From 99fc7d8689731070cc4a7425cf2f1c02e4ea1023 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Tue, 6 Jul 2021 13:54:21 +0930
Subject: [PATCH 01/18] Update cv_oem.R

---
 R/cv_oem.R | 35 ++++++++++++++++++++++++++++-------
 1 file changed, 28 insertions(+), 7 deletions(-)

diff --git a/R/cv_oem.R b/R/cv_oem.R
index 92f33ac..24d058b 100644
--- a/R/cv_oem.R
+++ b/R/cv_oem.R
@@ -61,7 +61,7 @@ cv.oem <- function (x, y, penalty = c("elastic.net",
                                       "grp.mcp.net",   "grp.scad.net",
                                       "sparse.grp.lasso"),
                     weights = numeric(0), lambda = NULL, 
-                    type.measure = c("mse", "deviance", "class", "auc", "mae"), nfolds = 10, foldid = NULL, 
+                    type.measure = c("mse", "deviance", "class", "auc", "auprc", "mae"), nfolds = 10, foldid = NULL, 
                     grouped = TRUE, keep = FALSE, parallel = FALSE, ncores = -1, ...) 
 {
     ## code modified from "glmnet" package
@@ -209,7 +209,7 @@ cv.oem <- function (x, y, penalty = c("elastic.net",
                nzero = nz, name = cvname, oem.fit = oem.object)
     if (keep) 
         out = c(out, list(fit.preval = cvstuff$fit.preval, foldid = foldid))
-    lamin <- if(cvname == "AUC") getmin(lambda, lapply(cvm, function(ccvvmm) -ccvvmm), cvsd)
+    lamin <- if(cvname == "AUC" | cvname == "AUPRC") getmin(lambda, lapply(cvm, function(ccvvmm) -ccvvmm), cvsd)
     else getmin(lambda, cvm, cvsd)
     obj <- c(out, as.list(lamin))
     obj$best.model <- penalty[obj$model.min]
@@ -223,13 +223,13 @@ cv.oemfit_binomial <- function (outlist, lambda, x, y, weights, foldid, type.mea
 {
     ## code modified from "glmnet" package
     typenames = c(mse = "Mean-Squared Error", mae = "Mean Absolute Error", 
-                  deviance = "Binomial Deviance", auc = "AUC", class = "Misclassification Error")
+                  deviance = "Binomial Deviance", auc = "AUC", auprc = "AUPRC", class = "Misclassification Error")
     if (type.measure == "default") 
         type.measure = "deviance"
-    if (!match(type.measure, c("mse", "mae", "deviance", "auc", 
+    if (!match(type.measure, c("mse", "mae", "deviance", "auc", "auprc",
                                "class"), FALSE)) 
     {
-        warning("Only 'deviance', 'class', 'auc', 'mse' or 'mae'  available for binomial models; 'deviance' used")
+        warning("Only 'deviance', 'class', 'auc', 'auprc', 'mse' or 'mae'  available for binomial models; 'deviance' used")
         type.measure = "deviance"
     }
     prob_min = 1e-05
@@ -303,7 +303,28 @@ cv.oemfit_binomial <- function (outlist, lambda, x, y, weights, foldid, type.mea
         }
         weights = tapply(weights, foldid, sum)
         weights = rep(list(weights), nmodels)
-    } else 
+    } 
+     
+    if (type.measure == "auprc") {
+    cvraw <- rep(list(matrix(NA, nfolds, length(lambda[[1]]))), 
+                 nmodels)
+    N <- vector(mode = "list", length = nmodels)
+    for (m in 1:nmodels) {
+      good <- matrix(0, nfolds, length(lambda[[1]]))
+      for (i in seq(nfolds)) {
+        good[i, seq(nlams[i])] = 1
+        which <- foldid == i
+        for (j in seq(nlams[i])) {
+          cvraw[[m]][i, j] = precrec::auc(evalmod(scores = predlist[[m]][which,j] , labels = y[which,2]))[4][2,]
+        }
+      }
+        N[[m]] = apply(good, 2, sum)
+      }
+      weights = tapply(weights, foldid, sum)
+      weights = rep(list(weights), nmodels)
+   }
+                                     
+   else 
     {
         ywt <- apply(y, 1, sum)
         y <- y / ywt
@@ -418,4 +439,4 @@ cv.oemfit_gaussian <- function (outlist, lambda, x, y, weights, foldid, type.mea
     if (keep) 
         out$fit.preval <- predlist
     out
-}
\ No newline at end of file
+}

