From 9b10fe9c6a4027e2be2530c9a0cf849bb2e77fdb Mon Sep 17 00:00:00 2001
From: WANG Zhiwei <48282751+statwangz@users.noreply.github.com>
Date: Thu, 12 Oct 2023 22:37:35 +0800
Subject: [PATCH] Change the function name

---
 NAMESPACE                                     |  4 ++--
 R/softImputeCV.R                              | 22 +++++++++----------
 ...{softImputeCV.Rd => softImputeCrossVal.Rd} |  6 ++---
 ..._sparse.Rd => softImputeCrossValSparse.Rd} |  6 ++---
 4 files changed, 18 insertions(+), 20 deletions(-)
 rename man/{softImputeCV.Rd => softImputeCrossVal.Rd} (90%)
 rename man/{softImputeCV_sparse.Rd => softImputeCrossValSparse.Rd} (89%)

diff --git a/NAMESPACE b/NAMESPACE
index a930419..5520b42 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,8 +8,8 @@ export(getELBO)
 export(getImportance)
 export(initSF)
 export(predictFX)
-export(softImputeCV)
-export(softImputeCV_sparse)
+export(softImputeCrossVal)
+export(softImputeCrossValSparse)
 export(updateMFAIR)
 exportClasses(MFAIR)
 exportClasses(MFAIRSingleFactor)
diff --git a/R/softImputeCV.R b/R/softImputeCV.R
index 3d8b576..297ec18 100644
--- a/R/softImputeCV.R
+++ b/R/softImputeCV.R
@@ -11,10 +11,10 @@
 #' @return A list containing the cross-validation results.
 #' @export
 #'
-softImputeCV <- function(Y, rank_max = NULL, lambda_range = NULL,
-                         nfold = 10, para_length = 100) {
-  N <- dim(Y)[1]
-  M <- dim(Y)[2]
+softImputeCrossVal <- function(Y, rank_max = NULL, lambda_range = NULL,
+                               nfold = 10, para_length = 100) {
+  N <- nrow(Y)
+  M <- ncol(Y)
   # Report settings
   message("Info: Matrix dimension: ", N, " * ", M)
   message("Info: Number of cv folds: ", nfold)
@@ -103,10 +103,10 @@ softImputeCV <- function(Y, rank_max = NULL, lambda_range = NULL,
 #' @return A list containing the cross-validation results.
 #' @export
 #'
-softImputeCV_sparse <- function(Y, rank_max = NULL, lambda_range = NULL,
-                                nfold = 10, para_length = 100) {
-  N <- dim(Y)[1]
-  M <- dim(Y)[2]
+softImputeCrossValSparse <- function(Y, rank_max = NULL, lambda_range = NULL,
+                                     nfold = 10, para_length = 100) {
+  N <- nrow(Y)
+  M <- ncol(Y)
   # Report settings
   message("Info: Matrix dimension: ", N, " * ", M)
   message("Info: Number of cv folds: ", nfold)
@@ -152,9 +152,6 @@ softImputeCV_sparse <- function(Y, rank_max = NULL, lambda_range = NULL,
       j = idx_all[train_idx, 2],
       x = Y@x[train_idx] - train_mean
     )
-    # Y_test <- Incomplete(i = idx_all[-train_idx, 1],
-    #                       j = idx_all[-train_idx, 2],
-    #                       x = Y@x[-train_idx])
 
     for (j in seq(from = para_length, to = 1, by = -1)) {
       if (j == para_length) {
@@ -170,10 +167,11 @@ softImputeCV_sparse <- function(Y, rank_max = NULL, lambda_range = NULL,
         )
       }
 
+      # The prediction corresponding to the test set
       Y_hat <- impute(
         si_fit,
         i = idx_all[-train_idx, 1], j = idx_all[-train_idx, 2]
-      ) + train_mean # The prediction cooresponding to the test set
+      ) + train_mean
       test_err[i, j] <- sqrt(mean((Y@x[-train_idx] - Y_hat)^2))
     }
   }
diff --git a/man/softImputeCV.Rd b/man/softImputeCrossVal.Rd
similarity index 90%
rename from man/softImputeCV.Rd
rename to man/softImputeCrossVal.Rd
index 733eb0c..366e464 100644
--- a/man/softImputeCV.Rd
+++ b/man/softImputeCrossVal.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/softImputeCV.R
-\name{softImputeCV}
-\alias{softImputeCV}
+\name{softImputeCrossVal}
+\alias{softImputeCrossVal}
 \title{Cross-validation for softImpute}
 \usage{
-softImputeCV(
+softImputeCrossVal(
   Y,
   rank_max = NULL,
   lambda_range = NULL,
diff --git a/man/softImputeCV_sparse.Rd b/man/softImputeCrossValSparse.Rd
similarity index 89%
rename from man/softImputeCV_sparse.Rd
rename to man/softImputeCrossValSparse.Rd
index e47aa99..4d08fc6 100644
--- a/man/softImputeCV_sparse.Rd
+++ b/man/softImputeCrossValSparse.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/softImputeCV.R
-\name{softImputeCV_sparse}
-\alias{softImputeCV_sparse}
+\name{softImputeCrossValSparse}
+\alias{softImputeCrossValSparse}
 \title{Sparse version of cross-validation for softImpute}
 \usage{
-softImputeCV_sparse(
+softImputeCrossValSparse(
   Y,
   rank_max = NULL,
   lambda_range = NULL,