Commit 1aefa792 authored by Reinhard Furrer's avatar Reinhard Furrer
Browse files

trinROC update

parent 6cac20c4
No preview for this file type
Package: trinROC
Title: Statistical Tests for Assessing Trinormal ROC Data
Version: 0.5
Date: 2021-01-04
Version: 0.5.1
Date: 2021-06-29
Authors@R: c(person("Samuel", "Noll", email = "uncle.sam@gmx.net", role = c("aut")), person("Reinhard", "Furrer", role = c("cre", "aut"), email = "reinhard.furrer@math.uzh.ch"), person("Benjamin", "Reiser", role = c("ctb")), person("Christos T.", "Nakas", role = c("ctb"), email = "cnakas@uth.gr"))
Description: Several statistical test functions as well as a function for exploratory data analysis to investigate classifiers allocating individuals to one of three disjoint and ordered classes. In a single classifier assessment the discriminatory power is compared to classification by chance. In a comparison of two classifiers the null hypothesis corresponds to equal discriminatory power of the two classifiers.
Depends:
......
......@@ -62,7 +62,7 @@
#' @export
#' @references Nakas, C. T. and C. T. Yiannoutsos (2004). Ordered multiple-class
#' ROC analysis with continuous measurements. \emph{Statistics in
#' Medicine} \bold{23}(22), 3437–3449.
#' Medicine}, \bold{23}(22), 3437–3449.
#' @examples
#' data(cancer)
#' data(krebs)
......
......@@ -211,7 +211,7 @@ roc.eda <- function(x, y, z, dat = NULL, type = c("empirical", "trinormal"),
histROC <- ggplot(data, aes_string(x = "value", colour="trueClass", fill="trueClass")) +
geom_histogram(aes_string(y ="..density.."), binwidth=(max(data$value)-min(data$value))/15,
position = "dodge", alpha=0.7, show.legend = FALSE) +
scale_colour_manual(values=c("#79AB67", "#6EA3D0", "#D68898"), guide = FALSE) +
scale_colour_manual(values=c("#79AB67", "#6EA3D0", "#D68898"), guide = "none") +
scale_fill_manual(values=c("#79AB67", "#6EA3D0", "#D68898"), name = "Class") +
labs(y="Count",x=paste(Marker, "measurements")) +
#facet_grid(. ~ trueClass, scales = "free") +
......@@ -222,7 +222,7 @@ roc.eda <- function(x, y, z, dat = NULL, type = c("empirical", "trinormal"),
histROC <- ggplot(data, aes_string(x = "value", colour="trueClass", fill="trueClass")) +
geom_histogram(aes_string(y = "..density.."),binwidth=(max(data$value)-min(data$value))/30,
show.legend = FALSE) +
scale_colour_manual(values=c("#79AB67", "#6EA3D0", "#D68898"), guide = FALSE) +
scale_colour_manual(values=c("#79AB67", "#6EA3D0", "#D68898"), guide = "none") +
scale_fill_manual(values=c("#79AB67", "#6EA3D0", "#D68898"), name="Class") +
labs(y="Density",x=paste(Marker, "measurements")) +
facet_grid(. ~ trueClass, scales = "free") +
......@@ -233,14 +233,14 @@ roc.eda <- function(x, y, z, dat = NULL, type = c("empirical", "trinormal"),
# boxplots:
meas.overview <- ggplot(data, aes_string(y="value", x="trueClass", fill = "trueClass")) +
stat_boxplot(geom ='errorbar') + geom_boxplot() +
scale_fill_manual(values=c("#79AB67", "#6EA3D0", "#D68898"), guide = FALSE) +
scale_fill_manual(values=c("#79AB67", "#6EA3D0", "#D68898"), guide = "none") +
coord_flip() + labs(x="", y=paste(Marker, "measurements"))
} else {
# scattter plot of data:
meas.overview <- ggplot(data, aes_string(y="value", x="trueClass", color = "trueClass")) +
geom_jitter(width = 0.25) +
scale_colour_manual(values=c("#79AB67", "#6EA3D0", "#D68898"), guide = FALSE) +
scale_colour_manual(values=c("#79AB67", "#6EA3D0", "#D68898"), guide = "none") +
coord_flip() + labs(x="", y=paste(Marker, "measurements"))
}
......
......@@ -3,5 +3,5 @@
#' estimates by setting \code{options(trinROC.MLE = FALSE)}
#' @references Noll, S., Furrer, R., Reiser, B. and Nakas, C. T. (2019).
#' Inference in ROC surface analysis via a trinormal model-based testing approach.
#' \emph{Stat}, accepted.
#' \emph{Stat}, \bold{8}(1), e249.
"_PACKAGE"
......@@ -71,7 +71,7 @@
#' geom_density geom_histogram geom_jitter labs scale_colour_manual
#' scale_fill_manual stat_boxplot aes_string
#' @param conf.level confidence level of the interval. A numeric value between (0,1)
#' yielding the significance level \eqn{\alpha=1-\code{conf.level}}.
