DOI: 10.5061/dryad.kd51c5bg5
title: Data from: Biologging in a free-ranging mammal reveals apparent energetic trade-offs among physiological and behavioral components of the acute phase response

description: The acute phase response (APR) is an adaptive emergency life-history
 stage, wherein vertebrates exhibit fever and anorexia to survive an
 infection. However, induced immune responses are energetically costly and
 sick animals may reduce physical activity to compensate. Tests of this
 predicted energetic trade-off in free-ranging animals are rare due to
 difficulties in measuring individual physiology and behavior under immune
 challenge in natural settings. However, recent advances in biologging
 technology now make such studies possible. We surgically implanted heart
 rate/temperature loggers in free-ranging adult male Arctic ground
 squirrels, fitted the squirrels with collar-mounted accelerometers and
 light/temperature loggers, and injected animals with lipopolysaccharide
 (LPS) to simulate an immune challenge. LPS-injected squirrels exhibited ~1
 °C overnight fevers accompanied by slightly elevated (~10 bpm) heart
 rates; LPS-injected squirrels also spent ~20% less of their time
 aboveground the following day and reduced overall movement by ~40%
 compared to saline-injected controls. Thus, we found support for an
 energetic trade-off between functional immune responses (fever and
 anorexia) and lethargic sickness behavior within the APR of a free-ranging
 mammal. Moreover, our results suggest animal-borne devices can play an
 important role in future studies of vertebrate immunity and disease
 dynamics.
description: The acute phase response (APR) is an adaptive emergency
 life-history stage, wherein vertebrates exhibit fever and anorexia to
 survive an infection. However, induced immune responses are energetically
 costly and sick animals may reduce physical activity to compensate. Tests
 of this predicted energetic trade-off in free-ranging animals are rare due
 to difficulties in measuring individual physiology and behavior under
 immune challenge in natural settings. However, recent advances in
 biologging technology now make such studies possible. We surgically
 implanted heart rate/temperature loggers in free-ranging adult male Arctic
 ground squirrels, fitted the squirrels with collar-mounted accelerometers
 and light/temperature loggers, and injected animals with
 lipopolysaccharide (LPS) to simulate an immune challenge. LPS-injected
 squirrels exhibited ~1 °C overnight fevers accompanied by slightly
 elevated (~10 bpm) heart rates; LPS-injected squirrels also spent ~20%
 less of their time aboveground the following day and reduced overall
 movement by ~40% compared to saline-injected controls. Thus, we found
 support for an energetic trade-off between functional immune responses
 (fever and anorexia) and lethargic sickness behavior within the APR of a
 free-ranging mammal. Moreover, our results suggest animal-borne devices
 can play an important role in future studies of vertebrate immunity and
 disease dynamics.
description: # Data from: Biologging in a free-ranging mammal reveals an energetic
 trade-off between physiological and behavioral components of the acute
 phase response
 [https://doi.org/10.5061/dryad.kd51c5bg5](https://doi.org/10.5061/dryad.kd51c5bg5) ## Dataset Description Data are provided as CSV files. The processed data CSV files are ready to be used in conjunction with the R code files to replicate analysis and generate figures from the manuscript. Only small changes in the file pathways should be required to replicate results. These files are not intended for interpretation outside the context of the associated manuscript, although some of the raw data may be useful in other contexts as mentioned above. ## File Descriptions ###### AGS\_IndividualAPR\_Data Data is structured for correlation analysis in R and for plotting via ggplot2 in R. Columns: * ID: individual squirrel identification number * Tb: mean overnight body temperature (measured by collar-mounted temperature loggers) in degrees Celsius during the first night following a LPS injection * VEDBA: mean daily VeDBA (measured by collar-mounted accelerometers) on the first day following a LPS injection; VeDBA is a measure of movement derived from tri-axial accelerometry data ###### AGS\_*LPS\_HR\_Excluded* Data is structured for plotting via ggplot2 in R. Columns: * Time: time of day in hourly bins (e.g., 00:00-01:00), denoted by the midpoint of the bin (e.g., 00:30) * Removed: percentage of heart rate values excluded during a given hourly time bin * Fill: denotes whether day from a given time bin was included in our generalized additive mixed-effects models ###### AGS\_LPS\_HR\_ProcessedData Data is structured for generalized additive mixed-effects model analysis via the the mgcv package in R. Columns: * Date: date (m/d/yyyy) * Datetime: date and time of day * Time: time of day (12-hour clock) * AM.PM: denotes whether time is morning or afternoon (AM = morning, PM = afternoon) * TB: instantaneous squirrel internal body temperature (measured by implanted temperature loggers) in degrees Celsius * HR: instantaneous squirrel heart rate (measured by implanted heart rate loggers) in beats per minute * QI: the quality index assigned to a given heart rate record by the internal heart rate logger (0 = highest quality, 3 = lowest quality) * ID: individual squirrel identification number * Injection.Type: the type of injection administered to a squirrel (saline = saline, LPS = LPS) * Inject.ID: a combination of a given squirrel's ID number and the injection type (distinguishes