Added lr_pos and lr_neg to coords (#102)

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pROC
 Type: Package
 Title: Display and Analyze ROC Curves
-Version: 1.18.5
-Date: 2023-11-01
+Version: 1.18.9999
+Date: 2024-07-07
 Encoding: UTF-8
 Depends: R (>= 2.14)
 Imports: methods, plyr, Rcpp (>= 0.11.1)

NEWS

@@ -1,3 +1,6 @@
+1.18.9999
+  * Added "lr_pos" and "lr_neg" to 'coords' (issue #102)
+
 1.18.5 (2023-11-01):
   * Fixed formula input when given as variable and combined with `with` (issue #111)
   * Fixed formula containing variables with spaces (issue #120)

R/roc.utils.R

@@ -309,7 +309,7 @@ roc.utils.valid.coords <- c("specificity", "sensitivity", "accuracy",
 	"npv", "ppv", "fdr",
 	"fpr", "tpr", "tnr", "fnr", 
 	"1-specificity", "1-sensitivity", "1-accuracy", "1-npv", "1-ppv",
-	"precision", "recall",
+	"precision", "recall", "lr_pos", "lr_neg",
 	"youden", "closest.topleft")
 
 # Arguments which can be returned by coords
@@ -472,6 +472,8 @@ roc_utils_calc_coords <- function(roc, thr, se, sp, best.weights) {
 		"1-ppv"=substr.percent-ppv,
 		precision=precision,
 		recall=recall,
+		"lr_pos"=(se / substr.percent) / (1 - sp / substr.percent),
+		"lr_neg"=(1 - se / substr.percent) / (sp / substr.percent),
 		youden=youden,
 		closest.topleft=closest.topleft
 	))
@@ -565,6 +567,8 @@ coord.is.monotone <- c(
 	"1-ppv"=FALSE,
 	"precision"=FALSE,
 	"recall"=TRUE,
+	"lr_pos"=FALSE,
+	"lr_neg"=FALSE,
 	"youden"=FALSE,
 	"closest.topleft"=FALSE
 )
@@ -592,6 +596,8 @@ coord.is.decreasing <- c(
 	"1-ppv"=NA,
 	"precision"=NA,
 	"recall"=TRUE,
+	"lr_pos"=NA,
+	"lr_neg"=NA,
 	"youden"=NA,
 	"closest.topleft"=NA
 )

man/coords.Rd

@@ -184,6 +184,8 @@ as.matrix=FALSE, ...)
 		\code{tnr} \tab True Negative Rate \tab tn / (tn + fp) \tab specificity \tab Yes \cr
 		\code{fnr} \tab False Negative Rate \tab fn / (tp + fn) \tab 1-sensitivity \tab Yes \cr
 		\code{fdr} \tab False Discovery Rate \tab fp / (tp + fp) \tab 1-ppv \tab No \cr
+		\code{lr_pos} \tab Positive Likelihood Ratio \tab se / (1 - sp) \tab - \tab No \cr
+		\code{lr_neg} \tab Negative Likelihood Ratio \tab (1 - se) / (sp) \tab - \tab No \cr
 		\code{youden} \tab Youden Index \tab 
 			se + r * sp
 			\tab - \tab No \cr

tests/testthat/helper-roc.utils-expected.R

@@ -1,37 +1,46 @@
 expected_roc_utils_calc_coords <-
-structure(c(-1, -2, -3, -4, 1, 0.5, 0.1, 0, 0, 0.5, 0.9, 1, 0.36283185840708, 
-0.5, 0.609734513274336, 0.63716814159292, 0, 36, 64.8, 72, 41, 
-20.5, 4.1, 0, 0, 20.5, 36.9, 41, 72, 36, 7.2, 0, NaN, 0.63716814159292, 
-0.63716814159292, 0.63716814159292, 0.36283185840708, 0.36283185840708, 
-0.36283185840708, NaN, 1, 0.5, 0.1, 0, 0, 0.5, 0.9, 1, 1, 0.5, 
-0.1, 0, 0, 0.5, 0.9, 1, 0.63716814159292, 0.63716814159292, 0.63716814159292, 
-NaN, 1, 0.5, 0.1, 0, 0, 0.5, 0.9, 1, 0.63716814159292, 0.5, 0.390265486725664, 
-0.36283185840708, NaN, 0.36283185840708, 0.36283185840708, 0.36283185840708, 
-0.63716814159292, 0.63716814159292, 0.63716814159292, NaN, 0.36283185840708, 
-0.36283185840708, 0.36283185840708, NaN, 1, 0.5, 0.1, 0, 1, 0.50462962962963, 
-0.108333333333333, 0.00925925925925926, 0.00925925925925926, 
-0.252314814814815, 0.810092592592593, 1), .Dim = c(4L, 24L), .Dimnames = list(
-NULL, c("threshold", "sensitivity", "specificity", "accuracy", 
-"tn", "tp", "fn", "fp", "npv", "ppv", "tpr", "tnr", "fpr", 
-"fnr", "fdr", "1-specificity", "1-sensitivity", "1-accuracy", 
-"1-npv", "1-ppv", "precision", "recall", "youden", "closest.topleft"
-)))
+structure(c(-1, -2, -3, -4, 1, 0.5, 0.10000000000000001, 0, 0, 
+0.5, 0.90000000000000002, 1, 0.36283185840707965, 0.5, 0.60973451327433625, 
+0.63716814159292035, 0, 36, 64.799999999999997, 72, 41, 20.5, 
+4.1000000000000005, 0, 0, 20.5, 36.899999999999999, 41, 72, 36, 
+7.2000000000000028, 0, NaN, 0.63716814159292035, 0.63716814159292035, 
+0.63716814159292035, 0.36283185840707965, 0.36283185840707965, 
+0.36283185840707954, NaN, 1, 0.5, 0.10000000000000001, 0, 0, 
+0.5, 0.90000000000000002, 1, 1, 0.5, 0.099999999999999978, 0, 
+0, 0.5, 0.89999999999999991, 1, 0.63716814159292035, 0.63716814159292035, 
+0.63716814159292035, NaN, 1, 0.5, 0.099999999999999978, 0, 0, 
+0.5, 0.90000000000000002, 1, 0.63716814159292035, 0.5, 0.39026548672566375, 
+0.36283185840707965, NaN, 0.36283185840707965, 0.36283185840707965, 
+0.36283185840707965, 0.63716814159292035, 0.63716814159292035, 
+0.63716814159292046, NaN, 0.36283185840707965, 0.36283185840707965, 
+0.36283185840707954, NaN, 1, 0.5, 0.10000000000000001, 0, 1, 
+1, 1.0000000000000002, NaN, NaN, 1, 1, 1, 1, 0.50462962962962965, 
+0.10833333333333334, 0.009259259259259257, 0.009259259259259257, 
+0.25231481481481483, 0.8100925925925927, 1), .Dim = c(4L, 26L
+), .Dimnames = list(NULL, c("threshold", "sensitivity", "specificity", 
+"accuracy", "tn", "tp", "fn", "fp", "npv", "ppv", "tpr", "tnr", 
+"fpr", "fnr", "fdr", "1-specificity", "1-sensitivity", "1-accuracy", 
+"1-npv", "1-ppv", "precision", "recall", "lr_pos", "lr_neg", 
+"youden", "closest.topleft")))
 
