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 > 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.