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Merged
roninsightrx merged 3 commits into from
Oct 10, 2025
Merged

Add more statistics to the output table #28

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414fb74
add ofv and ss
roninsightrx Oct 9, 2025
46e1d0e
add test
roninsightrx Oct 9, 2025
1c4546b
Update R/run_eval_core.R
roninsightrx Oct 10, 2025
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16 changes: 16 additions & 0 deletions R/misc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -67,3 +67,19 @@ mape <- function (obs, pred) {
mpe <- function (obs, pred) {
sum((obs - pred)/obs)/length(obs)
}

#' Weighted sum-of-squares of residuals
#'
#' @inheritParams rmse
#' @param w weights
#'
ss <- function(obs, pred, w = NULL) {
if(is.null(w)) {
w <- rep(1, length(obs))
}
if (length(obs) != length(pred) || length(obs) != length(w)) {
cli::cli_abort("`obs`, `pred`, and `w` must have the same length")
}
if(sum(w) == 0) return(NA)
sum(w * (obs - pred)^2)
}
Comment on lines +71 to +85
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@mccarthy-m-g mccarthy-m-g Oct 10, 2025

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Suggestion for something more concise (you can take or leave). vctrs::vec_recycle_common() will throw an informative error if any of the lengths are different, e.g.:

ss(obs = 1:5, pred = 5:1, w = 1:3)
#> Error in `ss()`:
#> ! Can't recycle `obs` (size 5) to match `w` (size 3).
Suggested change
#' Weighted sum-of-squares of residuals
#'
#' @inheritParams rmse
#' @param w weights
#'
ss <- function(obs, pred, w = NULL) {
if(is.null(w)) {
w <- rep(1, length(obs))
}
if (length(obs) != length(pred) || length(obs) != length(w)) {
cli::cli_abort("`obs`, `pred`, and `w` must have the same length")
}
if(sum(w) == 0) return(NA)
sum(w * (obs - pred)^2)
}
#' Weighted sum-of-squares of residuals
#'
#' @inheritParams rmse
#' @param w A numeric vector of weights the same size as `obs` and `pred`.
#' Vectors of size 1 will be recycled to the size of `obs` and `pred`.
#'
ss <- function(obs, pred, w = 1) {
args <- vctrs::vec_recycle_common(obs = obs, pred = pred, w = w)
if(sum(args[["w"]]) == 0) return(NA)
sum(args[["w"]] * (args[["obs"]] - args[["pred"]])^2)
}

Here are some tests you could add for this too:

test_that("recycling + incompatible size error works", {
  expect_equal(ss(obs = 1:3, pred = 3:1, w = 1), 8)
  expect_equal(ss(obs = 1:3, pred = 3:1, w = c(1, 1, 0.5)), 6)
  expect_error(
    ss(obs = 1:5, pred = 5:1, w = 1:3), class = "vctrs_error_incompatible_size"
  )
})

10 changes: 8 additions & 2 deletions R/run_eval_core.R
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Expand Up @@ -75,6 +75,8 @@ run_eval_core <- function(
dv = fit$dv,
ipred = fit$ipred,
pred = fit$pred,
ofv = fit$fit$value,
ss_w = ss(fit$dv, fit$ipred, weights),
`_iteration` = iterations[i],
`_grouper` = obs_data$`_grouper`
)
Expand Down Expand Up @@ -111,6 +113,8 @@ run_eval_core <- function(
dv = fit_map$dv,
ipred = fit_map$ipred,
pred = fit_map$pred,
ofv = fit_map$fit$value,
ss_w = ss(fit_map$dv, fit_map$ipred, w = NULL),
`_iteration` = iterations[i],
`_grouper` = obs_data$`_grouper`
)
Expand All @@ -127,7 +131,9 @@ run_eval_core <- function(
dplyr::filter(.data$`_iteration` == 1) |>
dplyr::mutate(
`_iteration` = 0,
ipred = .data$pred
ipred = .data$pred,
ofv = NA,
ss_w = NA
) |> # set to population parameters, not individual estimates
dplyr::select(-!!names(mod_obj$parameters)) |>
dplyr::left_join(
Expand All @@ -144,12 +150,12 @@ run_eval_core <- function(
) |>
dplyr::select(
"id", "_iteration", "_grouper", "t", "dv", "pred", "map_ipred",
"ofv", "ss_w",
"iter_ipred", "apriori",
!!names(mod_obj$parameters)
)

out

}

#' Handle covariate censoring
Expand Down
18 changes: 18 additions & 0 deletions man/ss.Rd
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14 changes: 14 additions & 0 deletions tests/testthat/test-run_eval.R
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Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,24 @@ test_that("Basic run with vanco data + model works", {
expect_equal(names(res), c("results", "mod_obj", "data", "sim", "stats_summ", "shrinkage", "bayesian_impact"))
expect_s3_class(res$results, c("tbl_df", "tbl", "data.frame"))
expect_s3_class(res$stats_summ, c("tbl_df", "tbl", "data.frame"))
expect_equal(
names(res$results),
c("id", "_iteration", "_grouper", "t", "dv", "pred", "map_ipred",
"ofv", "ss_w", "iter_ipred", "apriori", "CL", "V", "TH_CRCL",
"Q", "V2")
)
expect_equal(
round(res$results$CL[1:5], 3),
c(2.99, 2.685, 2.462, 2.430, 2.439)
)
expect_equal(
round(res$results$ofv[1:5], 3),
c(NA, 6.196, 11.846, 17.046, 21.563)
)
expect_equal(
round(res$results$ss_w[1:5], 3),
c(NA, 16.839, 11.241, 27.358, 30.944)
)

# Using PKPDsim model library:
res_2 <- run_eval(
Expand Down