Centralise validation of mvepiestim inputs #245
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| #' Check incidence input for MV-EpiEstim | ||
| #' | ||
| #' Check that incid is a 3-dimensional array with non-negatuve enteries. | ||
| #' | ||
| #' @inheritParams estimate_advantage | ||
| #' @returns Silently returns TRUE if the checks are passed, otherwise throws an | ||
| #' error. | ||
| #' @author Sangeeta Bhatia | ||
| #' @keywords internal | ||
| check_incidence <- function(incid) { | ||
| if (any(incid < 0)) { | ||
| stop("incid must be >=0") | ||
| } | ||
| if (!is.array(incid) || length(dim(incid)) != 3) { | ||
| stop( | ||
| "incid must be a 3-dimensional array with dimensions time, location, variant", | ||
| .call = FALSE | ||
| ) | ||
| } | ||
| invisible(TRUE) | ||
| } | ||
|
|
||
|
|
||
| #' Check priors for MV-EpiEstim | ||
| #' | ||
| #' Check that priors is a list of the correct format and that the mean of the | ||
| #' prior for epsilon is 1 (as currently only priors with mean of epsilon equal | ||
| #' to 1 is supported). | ||
| #' | ||
| #' @inheritParams estimate_advantage | ||
| #' @returns Silently returns TRUE if the checks are passed, otherwise throws an | ||
| #' error. | ||
| #' @author Sangeeta Bhatia | ||
| #' @keywords internal | ||
| check_priors <- function(priors) { | ||
|
|
||
| if (!identical(priors, default_priors())) { | ||
| warning( | ||
| "Priors where the mean of epsilon is different from 1 are not currently supported.", | ||
| .call = FALSE | ||
| ) | ||
| } | ||
| invisible(TRUE) | ||
| } | ||
|
|
||
| #' Check MCMC control parameters for MV-EpiEstim | ||
| #' | ||
| #' Check that (1) mcmc_control is a list of the correct format, (2) n_iter, burnin | ||
| #' and thin are positive integers and (3) n_iter is greater than burnin + thin. | ||
| #' | ||
| #' @inheritParams estimate_advantage | ||
| #' @returns Silently returns TRUE if the checks are passed, otherwise throws an | ||
| #' error. | ||
| #' @author Sangeeta Bhatia | ||
| #' @keywords internal | ||
| check_mcmc_control <- function(mcmc_control) { | ||
|
|
||
| if (mcmc_control$n_iter < 0 || !is.integer(mcmc_control$n_iter)) { | ||
| stop("n_iter in mcmc_control must be a positive integer", .call = FALSE) | ||
| } | ||
| if (mcmc_control$burnin < 0 || !is.integer(mcmc_control$burnin)) { | ||
| stop("burnin in mcmc_control must be a positive integer", .call = FALSE) | ||
| } | ||
| if (mcmc_control$thin < 0 || !is.integer(mcmc_control$thin)) { | ||
| stop("thin in mcmc_control must be a positive integer", .call = FALSE) | ||
| } | ||
| if (mcmc_control$n_iter < mcmc_control$burnin + mcmc_control$thin) { | ||
| stop("In mcmc_control, n_iter must be greater than burnin + thin", .call = FALSE) | ||
| } | ||
| invisible(TRUE) | ||
| } | ||
|
|
||
| #' Validate t_min and t_max inputs for MV-EpiEstim | ||
| #' | ||
| #' Check that (1) t_min and t_max are integers, (2) that they are >= 2, that | ||
| #' they are <= nrow(incid) and (3) t_min is not greater than t_max. | ||
| #' | ||
| #' @inheritParams estimate_advantage | ||
| #' @returns Silently returns TRUE if the checks are passed, otherwise throws an | ||
| #' error. | ||
| #' @author Sangeeta Bhatia | ||
| #' @keywords internal | ||
| check_t_min_t_max <- function(t_min, t_max, incid) { | ||
| if (!is.integer(t_min) || !is.integer(t_max)) { | ||
| stop("t_min and t_max must be integers", .call = FALSE) | ||
| } | ||
| if (t_min < 2 || t_max < 2) { | ||
| stop("t_min and t_max must be >=2", .call = FALSE) | ||
| } | ||
| if (t_min > nrow(incid) || t_max > nrow(incid)) { | ||
| stop("t_min and t_max must be <= nrow(incid)", .call = FALSE) | ||
| } | ||
| if (t_min > t_max) { | ||
| stop( | ||
| "t_min is greater than t_max. You can specify a smaller t_min or increase t_max.", | ||
| .call = FALSE | ||
| ) | ||
| } | ||
| invisible(TRUE) | ||
| } | ||
|
|
||
|
|
||
| #' Validate seed input for MV-EpiEstim | ||
| #' | ||
| #' Validate that the seed is not null and is numeric | ||
| #' | ||
| #' @inheritParams estimate_advantage | ||
| #' @return Silently returns TRUE if the checks are passed, otherwise throws an error. | ||
| #' @author Sangeeta Bhatia | ||
| #' @keywords internal | ||
| check_seed <- function(seed) { | ||
| if (!is.null(seed) && !is.numeric(seed)) { | ||
| stop("supplied seed is not a valid integer", .call = FALSE) | ||
| } | ||
| if (!is.null(seed)) set.seed(seed) | ||
| invisible(TRUE) | ||
| } | ||
|
|
||
|
|
||
| #' Validate inputs to estimate_advantage | ||
| #' | ||
| #' Runs all available input checks for \code{\link{estimate_advantage}} based on | ||
| #' the supplied arguments. Each check is called only if the corresponding | ||
| #' argument is present. | ||
| #' | ||
| #' @param ... Named arguments passed to \code{\link{estimate_advantage}}. | ||
| #' @returns Invisibly returns \code{NULL}; throws an error if any input check | ||
| #' fails. | ||
| #' @author Sangeeta Bhatia | ||
| #' @keywords internal | ||
| check_estimate_advantage_inputs <- function(...) { | ||
| estimate_advantage_args <- list(...) | ||
| arg_names <- names(estimate_advantage_args) | ||
| if ("incid" %in% arg_names) | ||
| check_incidence(estimate_advantage_args$incid) | ||
|
|
||
| if ("si" %in% arg_names) | ||
| apply(estimate_advantage_args$si_distr, 2, check_si_distr) | ||
|
|
||
| if ("priors" %in% arg_names) | ||
| check_priors(estimate_advantage_args$priors) | ||
|
|
||
| if ("mcmc_control" %in% arg_names) | ||
| check_mcmc_control(estimate_advantage_args$mcmc_control) | ||
|
|
||
| if (all(c("t_min", "t_max", "incid") %in% arg_names)) { | ||
| check_t_min_t_max( | ||
| estimate_advantage_args$t_min, estimate_advantage_args$t_max, | ||
| estimate_advantage_args$incid | ||
| ) | ||
| } | ||
| if ("seed" %in% arg_names) | ||
| check_seed(estimate_advantage_args$seed) | ||
| } |
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Uh oh!
There was an error while loading. Please reload this page.