Calculate start/end of season metrics for time series from multiple sites and groups

Reads remote sensing index time series files from the clean/ subdirectory within the specified dir. For each site, group, and year combination, the function extends the time series to include the end of the previous year and the beginning of the next year (to capture early- and late-year events), then calls calculate_season_metrics() to calculate start/end of season metrics for each time series, which are measured by the day-of-year (DOY) when the index first goes above or goes below specified threshold(s). Results are saved as .rds files under the doy/ subdirectory within dir, prefixed doy_.

Usage

calculate_season_metrics_batch(
  dir,
  v_site = NULL,
  v_group = NULL,
  v_year = NULL,
  df_thres = NULL,
  var_index = "evi",
  min_days = 80,
  check_seasonality = T,
  extend_to_previous_year = 275,
  extend_to_next_year = 90,
  num_cores = 3
)

Arguments

dir

Character. Base directory containing remote sensing index files (expects clean/ subdirectory).

v_site

Character vector, optional. Site identifiers to process; if NULL, all sites are included.

v_group

Character vector, optional. Group identifiers to process; if NULL, all groups are included.

v_year

Integer vector, optional. Years to process; if NULL, all years in the data are included.

df_thres

Data frame of thresholds as from set_thresholds(); if NULL, uses default thresholds.

var_index

Character. Name of the remote sensing index column in the input data frame df_index to analyze (default: "evi").

min_days

Numeric. Minimum required number of non-NA data points in one year (default: 80).

check_seasonality

Logical. If TRUE, tests for significant seasonal changes before calculating start/end of season metrics (default: TRUE).

extend_to_previous_year

Integer. Day of year to extend backward to, to capture early-year events (default: 275).

extend_to_next_year

Integer. Day of year to extend forward to, to capture late-year events (default: 90).

num_cores

Integer. Number of parallel workers for processing (default: 3).

Value

Invisibly returns NULL and saves calculated start/end of season metrics as .rds files in the doy/ subdirectory of dir.

Examples

if (FALSE) { # \dontrun{
# Example: Calculate start of season metrics for two sites and two groups
df_thres <- set_thresholds(thres_up = c(0.3, 0.5))
calculate_season_metrics_batch(
  dir = "alldata/PSdata/",
  v_site = c("Site1", "Site2"),
  v_group = c("Group1", "Group2"),
  v_year = c(2023, 2024),
  df_thres = df_thres,
  var_index = "evi",
  min_days = 80,
  check_seasonality = TRUE,
  extend_to_previous_year = 275,
  extend_to_next_year = 90,
  num_cores = 3
)
} # }