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Filter data for touchstones or diseases

Source: R/fn_impact_diagnostics.R
filter_impact_data.Rd

A pair of helper functions allowing filtering out of recent touchstone values and excluded diseases.

Usage

filter_recent_ts(df, threshold = DEF_TOUCHSTONE_NEW)

filter_excluded_diseases_ts(df, threshold = DEF_TOUCHSTONE_OLD_OLD)

flag_duplicates(df, key_cols = COLNAMES_KEY_PRESSURE_TEST)

filter_invalid_trajectories(
  df,
  prev_data,
  outcome = c("deaths_averted", "dalys_averted")
)

Arguments

df

A <data.frame> holding impact data. This data.frame is not checked for contents

threshold

A six-digit number that is checked as a valid touchstone identifier (YYYYMM format) using validate_ts_year(). Defaults to DEF_TOUCHSTONE_NEW ("202310").

key_cols

Key columns in df to check for duplicates.

prev_data

A <data.frame> holding data from a previous touchstone for the same scenarios as df.

outcome

A string giving the outcome of interest; may be one of "deaths_averted" or "dalys_averted".

Value

A filtered <data.frame>.

  • filter_recent_ts() returns df with rows where the touchstone condition is not met excluded.

  • filter_excluded_diseases_ts() returns df with rows where rows relating to the EXCLUDED_DISEASES, when the touchstone year in df is less than the threshold, excluded.

  • flag_duplicates() returns df with duplicated combinations of key_cols flagged using the column n_key (or a user-defined name).

  • filter_invalid_trajectories() returns df with bad outcome trajectories (NA to non-NA) removed.