incRscan_v3: Scoring of incubation based on combination of dynamic (as in...

In PabloCapilla/incR: Analysis of Incubation Data

Scoring of incubation based on combination of dynamic (as in incRscan) and fixed temperature thresholds (as in incRscan_v2

Description

Modified version of incRscan. It combines the assignment of incubation on/off-bout implemented in incRscan and incRscan_v2.

Usage

incRscan_v3(
  data,
  temp.name,
  temperature_threshold,
  lower.time,
  upper.time,
  sensitivity,
  temp.diff,
  temp.diff.threshold,
  maxNightVariation,
  env.temp
)

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.
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. Only applies for days when a calibration window is not available or temp.diff.threshold is exceeded.
lower.time	lower limit of time window for calibration (numeric).
upper.time	upper limit of time window for calibration (numeric).
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).
temp.diff	deprecated. Use temp.diff.threshold.
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.

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

Author(s)

Pablo Capilla-Lasheras

See Also

incRscan incRscan_v2

PabloCapilla/incR documentation built on July 22, 2023, 12:18 p.m.