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Issue #536: Setting the threshold to Inf message #537

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Issue #536: Setting the threshold to Inf message #537

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46ceee2
Change to cli message
athowes Feb 19, 2025
913a01c
Make more concise
athowes Feb 19, 2025
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10 changes: 5 additions & 5 deletions R/marginal_model.R
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@
data, obs_time_threshold = 2, weight = NULL, ...) {
assert_epidist.epidist_linelist_data(data)

data <- data |>

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file=R/marginal_model.R,line=68,col=11,[one_call_pipe_linter] Avoid pipe |> for expressions with only a single call.
mutate(
pwindow = .data$ptime_upr - .data$ptime_lwr,
swindow = .data$stime_upr - .data$stime_lwr,
Expand All @@ -87,11 +87,11 @@
if (n_beyond > 0) {
cli::cli_inform(c(
"!" = paste0(
"Setting {n_beyond} observation time{?s} beyond ",
"{threshold} (={obs_time_threshold}x max delay) to Inf. ",
"This improves model efficiency by reducing unique observation times ",
"while maintaining model accuracy as these times should have ",
"negligible impact."
"{n_beyond} relative observation time{?s} beyond {threshold} ",
"(= {obs_time_threshold} x max delay) set to Inf ",
"See {.var obs_time_threshold}. This improves efficiency by ",
"reducing unique data points. Impact on accuracy is neglible ",
"if right truncation bias for these data points is limited."
)
))
data$relative_obs_time[data$relative_obs_time > threshold] <- Inf
Expand Down Expand Up @@ -145,7 +145,7 @@
#' @export
new_epidist_marginal_model <- function(data) {
class(data) <- c("epidist_marginal_model", class(data))
return(data)

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file=R/marginal_model.R,line=148,col=3,[return_linter] Use implicit return behavior; explicit return() is not needed.
}

#' @method assert_epidist epidist_marginal_model
Expand All @@ -170,7 +170,7 @@
)
}
assert_numeric(data$n, lower = 1)
return(invisible(NULL))

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file=R/marginal_model.R,line=173,col=3,[return_linter] Use implicit return behavior; explicit return() is not needed.
}

#' Check if data has the `epidist_marginal_model` class
Expand All @@ -179,7 +179,7 @@
#' @family marginal_model
#' @export
is_epidist_marginal_model <- function(data) {
return(inherits(data, "epidist_marginal_model"))

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file=R/marginal_model.R,line=182,col=3,[return_linter] Use implicit return behavior; explicit return() is not needed.
}

#' Create the model-specific component of an `epidist` custom family
Expand Down Expand Up @@ -208,7 +208,7 @@
posterior_predict = epidist_gen_posterior_predict(family),
posterior_epred = epidist_gen_posterior_epred(family)
)
return(custom_family)

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file=R/marginal_model.R,line=211,col=3,[return_linter] Use implicit return behavior; explicit return() is not needed.
}

#' Define the model-specific component of an `epidist` custom formula for the
Expand All @@ -228,7 +228,7 @@
formula, delay_lwr | weights(n) +
vreal(relative_obs_time, pwindow, swindow, delay_upr) ~ .
)
return(formula)

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file=R/marginal_model.R,line=231,col=3,[return_linter] Use implicit return behavior; explicit return() is not needed.
}

#' Transform data for the marginal model
Expand Down Expand Up @@ -261,7 +261,7 @@

.inform_data_summarised(data, trans_data, c(required_cols))

return(trans_data)

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file=R/marginal_model.R,line=264,col=3,[return_linter] Use implicit return behavior; explicit return() is not needed.
}

#' @method epidist_stancode epidist_marginal_model
Expand Down Expand Up @@ -289,7 +289,7 @@
fixed = TRUE
)

if (family_name == "lognormal") {

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file=R/marginal_model.R,line=292,col=3,[if_switch_linter] Prefer switch() statements over repeated if/else equality tests, e.g., switch(x, a = 1, b = 2) over if (x == "a") 1 else if (x == "b") 2.
dist_id <- 1
} else if (family_name == "gamma") {
dist_id <- 2
Expand Down Expand Up @@ -341,7 +341,7 @@
}

.marginal_required_cols <- function() {
return(c(

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file=R/marginal_model.R,line=344,col=3,[return_linter] Use implicit return behavior; explicit return() is not needed.
"delay_lwr", "delay_upr", "relative_obs_time", "pwindow", "swindow", "n"
))
}
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