From e7ad6b9422e6d698f50b75d62f349cf8b14a8859 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Tue, 6 Jul 2021 15:38:08 +0930
Subject: [PATCH 02/18] Update cv_oem.R

---
 R/cv_oem.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cv_oem.R b/R/cv_oem.R
index 24d058b..24d0503 100644
--- a/R/cv_oem.R
+++ b/R/cv_oem.R
@@ -315,7 +315,7 @@ cv.oemfit_binomial <- function (outlist, lambda, x, y, weights, foldid, type.mea
         good[i, seq(nlams[i])] = 1
         which <- foldid == i
         for (j in seq(nlams[i])) {
-          cvraw[[m]][i, j] = precrec::auc(evalmod(scores = predlist[[m]][which,j] , labels = y[which,2]))[4][2,]
+          cvraw[[m]][i, j] = precrec::auc(precrec::evalmod(scores = predlist[[m]][which,j] , labels = y[which,2]))[4][2,]
         }
       }
         N[[m]] = apply(good, 2, sum)

From b2b044c0ed9f33cf2fc479c31e613612a2200e0c Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Tue, 6 Jul 2021 15:47:59 +0930
Subject: [PATCH 03/18] Update cv_oem.R

---
 R/cv_oem.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cv_oem.R b/R/cv_oem.R
index 24d0503..24d058b 100644
--- a/R/cv_oem.R
+++ b/R/cv_oem.R
@@ -315,7 +315,7 @@ cv.oemfit_binomial <- function (outlist, lambda, x, y, weights, foldid, type.mea
         good[i, seq(nlams[i])] = 1
         which <- foldid == i
         for (j in seq(nlams[i])) {
-          cvraw[[m]][i, j] = precrec::auc(precrec::evalmod(scores = predlist[[m]][which,j] , labels = y[which,2]))[4][2,]
+          cvraw[[m]][i, j] = precrec::auc(evalmod(scores = predlist[[m]][which,j] , labels = y[which,2]))[4][2,]
         }
       }
         N[[m]] = apply(good, 2, sum)

From d139154c4bcc3a78b1211c82cfb0ac71d16d688b Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Tue, 6 Jul 2021 16:01:54 +0930
Subject: [PATCH 04/18] Update cv_oem.R

---
 R/cv_oem.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/cv_oem.R b/R/cv_oem.R
index 24d058b..b83da5e 100644
--- a/R/cv_oem.R
+++ b/R/cv_oem.R
@@ -84,6 +84,8 @@ cv.oem <- function (x, y, penalty = c("elastic.net",
     else type.measure = match.arg(type.measure)
     if (!is.null(lambda) && length(lambda) < 2) 
         stop("Need more than one value of lambda for cv.oem")
+    if (length(weights)!=0 & type.measure=="auprc") 
+      stop("Cross-validation based on AUPRC is not available with sampling weights")
     N = nrow(x)
     if (length(weights)) 
         weights = as.double(weights)

From 29d93ad3241b50d4ac1189cb5b21dda9937f79b5 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Tue, 6 Jul 2021 16:16:40 +0930
Subject: [PATCH 05/18] Update DESCRIPTION

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 45f8a59..91f1538 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,7 +32,8 @@ Imports:
     Rcpp (>= 0.11.0),
     Matrix,
     foreach,
-    methods
+    methods,
+    precrec
 LinkingTo: Rcpp,
     RcppEigen,
     BH,

From a9c59cb8a38ec8a94907ab28d7fdb132da6bb496 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Tue, 6 Jul 2021 16:32:21 +0930
Subject: [PATCH 06/18] Update NAMESPACE

