epict_flag_spurious_obs: Flag potentially spurious observations

In seabbs/epict: Flexible Cycle Threshold Modelling

Flag potentially spurious observations

Description

Flag potentially spurious observations

Usage

epict_flag_spurious_obs(
  obs,
  max_t_rel_uncensored = 60,
  max_onset_t_rel_uncensored = 15,
  flag = TRUE,
  drop = TRUE,
  return_spurious = FALSE
)

Arguments

obs	A data.frame with the following variables: t_rel_uncensored: Time of test relative to the first uncensored Ct value for that id. onset_t_rel_uncensored: Time of onset relative to the first uncensored Ct value for that id. (optional). NA if unavailable/asymptomatic.
max_t_rel_uncensored	Numeric defaults to 60 days. Flags the maximum absolute relative time that is considered plausible for tests to be spaced by per ID.
max_onset_t_rel_uncensored	Numeric defaults to 15 days. Flags the maximum absolute relative time that is considered plausible for symptom onset from the first uncensored test per ID.
flag	Logical, defaults to TRUE. Should spurious tests be flagged
drop	Logical, defaults to TRUE. Should spurious tests and onsets be dropped (set to NA for onsets and filtered out for tests).
return_spurious	Logical, defaults to FALSE. Rather than returning observations should observations flagged as spurious be returned.

Value

A data.table of observations

Author(s)

Sam Abbott

See Also

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

Examples

obs <- data.frame(t_rel_uncensored = c(0, 2, 10, 60, 100, 30))

# Run with defaults
fil_obs <- epict_flag_spurious_obs(obs)
fil_obs
epict_flag_spurious_obs(fil_obs)

# Add onsets and repeat
obs$onset_t_rel_uncensored <- c(0, 15, 2, NA, 40, 5)
fil_obs <- epict_flag_spurious_obs(obs)
fil_obs
epict_flag_spurious_obs(fil_obs)

# Return spurious observations
epict_flag_spurious_obs(obs, return_spurious = TRUE)

# Flag spurious results but don't drop
epict_flag_spurious_obs(obs, drop = FALSE)

# Siltently drop
epict_flag_spurious_obs(obs, flag = FALSE)

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