#' yielding the significance level \eqn{\alpha=1-}\code{conf.level}.
#'
#' @return A list of class \code{"htest"} containing the following components:
#' \item{statistic}{the value of the chi-squared statistic.}
......@@ -89,9 +89,9 @@
#' \item{Summary}{a data frame representing the number of NA's as well as
#' the means and the standard deviations per class.}
#'
#' @references Noll, S., Furrer, R., Reiser, B. and Nakas, C. T. (2018).
#' @references Noll, S., Furrer, R., Reiser, B. and Nakas, C. T. (2019).
#' Inference in ROC surface analysis via a trinormal model-based testing approach.
#' \emph{Submitted}.
#' \emph{Stat}, \bold{8}(1), e249.
#' @seealso \code{\link{trinVUS.test}}, \code{\link{boot.test}}.
#'
#' @export
......
......@@ -82,7 +82,7 @@
#'
#' @references Xiong, C., van Belle, G., Miller, J. P., Yan, Y., Gao, F., Yu, K., and Morris, J. C. (2007). A parametric comparison
#' of diagnostic accuracy with three ordinal diagnostic groups.
#' \emph{Biometrical Journal}, \bold{49}(5), 682–693. \url{https://doi.org/10.1002/bimj.200610359}.
#' \emph{Biometrical Journal}, \bold{49}(5), 682–693. \doi{10.1002/bimj.200610359}.
#' @examples
#' data(cancer)
#' data(krebs)
......
......@@ -111,7 +111,7 @@ z2 <- with(krebs, krebs[trueClass=="diseased", 5])
\references{
Nakas, C. T. and C. T. Yiannoutsos (2004). Ordered multiple-class
ROC analysis with continuous measurements. \emph{Statistics in
Medicine} \bold{23}(22), 3437–3449.
Medicine}, \bold{23}(22), 3437–3449.
}
\seealso{
\code{\link{trinROC.test}}, \code{\link{trinVUS.test}}.
......
......@@ -16,7 +16,7 @@ See \code{vignette("Overview", package = "trinROC")} for an overview of the pack
\references{
Noll, S., Furrer, R., Reiser, B. and Nakas, C. T. (2019).
Inference in ROC surface analysis via a trinormal model-based testing approach.
\emph{Stat}, accepted.
\emph{Stat}, \bold{8}(1), e249.
}
\seealso{
Useful links:
......
......@@ -36,7 +36,7 @@ If \code{TRUE}, each class must have equal sample size for both
classifiers.}
\item{conf.level}{confidence level of the interval. A numeric value between (0,1)
yielding the significance level \eqn{\alpha=1-\code{conf.level}}.}
yielding the significance level \eqn{\alpha=1-}\code{conf.level}.}
}
\value{
A list of class \code{"htest"} containing the following components:
......@@ -121,9 +121,9 @@ z2 <- with(cancer, cancer[trueClass=="diseased", 5])
trinROC.test(x1, y1, z1, x2, y2, z2, paired = TRUE)
}
\references{
Noll, S., Furrer, R., Reiser, B. and Nakas, C. T. (2018).
Noll, S., Furrer, R., Reiser, B. and Nakas, C. T. (2019).
Inference in ROC surface analysis via a trinormal model-based testing approach.
\emph{Submitted}.
\emph{Stat}, \bold{8}(1), e249.
}
\seealso{
\code{\link{trinVUS.test}}, \code{\link{boot.test}}.
......
......@@ -108,7 +108,7 @@ Xiong, C., Van Belle, G. Miller J. P., Morris, J. C. (2006). Measuring and esti
Xiong, C., van Belle, G., Miller, J. P., Yan, Y., Gao, F., Yu, K., and Morris, J. C. (2007). A parametric comparison
of diagnostic accuracy with three ordinal diagnostic groups.
\emph{Biometrical Journal}, \bold{49}(5), 682–693. \url{https://doi.org/10.1002/bimj.200610359}.
\emph{Biometrical Journal}, \bold{49}(5), 682–693. \doi{10.1002/bimj.200610359}.
}
\seealso{
\code{\link{trinROC.test}}, \code{\link{boot.test}}.
......
R Under development (unstable) (2020-12-04 r79564) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
R Under development (unstable) (2021-05-23 r80364) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
......@@ -535,7 +535,7 @@ VUS of Classifier 1 VUS of Classifier 2
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed: 5.28 0.092 5.748 0.004 0
Time elapsed: 5.689 0.105 6.06 0.001 0.001
> grDevices::dev.off()
null device
1
......
R Under development (unstable) (2020-12-04 r79564) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
R Under development (unstable) (2021-05-23 r80364) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
......@@ -53,9 +53,8 @@ Parameters:
a b c d
0.6959 -0.2546 0.4462 0.1083
---------------------------------------------------------------------
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 43 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
>
> proc.time()
user system elapsed
4.768 0.144 4.905
5.297 0.111 5.399
This source diff could not be displayed because it is too large. You can view the blob instead.
This diff is collapsed.
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment