epict_filter_ids: Filter infection IDs based on characteristics

In seabbs/epict: Flexible Cycle Threshold Modelling

Filter infection IDs based on characteristics

Description

Filter infection IDs based on characteristics

Usage

epict_filter_ids(
  obs,
  min_uncensored_tests = 2,
  min_days_with_uncensored = 2,
  invert = FALSE
)

Arguments

obs	A data.frame with the following variables: id: An integer vector uniquely identifying each infection. t: Time of test relative to a baseline date. censored: Logical, indicating if the Ct has been censored.
min_uncensored_tests	Numeric defaults to 2. The minimum number of uncensored tests an ID must have in order to be included in the processed dataset.
min_days_with_uncensored	Numeric defaults to 2. The minimum number of days tests per ID must span in order to be included in the processed dataset.
invert	Logical, defaults to FALSE. Should the filtering requirements be inverted. This switches from excluding to including and can be used for debugging and data exploration.

Value

A data.table with IDs failing/meeting the specified criteria removed.

Author(s)

Sam Abbott

See Also

Preprocessing functions epict_check_obs(), epict_check_raw_obs(), epict_clean_factors(), epict_drop_na_ct(), epict_flag_spurious_obs(), epict_make_time_rel_to_first_uncensored(), epict_make_time_rel()

Examples

obs <- data.frame(
 censored = c(TRUE, rep(FALSE, 3), TRUE, rep(FALSE, 4)),
 id = c(1, 1, 1, 2, 3, 3, 4, 4, 4), t = c(0, 0, 1, 1, 1, 2, 1, 1, 1)
)

# Use defaults
epict_filter_ids(obs)

# Invert with defaults
epict_filter_ids(obs, invert = TRUE)

# Remove IDs with less than 3 tests
epict_filter_ids(obs, min_uncensored_tests = 3, min_days_with_uncensored = 1)

# Remove IDs with less than 3 tests - this will be all available data
epict_filter_ids(obs, min_days_with_uncensored = 3)

seabbs/epict documentation built on July 3, 2023, 6:42 a.m.