From 81e29f66dc94244e359e199bd098db555c9d7548 Mon Sep 17 00:00:00 2001
From: WANG Zhiwei <48282751+statwangz@users.noreply.github.com>
Date: Mon, 30 Oct 2023 17:54:54 +0800
Subject: [PATCH] Move softImpute code to others folder

---
 .Rbuildignore                   |  1 +
 DESCRIPTION                     |  3 +--
 NAMESPACE                       |  3 ---
 man/softImputeCrossVal.Rd       | 31 -------------------------------
 man/softImputeCrossValSparse.Rd | 31 -------------------------------
 {R => others}/softImputeCV.R    |  0
 6 files changed, 2 insertions(+), 67 deletions(-)
 delete mode 100644 man/softImputeCrossVal.Rd
 delete mode 100644 man/softImputeCrossValSparse.Rd
 rename {R => others}/softImputeCV.R (100%)

diff --git a/.Rbuildignore b/.Rbuildignore
index 9ce5453..bf845ce 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -10,3 +10,4 @@
 ^pkgdown$
 ^codecov\.yml$
 ^\.github$
+^others$
diff --git a/DESCRIPTION b/DESCRIPTION
index bce9811..5b98635 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -13,8 +13,7 @@ Imports:
     dplyr,
     Matrix,
     methods,
-    rpart,
-    softImpute
+    rpart
 Depends: 
     R (>= 2.10),
 LazyData: true
diff --git a/NAMESPACE b/NAMESPACE
index 5520b42..86c4a8a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,14 +8,11 @@ export(getELBO)
 export(getImportance)
 export(initSF)
 export(predictFX)
-export(softImputeCrossVal)
-export(softImputeCrossValSparse)
 export(updateMFAIR)
 exportClasses(MFAIR)
 exportClasses(MFAIRSingleFactor)
 exportMethods(predict)
 import(Matrix)
-import(softImpute)
 importFrom(dplyr,left_join)
 importFrom(methods,new)
 importFrom(rpart,rpart)
diff --git a/man/softImputeCrossVal.Rd b/man/softImputeCrossVal.Rd
deleted file mode 100644
index 6d43a02..0000000
--- a/man/softImputeCrossVal.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/softImputeCV.R
-\name{softImputeCrossVal}
-\alias{softImputeCrossVal}
-\title{Cross-validation for softImpute.}
-\usage{
-softImputeCrossVal(
-  Y,
-  rank_max = NULL,
-  lambda_range = NULL,
-  nfold = 10,
-  para_length = 100
-)
-}
-\arguments{
-\item{Y}{A matrix. The main data matrix of N samples and M features.}
-
-\item{rank_max}{An integer. The maximum rank allowed.}
-
-\item{lambda_range}{A vector containing the minimal and maximal value of the parameter lambda.}
-
-\item{nfold}{An integer. The total number of validation sets.}
-
-\item{para_length}{An integer. The total number of parameter lambda.}
-}
-\value{
-A list containing the cross-validation results.
-}
-\description{
-Cross-validation for softImpute.
-}
diff --git a/man/softImputeCrossValSparse.Rd b/man/softImputeCrossValSparse.Rd
deleted file mode 100644
index a6a53cf..0000000
--- a/man/softImputeCrossValSparse.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/softImputeCV.R
-\name{softImputeCrossValSparse}
-\alias{softImputeCrossValSparse}
-\title{Sparse version of cross-validation for softImpute.}
-\usage{
-softImputeCrossValSparse(
-  Y,
-  rank_max = NULL,
-  lambda_range = NULL,
-  nfold = 10,
-  para_length = 100
-)
-}
-\arguments{
-\item{Y}{A Matrix::dgCMatrix. The main data matrix of N samples and M features.}
-
-\item{rank_max}{An integer. The maximum rank allowed.}
-
-\item{lambda_range}{A vector containing the minimal and maximal value of the parameter lambda.}
-
-\item{nfold}{An integer. The total number of validation sets.}
-
-\item{para_length}{An integer. The total number of parameter lambda.}
-}
-\value{
-A list containing the cross-validation results.
-}
-\description{
-Sparse version of cross-validation for softImpute.
-}
diff --git a/R/softImputeCV.R b/others/softImputeCV.R
similarity index 100%
rename from R/softImputeCV.R
rename to others/softImputeCV.R