between saline and LPS injections in squirrels that received both during the experiment) * Injection.Time: the date and time of day at which a given injection was administered to the squirrel * Injection.Time.Diff: time difference between a given heart rate record and the injection time in hours * Injection.Night.Diff: binned time difference between heart rate records and the injection (0Pre = two nights prior to an injection, 1Post = first night post-injection, 2Post = second night post-injection, 3Post = third night post-injection * Time2: time of day as a numerical vector * Amb.Temp: mean overnight (00:00-04:00) ambient aboveground temperature ###### AGS\_LPS\_HR\_TB\_NightlyMedians\_Model Data is structured for linear mixed-effects model analysis via the lme4 package in R. Columns: * date: date (m/d/yyyy) * id: individual squirrel identification number * hr: median overnight squirrel heart rate (measured by implanted heart rate loggers) in beats per minute * tb: median overnight squirrel internal body temperature (measured by implanted temperature loggers) in degrees Celsius * cat: categorizes nights as the first night following an LPS injection (A), the first night following a saline injection (B), or other (C) ###### AGS\_LPS\_HR\_TB\_NightlyMedians\_Plot Data is structured for plotting via the ggplot2 package in R. Columns: * date: date (m/d/yyyy) * id: individual squirrel identification number * hr: median overnight squirrel heart rate (measured by implanted heart rate loggers) in beats per minute * tb: median overnight squirrel internal body temperature (measured by implanted temperature loggers) in degrees Celsius * cat: categorizes nights as the first night following an LPS injection (First Night Post-LPS), the first night following a saline injection (First Night Post-Saline), or other (Other) ###### AGS\_LPS\_HR\_Tb\_RawData Data is structured as downloaded from the internally implanted heart rate/temperature loggers. Columns: * Datetime: date and time of day * Date: date (m/d/yyyy) * time: time of day (12-hour clock) * am.pm: denotes whether time is morning or afternoon (AM = morning, PM = afternoon) * night: denotes whether a given set of values falls within the overnight period we modeled (00:00-04:00) * temp_c: instantaneous squirrel internal body temperature (measured by implanted temperature loggers) in degrees Celsius * HR_bpm: instantaneous squirrel heart rate (measured by implanted heart rate loggers) in beats per minute * QI: the quality index assigned to a given heart rate record by the internal heart rate logger (0 = highest quality, 3 = lowest quality) * filename: the name of the file downloaded from the device (file names include individual logger id numbers, which can be tied to individual squirrel id numbers) ###### AGS\_*LPS\_HR\_Validate* Date is structured for plotting via ggplot2 in R. Columns: * Automated: instantaneous squirrel heart rate values (bpm) automatically estimated by internal heart rate loggers * Manual: instantaneous squirrel heart rate values (bpm) manually estimated by us via PatternFinder software * ID: individual heart rate logger identification number ###### AGS\_LPS\_HR\_Validate\_Line Data is structured for plotting via ggplot2 in R. Columns: * Automated: hypothetical instantaneous squirrel heart rate values (bpm) automatically estimated by internal heart rate loggers to draw a 1:1 line on the plot (i.e., if automated values and manual values matched perfectly) * Manual: hypothetical instantaneous squirrel heart rate values (bpm) manually estimated by us via PatternFinder software to draw a 1:1 line on the plot (i.e., if automated values and manual values matched perfectly) ###### AGS\_LPS\_Light\_ProcessedData Data is structured for generalized additive mixed-effects model analysis via the the mgcv package in R. Columns: * Day.Time: a combination of the date and hourly time bins * Inject.ID: a combination of a given squirrel's ID number and the injection type (distinguishes between saline and LPS injections in squirrels that received both during the experiment) * Time.Block: hourly time of day bins * Time: time of day as a numerical vector * ID: individual squirrel identification number * Injection.Type: the type of injection administered to a squirrel (saline = saline, LPS = LPS) * Injection.Day.Diff: binned time difference between aboveground activity records and the injection (0Pre = two days prior to an injection, 1Post = first day post-injection, 2Post = second day post-injection, 3Post = third day post-injection * Injection.Time: the time at which a given injection was administered to the squirrel * Day: shorthand for the date (day of June 2019) * Date: date (m/d/yyyy) * Time.Up: number of trials within an hour a squirrel was above ground (lux &gt; 0 as measured by collar-mounted light loggers) * Prop.Up: proportion of trials within an hour a squirrel was above ground * Trials: number of trials in hour * Temp: mean ambient aboveground temperature within an hour in degrees Celsius * Precip: precipitation within an hour (cm) ###### AGS\_LPS\_LightLogger\_RawData Data is structured as downloaded from the collar-mounted light-loggers. Columns: * XXX: a unitless counting column * light: instantaneous light intensity (lux) readings measured by collar-mounted light loggers * ID: individual squirrel identification number * datetime_ak: date (m/d/yyyy) and time of day ###### AGS\_LPS\_Tb\_Collar\_ProcessedData Data is structured for generalized additive mixed-effects model analysis via the the mgcv package in R. Columns: * Date: date (m/d/yyyy) * Time: time of day (12-hour clock) * ID: individual