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Check proccessed observations meet the package specification

Source: R/preprocess.R
epict_check_obs.Rd

Checks the available proccessed observastionsfor required variables and returns informative errors, warnings, and messages about the structure of the observations.

Usage

epict_check_obs(obs, check_onset = FALSE)

Arguments

obs

A data.frame with the following variables:

  • id: An integer vector uniquely identifying eahc infection.

  • test_id: An integer vector uniquely identiying each test

  • ct_value: Numeric cycle threshold value.

  • t: Relative (to a baseline) time of the test yielding a Ct value.

  • t_rel_uncensored: Time of test relative to the first uncensored Ct value for that id.

  • onset_t: Relative (to a baseline) time of onset for each infection

  • onset_t_rel_uncensored: Time of onset relative to the first uncensored Ct value for that id. (optional). NA if unavailable/asymptomatic.

  • censored: Logical, indicating if the Ct has been censored.

check_onset

Logical, defaults to FALSE. Should observations be checked for the presence of symptom onset data.

Value

A data.table of observations ready for use in epict() and other package functions.

See also

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

Author

Sam Abbott