "low activity" (1 of the 8 behavior categories
 possible) for &gt; 80 % of the day (occurred within the first week of
 life; suggested to reflect an active tag that had not yet been placed on a
 calf for a full day) or failed entirely. * This file is used in the
 RMarkdown files "1_Descriptive_intake_and_figures_260122.Rmd"
 and "2_Age_at_reaching_thresholds_calculations_260122.Rmd". ```
 * "Grain" sheet; This sheet contains daily grain intake in
 grams. The "Grain_g" column is presented on a dry matter basis.
 All calves (20 Control, 29 Hay) are represented in this sheet. *
 "Hay" sheet; This sheet contains daily hay intake in grams. The
 "Hay_g" column is presented on a dry matter basis. Only Hay
 treatment calves (n = 29) are represented in this sheet. There are a few
 0s in this sheet; these are true 0s, i.e., calves did not consume any hay
 on that day. * "Water" sheet; This sheet contains daily water
 intake in liters ("Water_L" column). * "Rumination"
 sheet; This sheet contains rumination data ("Rumination_prop"
 column). This column represents the proportion of a 24-h day that the calf
 was recorded as ruminating. Tags collected data every minute continuously
 from the application until the end of the data collection period or the
 tag failed, whichever came first (see "Supplemental Table S1"
 for more details). NAs reflect missing data (either the tag did not record
 or recorded less than a full 24-h day), while 0s reflect true 0s, i.e.,
 the tag recorded that calf did not ruminate at all on that day. ``` \-
 *2_Age_at_reaching_thresholds.xlsx*; * This file is generated from
 "1_Intake_and_rumination_complete_daily_data.xlsx" in the
 RMarkdown file
 "2_Age_at_reaching_thresholds_calculations_260122.Rmd". It is
 used in the file "3_Onset_models_and_figures_260122.Rmd". * This
 file has the age at which calves reached each threshold for grain, water,
 hay intake and rumination. Daily intake and rumination data were analyzed
 to identify when each calf met or exceeded each threhold for at least 3
 consecutive days. The age reported in this file is the first day of that
 first 3 day period. * Missing data (NAs in the complete daily data) were
 excluded; i.e., if a calf ate 50 g of grain on day 1, 60 g on day 2, had
 an NA on day 3, then ate 55 g on day 4, they would not be recorded as
 having met the threshold for 3 consecutive days due to the presence of the
 NA. * "." in each sheet means that the calf did not reach that
 threshold, while "NA" means missing or excluded data. ``` *
 "Grain" sheet; This sheet contains age in days that calves
 reached 50, 100, 250, 500, and 900 g of grain intake. * "Hay"
 sheet; This sheet contains age in days that calves reached 25, 50, 100,
 150, and 200 g of hay intake. Only Hay Treatment calves are included on
 this sheet, as Control calves were never given access to hay. *
 "Water" sheet; This sheet contains age in days that calves
 reached 1, 2, 3, 4, and 5 L of water intake. * "Rumination"
 sheet; This sheet contains age in days that calves reached 5, 10, 15, and
 20 % of a 24-h day ruminating. Two calves (2942, 3045) have NA values
 reflecting missing or incomplete daily tag data that prevented their
 analysis for age of meeting thresholds. ``` #### Code All analyses were
 run in R using RStudio. Software versions, including those for all
 packages used, are included in each RMarkdown file. Each RMarkdown file is
 exported as a PDF as well, which has the same name. These PDF exports show
 both the code and outputs of the associated RMarkdown file, and are
 particularly useful for users that are not planning to run the code in
 real time, or are less familiar with R, but would like to view the
 processing steps. * *1_Descriptive_intake_and_figures_260122.Rmd*; This
 annotated RMarkdown script uses grain, water, and hay intake data
 collected daily in Holstein heifer calves from birth through the start of
 step-down weaning (~d 50) to calculate descriptive data on the development
 of hay, grain, and water intake, particularly in the first week of life,
 and create a figure of intake throughout the milk-fed period. *
 *1_Descriptive_intake_and_figures_260122.pdf*; This is the knit PDF output
 of the "1_Descriptive_intake_and_figures_260122.Rmd" coding
 file. * *2_Age_at_reaching_thresholds_calculations_260122.Rmd*; This file
 uses daily data
 ("1_Intake_and_rumination_complete_daily_data.xlsx") to
 determine calf age at reaching specific thresholds of intake and
 rumination. This code identifies the first of 3 consecutive days that each
 calf reached or surpassed each threshold. NA values do not count towards
 the 3 consecutive days. These ages are then exported
 ("2_Age_at_reaching_thresholds.xlsx"). *
 *2_Age_at_reaching_thresholds_calculations_260122.pdf*; This is the knit
 PDF output of the
 "2_Age_at_reaching_thresholds_calculations_260122.Rmd" script. *
 *3_Onset_models_and_figures_260122.Rmd*; This file uses data on the ages
 at which calves reached each threshold
 ("2_Age_at_reaching_thresholds.xlsx"; calculated and generated
 in the second RMarkdown file,
 "2_Age_at_reaching_thresholds_calculations_260122.Rmd") to model
 the effect of hay on likelihood of reaching grain, water, and rumination
