incRscan_v2: Scoring of incubation based on a fixed temperature threshold

Description

Modified version of incRscan. Data points are assigned to incubation on/off-bout based on a fixed temperature threshold for the difference in nest temperature expected when an off-bout starts.

Usage

incRscan_v2(
  data,
  temp.name,
  sensitivity,
  temperature_threshold,
  temp.diff.threshold,
  env.temp
)

Value

The function returns the original data frame with a new column named 'incR_score'. This new variable is formed by 1's and 0's, representing whether the incubating individual is inside ("1") or outside the nest ("0"). #' @section Details: See incRenv for more details

Arguments

data: data frame for analysis. It must contained four columns named as follow: date, temp1, dec_time and index, where temp1 is the difference between the ith and i-1th temperature recordings; dec_time is time in decimal hours; and index is a running number from 1 to N, N being the total number of observations. incRprep returns a data frame with these variables and the correct names, ready to be passed through incRscan.
temp.name: (character object) name of the column containing temperature data in data.
sensitivity: percentage of reduction in temperature threshold. When nest temperature does not drop close to environmental temperature, this value can be kept to 1. If nest temperature follows environmental temperature at any point, then, adjustment of this value may be required to detect short on/off-bouts at lower nest temperatures (see details).
temperature_threshold: Maximum temperature difference between two consecutive nest temperature recordings allowed for an on-bout. When the difference in nest temperature between two consecutive recordings is higher than this value, an off-bout is detected.
temp.diff.threshold: threshold for temperature difference between env.temp and an observation which triggers application of the sensitivity parameter.
env.temp: name of a column containing environmental temperatures.

Author

Pablo Capilla-Lasheras

Examples

Run this code

# incR_procdata is a data frame processed by incRprep and incRenv.
# It contains suitable information to run incRscan
data(incR_procdata)

incubation.analysis <- incRscan_v2 (data=incR_procdata, 
                                  temp.name="temperature",
                                  temperature_threshold = 0.75,
                                  sensitivity=0.15,
                                  temp.diff.threshold=5,
                                  env.temp="env_temp")