Skip to main content
  • Home
  • Development
  • Documentation
  • Donate
  • Operational login
  • Browse the archive

swh logo
SoftwareHeritage
Software
Heritage
Archive
Features
  • Search

  • Downloads

  • Save code now

  • Add forge now

  • Help

https://github.com/cran/cutpointr
12 May 2022, 17:57:39 UTC
  • Code
  • Branches (12)
  • Releases (0)
  • Visits
    • Branches
    • Releases
    • HEAD
    • refs/heads/master
    • refs/tags/0.7.2
    • refs/tags/0.7.3
    • refs/tags/0.7.4
    • refs/tags/0.7.6
    • refs/tags/1.0.0
    • refs/tags/1.0.1
    • refs/tags/1.0.2
    • refs/tags/1.0.32
    • refs/tags/1.1.0
    • refs/tags/1.1.1
    • refs/tags/1.1.2
    No releases to show
  • da13f07
  • /
  • R
  • /
  • plot_roc.R
Raw File Download
Take a new snapshot of a software origin

If the archived software origin currently browsed is not synchronized with its upstream version (for instance when new commits have been issued), you can explicitly request Software Heritage to take a new snapshot of it.

Use the form below to proceed. Once a request has been submitted and accepted, it will be processed as soon as possible. You can then check its processing state by visiting this dedicated page.
swh spinner

Processing "take a new snapshot" request ...

Permalinks

To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

  • content
  • directory
  • revision
  • snapshot
origin badgecontent badge Iframe embedding
swh:1:cnt:2e3453bef5aa12b0bc5ec384f2a0d482b16e7e2f
origin badgedirectory badge Iframe embedding
swh:1:dir:a9efd1deea485f19e4e36bfcd9b5108a56759d62
origin badgerevision badge
swh:1:rev:8883cb6d23c8c690e6eeb8a8d074a5508e76f3d7
origin badgesnapshot badge
swh:1:snp:59fa548f9fdef2e9cfbec66f8a33531d45433c4b
Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

  • content
  • directory
  • revision
  • snapshot
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
Tip revision: 8883cb6d23c8c690e6eeb8a8d074a5508e76f3d7 authored by Christian Thiele on 27 March 2019, 09:10:03 UTC
version 0.7.6
Tip revision: 8883cb6
plot_roc.R
#' Plot ROC curve from a cutpointr object
#'
#' Given a \code{cutpointr} object this function plots the ROC curve(s)
#' per subgroup, if given. Also plots a ROC curve from the output of \code{roc()}.
#' @param x A cutpointr or roc_cutpointr object.
#' @param display_cutpoint (logical) Whether or not to display the optimal
#' cutpoint as a dot on the ROC curve for cutpointr objects.
#' @param ... Additional arguments (unused).
#' @examples
#' opt_cut <- cutpointr(suicide, dsi, suicide)
#' plot_roc(opt_cut, display_cutpoint = FALSE)
#'
#' opt_cut_2groups <- cutpointr(suicide, dsi, suicide, gender)
#' plot_roc(opt_cut_2groups, display_cutpoint = TRUE)
#' @family cutpointr plotting functions
#' @export
plot_roc <- function(x, display_cutpoint = TRUE, ...) {
    args <- list(...)
    if ("cutpointr" %in% class(x)) {
        plot_roc_cp(x = x, display_cutpoint = display_cutpoint, args)
    } else if ("roc_cutpointr" %in% class(x)) {
        plot_roc_rcp(x = x, args)
    } else {
        stop(paste("Can not plot ROC curve form object of type",
                   paste(class(x), collapse = ", ")))
    }
}

plot_roc_cp <- function(x, display_cutpoint, ...) {
    predictor <- as.name(x$predictor[1])
    outcome <- as.name(x$outcome[1])

    if (!(has_column(x, "subgroup"))) {
        dts_roc <- "roc_curve"
        fll <- NULL
        clr <- NULL
        clr_roc <- NULL
        transparency <- 1
    } else {
        dts_roc <- c("roc_curve", "subgroup")
        fll <- "subgroup"
        clr <- "subgroup"
        clr_roc <- ~ subgroup
        transparency <- 0.6
    }

    if (!(has_column(x, "subgroup"))) {
        roc_title <- ggplot2::ggtitle("ROC curve")
    } else {
        roc_title <- ggplot2::ggtitle("ROC curve", "by class")
    }
    if (display_cutpoint) {
        optcut_coords <- apply(x, 1, function(r) {
            opt_ind <- get_opt_ind(roc_curve = r$roc_curve,
                                   oc = r$optimal_cutpoint,
                                   direction = r$direction)
            data.frame(tpr = r$roc_curve$tpr[opt_ind],
                       tnr = r$roc_curve$tnr[opt_ind])
        })
        optcut_coords <- do.call(rbind, optcut_coords)
    }
    res_unnested <- x %>%
        dplyr::select_(.dots = dts_roc) %>%
        tidyr::unnest_(unnest_cols = "roc_curve")
    roc <- ggplot2::ggplot(res_unnested,
                           ggplot2::aes_(x = ~ 1 - tnr, y = ~ tpr, color = clr_roc)) +
        ggplot2::geom_step() +
        roc_title +
        ggplot2::xlab("1 - Specificity") +
        ggplot2::ylab("Sensitivity") +
        ggplot2::theme(aspect.ratio = 1)
    if (display_cutpoint) {
        roc <- roc + ggplot2::geom_point(data = optcut_coords, color = "black")
    }
    return(roc)
}

plot_roc_rcp <- function(x, ...) {
    roc_title <- ggplot2::ggtitle("ROC curve")
    roc <- ggplot2::ggplot(x, ggplot2::aes_(x = ~ 1 - tnr, y = ~ tpr)) +
        ggplot2::geom_step() +
        roc_title +
        ggplot2::xlab("1 - Specificity") +
        ggplot2::ylab("Sensitivity") +
        ggplot2::theme(aspect.ratio = 1)
    return(roc)
}

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API

back to top