 thresholds, and whether, of the calves that met the thresholds, access to
 hay influenced the age at which calves reached these thresholds. This file
 also evaluates the development of hay intake in calves fed hay by
 describing the age at which hay intake thresholds were reached. *
 *3_Onset_models_and_figures_260122.pdf*; This is the knit PDF output of
 the "3_Onset_models_and_figures_260122.Rmd" script. ####
 Supplemental * *Supplemental_Tables_and_Figures.pdf*; This PDF contains 2
 supplemental tables and 1 supplemental figure. ``` * Supplemental Table
 S1.; This table shows accelerometer ear tag (MSD Animal Health Technology)
 active days for all calves. Calves were tagged in the right ear on d
 3±2 (mean±SD; range: d 0-7) of life. “First day tag was
 active” was considered the first full day the tag recorded after the tag
 was applied, or the first full day a tag reported a “low activity”
 percentage lower than 80 % after birth. “Low activity” values higher than
 80 % were considered to reflect time when the tag was active but not yet
 applied to the calf, or had not yet registered the calf’s movement
 correctly. Tags collected behavioral data continuously from this starting
 point until the start of weaning, or until the tag failed, whichever came
 first. In some cases, tags began recording a few days after birth, and
 failed before weaning. This table presents columns for "Year"
 (2018 or 2019; the year data collection occurred for each calf),
 "Calf" (calf ID), "Treatment" (Hay or Control),
 "First day tag was active" (calf's age in days when the tag
 first began recording behavior for a complete 1440 min day), "Last
 day tag was active" (calf's age in days when the tag stopped
 recording behavior), "Total number of days tag recorded"
 (difference between first and last days tag recorded), "Ideal number
 of days tag would have recorded" (number of days from birth until the
 day before weaning began; due to variable weaning days, calves would
 ideally have 49-51 days where the tag was active), and "% of data
 collection period with active tag" (percentage of the entire data
 collection period that the calf had an active, recording tag, calculated
 by dividing "Total number of days tag recorded" by "Ideal
 number of days tag would have recorded"). NAs reflect missing data,
 as 1 calf (2942) had complete tag failure and had no data recorded. *
 Supplemental Table S2.; This table shows model-predicted probabilities,
 means, and test statistics from hurdle models evaluating the effect of hay
 provision and year, in some cases, on the onset of grain and water intake
 and rumination in individually housed Holstein heifer calves fed milk
 replacer, water, and grain (Control, n = 20) and mountaingrass hay (Hay, n
 = 29). This table presents columns for "Outcome" (dependent
 variables, i.e. rumination, grain intake, and water intake),
 "Threshold" (predetermined levels of behavior or intake),
 "Likelihood of not reaching threshold" including model-predicted
 values (estimated marginal probabilities and standard error for Control
 and Hay calves at each threshold level for each outcome) and zero-inflated
 (ZI) model component test statistics (chi-square and P-value) for fixed
 effects (e.g. Treatment for all; Year and a Treatment:Year interaction for
 some models); "Age at reaching threshold (d)" including model
 predicted values (estimated marginal means and standard error for Control
 and Hay calves, or calves raised in 2018 and 2019, at each threshold level
 for each outcome) and conditional model component test statistics
 (chi-square and P-value), which was only evaluated when n (number of
 calves reaching the threshold) was greater than or equal to 2/treatment.
 "." reflects that model component not being run, i.e. in the
 "Likelihood of not reaching threshold" column it means that
 there were no zeros (all calves reached that threshold) and thus the ZI
 component was not evaluated; in the "Age at reaching threshold
 (d)" column it means that fewer than 2 calves per treatment reached
 that threshold and thus the conditional component was not evaluated. Test
 statistics for the ZI and conditional model components are also included
 in the associated manuscript, in a table alongside the observed (raw)
 means. * Supplemental Figure S1.; This figure shows the results of a
 linear regression comparing proportion of a 24-h day engaged in rumination
 obtained through live observations using 1-0 sampling at 5-s intervals
 compared with behavior monitoring accelerometer ear tags (SenseHub, Merck
 Animal Health). The figure includes a red line representing a perfect
 relationship (coefficient of determination = 1, slope = 1, intercept = 0)
 and dotted line representing the estimate generated by the tag comparison.
 Comparisons were made on a subset of 16 calves from 2019 who were observed
 on week 4 of life and had tag data available on the same day; each point
 represents an individual calf. Detailed information about live
 observations is available in Downey and Tucker (2023). Coefficient of
 determination, slope estimate, and intercept estimate generated by the
 linear regression are reported in the figure, and p-values comparing the
 slope to 1 and intercept to 0 are presented in the caption. ```