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Default vaccine efficacy estimates data

Source: R/aac-data-types.R
efficacy_default.Rd

A data frame containing default vaccine efficacy estimates per serotype for Poliovirus from published literature. Used as default when user-provided efficacy data is unavailable and the study concerns poliovirus OPV and IPV vaccines. This data also shows the vaccine efficacy estimates in its raw format.

Usage

efficacy_default

Format

A data frame with 10 rows and 7 columns:

serotype

[character] The disease serotype (Poliovirus in this case). Format: <disease><number> with <disease> being a string representing the disease (e.g., "PV" for Poliovirus) and <number> being 1, 2, ..., to distinguish serotypes, <number> can be a combination of numbers for multiple serotypes (e.g., "13" for PV1 and PV3).

vaccine_type

[character] Vaccine variant. Format: <prefix><vaccine> where prefix distinguishes variants (e.g., "tOPV", "bOPV", "mOPV1").

dose_num

[integer] Dose number (1, 2, 3, ...). Must conform to the rules specified for the dose_num column of dummy_vs_info.

efficacy

[numeric] Efficacy value between 0 and 1.

type

[character] Either 'per-dose' (measured per individual dose) or 'n-dose' (measured per number of doses).

from, to

[integer] First/last year this vaccine type was used. May be NA meaning 'from/to anytime'. This is used to handle historical vaccine changes (e.g., Poliovirus tOPV vaccine withdrawal in 2016). Overlapping vaccine use (e.g., tOPV and bOPV used in the same year) is not currently supported.

Source

Estimates retrieved from peer-reviewed literature. The exact references and their mapping to individual rows are not currently recorded in the repository and should be added to make the dataset fully traceable.

Details

Efficacy interpretation

  • per-dose: Efficacy applies to each individual dose. This is most of the time the same for all doses for the specific vaccine variant but is allowed to be different between doses as well. When the same, only the first dose needs to be specified.

  • n-dose: Efficacy applies to the cumulative number of doses received. An efficacy value should be given for each dose for the corresponding vaccine variant and should be non-decreasing with the number of doses. For example, if the efficacy for 1 dose is 0.5, the efficacy for 2 doses should be at least 0.5 and so on.

Serotype notation <disease><number>:

<disease> should be consistent for all serotypes.

  • PV1: Serotype 1 specific

  • PV3: Serotype 3 specific

  • PV13: Same efficacy applies to both serotypes 1 and 3. This is used when the efficacy is the same for more than one serotype for a given vaccine variant. This spares the user from having to specify the same efficacy value for each serotype separately which is also fine but might be more tedious.

If the disease has only one serotype or dealing with a single serotype, the serotype can just be the <disease> (e.g., "PV") without the number.

See also

prep_dummy_efficacy for the preprocessed, preprocess_efficacy() for preprocessing function, validate_efficacy() for validation function

Examples

# \donttest{
# View efficacy
head(efficacy_default)
#>   serotype     type vaccine_type dose_num efficacy from   to
#> 1     PV12 per dose         tOPV        0     0.39   NA 2015
#> 2      PV1 per dose         bOPV        0     0.63 2016   NA
#> 3      PV1  n-doses          IPV        1     0.35   NA   NA
#> 4      PV1  n-doses          IPV        2     0.60   NA   NA
#> 5      PV1  n-doses          IPV        3     0.84   NA   NA
#> 6      PV1  n-doses          IPV        4     0.94   NA   NA

# Validate efficacy estimates data
validate_efficacy(efficacy_default, dummy_vs_info, preprocessed = FALSE)

# Filter for OPV efficacy
efficacy_default |>
  dplyr::filter(grepl("OPV", vaccine_type))
#>   serotype     type vaccine_type dose_num efficacy from   to
#> 1     PV12 per dose         tOPV        0     0.39   NA 2015
#> 2      PV1 per dose         bOPV        0     0.63 2016   NA
# }