 expected_roc_utils_calc_coords.percent <-
-structure(c(-1, -2, -3, -4, 100, 50, 10, 0, 0, 50, 90, 100, 36.283185840708, 
-50, 60.9734513274336, 63.716814159292, 0, 36, 64.8, 72, 41, 20.5, 
-4.1, 0, 0, 20.5, 36.9, 41, 72, 36, 7.2, 0, NaN, 63.716814159292, 
-63.716814159292, 63.716814159292, 36.283185840708, 36.283185840708, 
-36.283185840708, NaN, 100, 50, 10, 0, 0, 50, 90, 100, 100, 50, 
-10, 0, 0, 50, 90, 100, 63.716814159292, 63.716814159292, 63.716814159292, 
-NaN, 100, 50, 10, 0, 0, 50, 90, 100, 63.716814159292, 50, 39.0265486725664, 
-36.283185840708, NaN, 36.283185840708, 36.283185840708, 36.283185840708, 
-63.716814159292, 63.716814159292, 63.716814159292, NaN, 36.283185840708, 
-36.283185840708, 36.283185840708, NaN, 100, 50, 10, 0, 100, 50.462962962963, 
-10.8333333333333, 0.925925925925926, 0.925925925925926, 25.2314814814815, 
-81.0092592592593, 100), .Dim = c(4L, 24L), .Dimnames = list(NULL, 
-c("threshold", "sensitivity", "specificity", "accuracy", 
-"tn", "tp", "fn", "fp", "npv", "ppv", "tpr", "tnr", "fpr", 
-"fnr", "fdr", "1-specificity", "1-sensitivity", "1-accuracy", 
-"1-npv", "1-ppv", "precision", "recall", "youden", "closest.topleft"
-)))
+structure(c(-1, -2, -3, -4, 100, 50, 10, 0, 0, 50, 90, 100, 36.283185840707965, 
+50, 60.973451327433622, 63.716814159292035, 0, 36, 64.799999999999997, 
+72, 41, 20.5, 4.0999999999999996, 0, 0, 20.5, 36.899999999999999, 
+41, 72, 36, 7.2000000000000028, 0, NaN, 63.716814159292035, 63.716814159292042, 
+63.716814159292035, 36.283185840707965, 36.283185840707965, 36.283185840707951, 
+NaN, 100, 50, 10, 0, 0, 50, 90, 100, 100, 50, 10, 0, 0, 50, 90, 
+100, 63.716814159292035, 63.716814159292035, 63.716814159292042, 
+NaN, 100, 50, 10, 0, 0, 50, 90, 100, 63.716814159292035, 50, 
+39.026548672566378, 36.283185840707965, NaN, 36.283185840707965, 
+36.283185840707958, 36.283185840707965, 63.716814159292035, 63.716814159292035, 
+63.716814159292049, NaN, 36.283185840707965, 36.283185840707965, 
+36.283185840707951, NaN, 100, 50, 10, 0, 1, 1, 1.0000000000000002, 
+NaN, NaN, 1, 1, 1, 100, 50.462962962962962, 10.833333333333334, 
+0.92592592592592571, 0.92592592592592571, 25.231481481481481, 
+81.009259259259267, 100), .Dim = c(4L, 26L), .Dimnames = list(
+    NULL, c("threshold", "sensitivity", "specificity", "accuracy", 
+    "tn", "tp", "fn", "fp", "npv", "ppv", "tpr", "tnr", "fpr", 
+    "fnr", "fdr", "1-specificity", "1-sensitivity", "1-accuracy", 
+    "1-npv", "1-ppv", "precision", "recall", "lr_pos", "lr_neg", 
+    "youden", "closest.topleft")))