apply_dd_filters: Apply filters to prepare data for degree-day calculation

In dempsey-CMAR/tgc: Thermal Growth Coefficient Model for Aquaculture

Apply filters to prepare data for degree-day calculation

Description

Apply filters to prepare data for degree-day calculation

Usage

apply_dd_filters(
  dat,
  trend_threshold = 4,
  superchill_threshold = -0.7,
  max_season = 540,
  full_season = TRUE,
  heat_threshold = 18,
  n_hours = 24
)

Arguments

dat	Data frame with at least three columns: TIMESTAMP (must be possible to convert to POSIXct), DEPTH, and VALUE. If column VARIABLE is included, it must have one unique entry. May also include columns with grouping variables passed to .... Other columns will be ignored.
trend_threshold	The threshold for "trending up". Default is trend_threshold = 4. The last observation above trend_threshold that does not return below trend_threshold triggers the beginning of the growing season for each DEPTH and group in ....
superchill_threshold	The threshold for "superchill". Default is superchill_threshold = -0.7. The first observation below superchill_threshold triggers the end of the growing season for each group in DEPTH and ....
max_season	The length of the growing season in months for groups that have no temperature observations below superchill_threshold. Default is max_season = 540 days (~18 months). Note: units are days because adding 18 months to August 30 or August 31 results in NA (because February 30 and February 31 are not real dates).
full_season	Logical argument. The default, full_season = TRUE will only return data for groups with a full season of data (e.g., START_SEASON and END_SEASON as returned by identify_growing_seasons(dat, full_season = TRUE) are both NOT NA). If full_season = FALSE, data for all groups will be returned; the START_SEASON and END_SEASON dates default to the first and last timestamp in ... and DEPTH.
heat_threshold	The threshold for heat stress. Default is heat_threshold = 18). Every observation above heat_threshold triggers an n-hour heat stress interval.
n_hours	Length of heat stress interval in hours (default is n_hours = 24).

Value

Returns dat filtered for days that will be used to calculate degree-days at DEPTH. Includes observations that start after the 4-degree trending up threshold and end 1 minute before the first observation of superchill for each season; observations that occur during a heat stress events are removed.

An additional column SEASON is included to label the growing seasons ("S1", "S2", ...). Some observations may be duplicated in consecutive seasons.

dempsey-CMAR/tgc documentation built on Oct. 20, 2023, 6:45 p.m.