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index 329409b..af5723b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -27,6 +27,7 @@ export(oem.xtx)
 export(oemfit)
 export(xval.oem)
 import(Matrix)
+import(precrec)
 import(Rcpp)
 import(bigmemory)
 import(foreach)

From e80c08a65f7f97dba6ebba76b4aed4dab1c5d3be Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Wed, 7 Jul 2021 08:50:19 +0930
Subject: [PATCH 07/18] Update cv_oem.R

---
 R/cv_oem.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cv_oem.R b/R/cv_oem.R
index b83da5e..9dbd890 100644
--- a/R/cv_oem.R
+++ b/R/cv_oem.R
@@ -221,7 +221,7 @@ cv.oem <- function (x, y, penalty = c("elastic.net",
 }
 
 
-cv.oemfit_binomial <- function (outlist, lambda, x, y, weights, foldid, type.measure, grouped, keep = FALSE) 
+ cv.oemfit_binomial <- function (outlist, lambda, x, y, weights, foldid, type.measure, grouped, keep = FALSE) 
 {
     ## code modified from "glmnet" package
     typenames = c(mse = "Mean-Squared Error", mae = "Mean Absolute Error", 

From f58daf2c616f29823dd4dc1bb1c023a2058674ed Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Wed, 7 Jul 2021 08:51:47 +0930
Subject: [PATCH 08/18] Update cv_oem.R

---
 R/cv_oem.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cv_oem.R b/R/cv_oem.R
index 9dbd890..b83da5e 100644
--- a/R/cv_oem.R
+++ b/R/cv_oem.R
@@ -221,7 +221,7 @@ cv.oem <- function (x, y, penalty = c("elastic.net",
 }
 
 
- cv.oemfit_binomial <- function (outlist, lambda, x, y, weights, foldid, type.measure, grouped, keep = FALSE) 
+cv.oemfit_binomial <- function (outlist, lambda, x, y, weights, foldid, type.measure, grouped, keep = FALSE) 
 {
     ## code modified from "glmnet" package
     typenames = c(mse = "Mean-Squared Error", mae = "Mean Absolute Error", 

From db98d67808e1075b7cd8543699b3cf669af7d479 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Wed, 7 Jul 2021 08:53:10 +0930
Subject: [PATCH 09/18] Update cv_oem.R

---
 R/cv_oem.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cv_oem.R b/R/cv_oem.R
index b83da5e..ab13655 100644
--- a/R/cv_oem.R
+++ b/R/cv_oem.R
@@ -85,7 +85,7 @@ cv.oem <- function (x, y, penalty = c("elastic.net",
     if (!is.null(lambda) && length(lambda) < 2) 
         stop("Need more than one value of lambda for cv.oem")
     if (length(weights)!=0 & type.measure=="auprc") 
-      stop("Cross-validation based on AUPRC is not available with sampling weights")
+      stop("Cross-validation based on AUPRC is not yet available with sampling weights")
     N = nrow(x)
     if (length(weights)) 
         weights = as.double(weights)

From 911e93ba59607b0ab40c0bc112089eb0521087e1 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Wed, 7 Jul 2021 10:27:42 +0930
Subject: [PATCH 10/18] Update cv_oem.R

---
 R/cv_oem.R | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/R/cv_oem.R b/R/cv_oem.R
index ab13655..e2c6d6a 100644
--- a/R/cv_oem.R
+++ b/R/cv_oem.R
@@ -305,9 +305,7 @@ cv.oemfit_binomial <- function (outlist, lambda, x, y, weights, foldid, type.mea
         }
         weights = tapply(weights, foldid, sum)
         weights = rep(list(weights), nmodels)
-    } 
-     
-    if (type.measure == "auprc") {
+    } else if (type.measure == "auprc") {
     cvraw <- rep(list(matrix(NA, nfolds, length(lambda[[1]]))), 
                  nmodels)
     N <- vector(mode = "list", length = nmodels)
@@ -324,9 +322,7 @@ cv.oemfit_binomial <- function (outlist, lambda, x, y, weights, foldid, type.mea
       }
       weights = tapply(weights, foldid, sum)
       weights = rep(list(weights), nmodels)
-   }
-                                     
-   else 
+   } else 
     {
         ywt <- apply(y, 1, sum)
         y <- y / ywt

