Skip to content

Update impute.R to 1) clarify impute_gmt_titers parameters and 2) enforce reproducibility #3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
TKMarkCheng wants to merge 3 commits into
base: main
Choose a base branch
from
Open

Update impute.R to 1) clarify impute_gmt_titers parameters and 2) enforce reproducibility #3

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
0743d74
Update impute.R to clarify impute_gmt_titers
TKMarkCheng Mar 19, 2025
1470155
Update impute.R to improve reproducibility
TKMarkCheng Mar 19, 2025
8004495
Update impute.R to remove random seed enforcement
TKMarkCheng Mar 19, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 5 additions & 5 deletions R/impute.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ rcensnorm <- function(mean, sd, lower_lims, upper_lims) {

min_p <- pnorm(lower_lims[bounded_titer], mean[bounded_titer], sd[bounded_titer])
max_p <- pnorm(upper_lims[bounded_titer], mean[bounded_titer], sd[bounded_titer])

samples <- runif(sum(bounded_titer), min_p, max_p)
output <- lower_lims
output[bounded_titer] <- qnorm(samples, mean[bounded_titer], sd[bounded_titer])
Expand All @@ -23,7 +23,7 @@ impute_gmt_logtiters <- function(result, titers) {
mean = result["mean", "estimate"],
sd = result["sd", "estimate"],
lower_lims = titerlims$min_titers,
upper_lims = titerlims$max_titers
upper_lims = titerlims$max_titers,
)

attr(result, "censoring") <- titerlims$censoring
Expand All @@ -34,12 +34,12 @@ impute_gmt_logtiters <- function(result, titers) {
#' Impute censored titers
#'
#' This function takes a vector of titers and imputes censored titers based on
#' the results of a geometric mean titer estimate from the `impute_gmt_titers()`
#' the results of a geometric mean titer estimate from the `titertools::gmt()`
#' function. Censored titers are drawn from a censored normal distribution with
#' mean and standard deviation parameters equal to those provided in the
#' result argument.
#'
#' @param result Results from a titer GMT estimate from `impute_gmt_titers()`
#' @param result Results from a titer GMT estimate from `titertools::gmt()`
#' @param titers A vector of titers for which to impute censored cases
#'
#' @return Returns a vector of titers with imputed values in place of censored
Expand Down Expand Up @@ -73,7 +73,7 @@ impute_log2diff <- function(
mean = result["mean", "estimate"],
sd = result["sd", "estimate"],
lower_lims = titerlims$min_diffs,
upper_lims = titerlims$max_diffs
upper_lims = titerlims$max_diffs,
)

attr(result, "censoring") <- titerlims$censoring
Expand Down