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Filter infection IDs based on characteristics

Source: R/preprocess.R
epict_filter_ids.Rd

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 exluding to including and can be used for debugging and data exploration.

Value

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

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()

Author

Sam Abbott

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)
#>    censored id t uncensored_tests days_with_uncensored
#> 1:     TRUE  1 0                2                    2
#> 2:    FALSE  1 0                2                    2
#> 3:    FALSE  1 1                2                    2

# Invert with defaults
epict_filter_ids(obs, invert = TRUE)
#>    censored id t uncensored_tests days_with_uncensored
#> 1:    FALSE  2 1                1                    1
#> 2:     TRUE  3 1                1                    1
#> 3:    FALSE  3 2                1                    1

# Remove IDs with less than 3 tests
epict_filter_ids(obs, min_uncensored_tests = 3, min_days_with_uncensored = 1)
#>    censored id t uncensored_tests days_with_uncensored
#> 1:    FALSE  4 1                3                    1
#> 2:    FALSE  4 1                3                    1
#> 3:    FALSE  4 1                3                    1

#' # Remove IDs with less than 3 tests - this will be all available data
epict_filter_ids(obs, min_days_with_uncensored = 3)
#> Empty data.table (0 rows and 5 cols): censored,id,t,uncensored_tests,days_with_uncensored