From ddb3b4ee30bc9c7132652727ed90fd487429721a Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Thu, 8 Jul 2021 16:54:03 +0930
Subject: [PATCH 11/18] Update cv_oem.R

---
 R/cv_oem.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cv_oem.R b/R/cv_oem.R
index e2c6d6a..36f4c24 100644
--- a/R/cv_oem.R
+++ b/R/cv_oem.R
@@ -17,7 +17,7 @@
 #' a value of lambda overrides this.
 #' @param type.measure measure to evaluate for cross-validation. The default is \code{type.measure = "deviance"}, 
 #' which uses squared-error for gaussian models (a.k.a \code{type.measure = "mse"} there), deviance for logistic
-#' regression. \code{type.measure = "class"} applies to binomial only. \code{type.measure = "auc"} is for two-class logistic 
+#' regression. \code{type.measure = "class"} applies to binomial only. \code{type.measure = "auc"} or \code{type.measure = "auprc"} are for two-class logistic 
 #' regression only. \code{type.measure = "mse"} or \code{type.measure = "mae"} (mean absolute error) can be used by all models;
 #' they measure the deviation from the fitted mean to the response.
 #' @param nfolds number of folds for cross-validation. default is 10. 3 is smallest value allowed. 

From daa6af1fc661c2ff03ba60caa2d1c957bd51e846 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Thu, 8 Jul 2021 17:08:38 +0930
Subject: [PATCH 12/18] Update cv.oem.Rd

---
 man/cv.oem.Rd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/cv.oem.Rd b/man/cv.oem.Rd
index eb8e9ed..20798e2 100644
--- a/man/cv.oem.Rd
+++ b/man/cv.oem.Rd
@@ -12,7 +12,7 @@ cv.oem(
     "sparse.grp.lasso"),
   weights = numeric(0),
   lambda = NULL,
-  type.measure = c("mse", "deviance", "class", "auc", "mae"),
+  type.measure = c("mse", "deviance", "class", "auc", "auprc", "mae"),
   nfolds = 10,
   foldid = NULL,
   grouped = TRUE,
@@ -42,7 +42,7 @@ a value of lambda overrides this.}
 
 \item{type.measure}{measure to evaluate for cross-validation. The default is \code{type.measure = "deviance"}, 
 which uses squared-error for gaussian models (a.k.a \code{type.measure = "mse"} there), deviance for logistic
-regression. \code{type.measure = "class"} applies to binomial only. \code{type.measure = "auc"} is for two-class logistic 
+regression. \code{type.measure = "class"} applies to binomial only. \code{type.measure = "auc"} and \code{type.measure = "auprc"} are for two-class logistic 
 regression only. \code{type.measure = "mse"} or \code{type.measure = "mae"} (mean absolute error) can be used by all models;
 they measure the deviation from the fitted mean to the response.}
 

From 4815129db9075ec811a90e2f5450a3ff3470c496 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Fri, 16 Jul 2021 17:18:20 +0930
Subject: [PATCH 13/18] Update cv_oem.R

---
 R/cv_oem.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cv_oem.R b/R/cv_oem.R
index 36f4c24..b72b1bf 100644
--- a/R/cv_oem.R
+++ b/R/cv_oem.R
@@ -89,7 +89,7 @@ cv.oem <- function (x, y, penalty = c("elastic.net",
     N = nrow(x)
     if (length(weights)) 
         weights = as.double(weights)
-    y = drop(y)
+    y = drop(y) 
     
     if (parallel & ncores != 1)
     {

From 8537820ec678d2088796c34337d36019bf382ff0 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Tue, 20 Jul 2021 09:18:39 +0930
Subject: [PATCH 14/18] Update DESCRIPTION