squirrel identification number * Tb: instantaneous squirrel body temperature (measured by collar-mounted temperature loggers) in degrees Celsius * Datetime: date and time of day * AM.PM: denotes whether time is morning or afternoon (AM = morning, PM = afternoon) * Injection.Type: the type of injection administered to a squirrel (saline = saline, LPS = LPS) * Injection.Datetime: the date and time of day at which a given injection was administered to the squirrel * Injection.Time.Diff: time difference between a given heart rate record and the injection time in hours * Inject.ID: a combination of a given squirrel's ID number and the injection type (distinguishes between saline and LPS injections in squirrels that received both during the experiment) * Injection.Night.Diff: binned time difference between body temperature records and the injection (0Pre = two nights prior to an injection, 1Post = first night post-injection, 2Post = second night post-injection, 3Post = third night post-injection * Time2: time of day as a numerical vector * Amb.Temp: mean overnight (00:00-04:00) ambient aboveground temperature ###### AGS\_LPS\_Tb\_Collar\_RawData Data is structured as downloaded from the collar-mounted light-loggers. Columns: * temp: instantaneous squirrel body temperature (measured by collar-mounted temperature loggers) in degrees Celsius * ID: individual squirrel identification number * datetime_ak: date (m/d/yyyy) and time of day ###### AGS\_LPS\_Tb\_ProcessedData Data is structured for generalized additive mixed-effects model analysis via the the mgcv package in R. Columns: * Date2: date (m/d/yyyy) * Datetime: date and time of day * Date: date (m/d/yyyy) * Time: time of day (12-hour clock) * AM.PM: denotes whether time is morning or afternoon (AM = morning, PM = afternoon) * Tb: instantaneous squirrel internal body temperature (measured by implanted temperature loggers) in degrees Celsius * HR: instantaneous squirrel heart rate (measured by implanted heart rate loggers) in beats per minute * QI: the quality index assigned to a given heart rate record by the internal heart rate logger (0 = highest quality, 3 = lowest quality) * ID: individual squirrel identification number * Injection.Type: the type of injection administered to a squirrel (saline = saline, LPS = LPS) * Inject.ID: a combination of a given squirrel's ID number and the injection type (distinguishes between saline and LPS injections in squirrels that received both during the experiment) * Mass: squirrel body mass (g) * Injection.Time: the date and time of day at which a given injection was administered to the squirrel * Injection.Time.Diff: time difference between a given body temperature record and the injection time in hours * Injection.Night.Diff: binned time difference between body temperature records and the injection (0Pre = two nights prior to an injection, 1Post = first night post-injection, 2Post = second night post-injection, 3Post = third night post-injection * Time2: time of day as a numerical vector * Amb.Temp: mean overnight (00:00-04:00) ambient aboveground temperature ###### AGS\_*LPS\_VEDBA\_ProcessedData* Data is structured for generalized additive mixed-effects model analysis via the the mgcv package in R. Columns: * Day.Time: a combination of the date and hourly time bins * ID: individual squirrel identification number * Injection.Type: the type of injection administered to a squirrel (saline = saline, LPS = LPS) * Inject.ID: a combination of a given squirrel's ID number and the injection type (distinguishes between saline and LPS injections in squirrels that received both during the experiment) * Day: shorthand for the date (day of June 2019) * Date: date (d/m/yyyy) * Injection.Time.Bin: binned (hourly) time difference between VeDBA records and the injection in hours * Injection.Time.Diff: time difference between a given VeDBA record and the injection time in hours * Injection.Day.Diff: binned time difference between aboveground activity records and the injection (0Pre = two days prior to an injection, 1Post = first day post-injection, 2Post = second day post-injection, 3Post = third day post-injection * Time.Block: hourly time of day bins * Time: time of day as a numerical vector * vedba: mean hourly squirrel VeDBA (measured by collar-mounted accelerometers); VeDBA is a measure of movement derived from tri-axial accelerometry data * Temp: mean ambient aboveground temperature within an hour in degrees Celsius * Precip: precipitation within an hour (cm) ###### AGS\_LPS\_Weather\_RawData Data is structured as downloaded from the weather station at our study site. Columns: * Datetime: date and time of day * Date: date (m/d/yyyy) * Precip: total precipitation (cm) within the previous 15 minutes * Temp: instantaneous ambient temperature (degrees Celsius) * RH: instantaneous relative humidity (%) * Wind.Dir: instantaneous wind direction (degrees; north = 0 degrees) * Wind.Spd: instantaneous sustained wind speed (m/s) * Gust.Spd: instantaneous wind gust speed (m/s) * Solar: instantaneous solar radiation (W/m2) ## Code/Software Description The R code files included in the dataset include the statistical analyses from the manuscript, which are primarily comprised of generalized additive mixed-effects models. The GAMM files can be used in conjunction with the processed data files. The R code files also include code to re-create figures from the manuscript. Note that some manual manipulation of CSV files occurred prior to plotting (primarily this consisted of renaming columns). No statistical analyses or changes to values occurred outside of the R environment. All R code is annotated.