---
 DESCRIPTION | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 91f1538..45f8a59 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,8 +32,7 @@ Imports:
     Rcpp (>= 0.11.0),
     Matrix,
     foreach,
-    methods,
-    precrec
+    methods
 LinkingTo: Rcpp,
     RcppEigen,
     BH,

From 5ab3c4888e5f4c6381bcc42e5733fdf1f83773c5 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Tue, 20 Jul 2021 10:40:37 +0930
Subject: [PATCH 15/18] Update DESCRIPTION

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 45f8a59..91f1538 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,7 +32,8 @@ Imports:
     Rcpp (>= 0.11.0),
     Matrix,
     foreach,
-    methods
+    methods,
+    precrec
 LinkingTo: Rcpp,
     RcppEigen,
     BH,

From 2948decf63fcb8a077318287b551002c591a717e Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Tue, 20 Jul 2021 10:40:53 +0930
Subject: [PATCH 16/18] Update NAMESPACE

---
 NAMESPACE | 1 -
 1 file changed, 1 deletion(-)

diff --git a/NAMESPACE b/NAMESPACE
index af5723b..329409b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -27,7 +27,6 @@ export(oem.xtx)
 export(oemfit)
 export(xval.oem)
 import(Matrix)
-import(precrec)
 import(Rcpp)
 import(bigmemory)
 import(foreach)

From e325bfc91a74530f05e1749d81d34a324bfc2677 Mon Sep 17 00:00:00 2001
From: pedro-ribeirosantiago
 <45943434+pedro-ribeirosantiago@users.noreply.github.com>
Date: Tue, 20 Jul 2021 11:42:45 +0930
Subject: [PATCH 17/18] Update NAMESPACE

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index 329409b..dd51f4e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -28,6 +28,7 @@ export(oemfit)
 export(xval.oem)
 import(Matrix)
 import(Rcpp)
+import(precrec)
 import(bigmemory)
 import(foreach)
 importFrom(bigmemory,is.big.matrix)

From c354581fb068d5c7d46cf5d6376528d7199df472 Mon Sep 17 00:00:00 2001
From: Pedro Henrique Ribeiro Santiago <a1714694@adelaide.edu.au>
Date: Mon, 17 Jul 2023 12:28:58 +0930
Subject: [PATCH 18/18] AUPRC available

---
 DESCRIPTION   | 2 +-
 NAMESPACE     | 1 -
 man/cv.oem.Rd | 2 +-
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f5d71a5..786abd6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -40,7 +40,7 @@ LinkingTo: Rcpp,
     BH,
     bigmemory,
     RcppArmadillo
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Suggests:
     knitr,
     rmarkdown
diff --git a/NAMESPACE b/NAMESPACE
index dd51f4e..329409b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -28,7 +28,6 @@ export(oemfit)
 export(xval.oem)
 import(Matrix)
 import(Rcpp)
-import(precrec)
 import(bigmemory)
 import(foreach)
 importFrom(bigmemory,is.big.matrix)
diff --git a/man/cv.oem.Rd b/man/cv.oem.Rd
index 9b9deec..4f0ec00 100644
--- a/man/cv.oem.Rd
+++ b/man/cv.oem.Rd
@@ -42,7 +42,7 @@ a value of lambda overrides this.}
 
 \item{type.measure}{measure to evaluate for cross-validation. The default is \code{type.measure = "deviance"}, 
 which uses squared-error for gaussian models (a.k.a \code{type.measure = "mse"} there), deviance for logistic
-regression. \code{type.measure = "class"} applies to binomial only. \code{type.measure = "auc"} and \code{type.measure = "auprc"} are for two-class logistic 
+regression. \code{type.measure = "class"} applies to binomial only. \code{type.measure = "auc"} or \code{type.measure = "auprc"} are for two-class logistic 
 regression only. \code{type.measure = "mse"} or \code{type.measure = "mae"} (mean absolute error) can be used by all models;
 they measure the deviation from the fitted mean to the response.}