@gvegayon @chipmanj My dirty work... I will get things done over the …

…weekend. Thank you! UofUEpiBio/PHS7045-advanced-programming#13

DESCRIPTION

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+Package: ImbLassoRcpp
+Type: Package
+Title: LASSO for Logistic Regression with Imbalanced Outcome by Rcpp (Title Case)
+Version: 0.1.0
+Author: Haojia Li
+Maintainer: Haojia Li <[email protected]>
+Description: More about what it does (maybe more than one line)
+    Use four spaces when indenting paragraphs within the Description.
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
+RoxygenNote: 7.2.3
+LinkingTo: 
+    Rcpp
+Imports: 
+    Rcpp

ImbLassoRcpp.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

LICENSE

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+YEAR: 2023
+COPYRIGHT HOLDER: Haojia Li

LICENSE.md

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+# MIT License
+
+Copyright (c) 2023 ImbLassoRcpp authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(lambda_gen)

R/RcppExports.R

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+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+coord_desc <- function(X, y, lambda, thresh = 1e-7, maxit = 1e5L) {
+    .Call('_ImbLassoRcpp_coord_desc', PACKAGE = 'ImbLassoRcpp', X, y, lambda, thresh, maxit)
+}
+
+logit_i <- function(X, b0, b) {
+    .Call('_ImbLassoRcpp_logit_i', PACKAGE = 'ImbLassoRcpp', X, b0, b)
+}
+
+#'run the coordinate descent algorithm on the penalized weighted-least-squares
+#'
+#'Update the quadratic approx
+#'
+#'@name single_coord_des
+#'
+#'@param X input matrix, of dimension nobs x nvars; each row is an observation vector.
+#'@param y binary response variable, positive outcome = 1 and negative outcome = 0.
+#'@param lambda A user supplied lambda
+#'@param thresh Convergence threshold for coordinate descent. Each inner coordinate-descent loop continues until the maximum change in the objective after any coefficient update is less than thresh times the null deviance. Defaults value is 1E-7.
+#'@param maxit Maximum number of passes over the data for all lambda values; default is 10^5.
+#'
+betamat <- function(X, y, lambda, thresh = 1e-7, maxit = 1e5L) {
+    .Call('_ImbLassoRcpp_betamat', PACKAGE = 'ImbLassoRcpp', X, y, lambda, thresh, maxit)
+}
+
+prob_i <- function(logit) {
+    .Call('_ImbLassoRcpp_prob_i', PACKAGE = 'ImbLassoRcpp', logit)
+}
+
+smoteCpp <- function(X, y, k, m) {
+    .Call('_ImbLassoRcpp_smoteCpp', PACKAGE = 'ImbLassoRcpp', X, y, k, m)
+}
+
+soft_thresh <- function(z, gamma) {
+    .Call('_ImbLassoRcpp_soft_thresh', PACKAGE = 'ImbLassoRcpp', z, gamma)
+}
+
+stratifiedCpp <- function(X, y, size) {
+    .Call('_ImbLassoRcpp_stratifiedCpp', PACKAGE = 'ImbLassoRcpp', X, y, size)
+}
+
+weight_i <- function(prob) {
+    .Call('_ImbLassoRcpp_weight_i', PACKAGE = 'ImbLassoRcpp', prob)
+}
+

README.Rmd

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+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# ImbLassoRcpp
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of ImbLassoRcpp is to ...
+
+## Installation
+
+You can install the development version of ImbLassoRcpp like so:
+
+``` r
+# FILL THIS IN! HOW CAN PEOPLE INSTALL YOUR DEV PACKAGE?
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+```{r example}
+library(ImbLassoRcpp)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:
+
+```{r cars}
+summary(cars)
+```
+
+You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. You could also use GitHub Actions to re-render `README.Rmd` every time you push. An example workflow can be found here: <https://github.com/r-lib/actions/tree/v1/examples>.
+
+You can also embed plots, for example:
+
+```{r pressure, echo = FALSE}
+plot(pressure)
+```
+
+In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN.

README.md

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+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# ImbLassoRcpp
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of ImbLassoRcpp is to …
+
+## Installation
+
+You can install the development version of ImbLassoRcpp like so:
+
+``` r
+# FILL THIS IN! HOW CAN PEOPLE INSTALL YOUR DEV PACKAGE?
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+library(ImbLassoRcpp)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`?
+You can include R chunks like so:
+
+``` r
+summary(cars)
+#>      speed           dist       
+#>  Min.   : 4.0   Min.   :  2.00  
+#>  1st Qu.:12.0   1st Qu.: 26.00  
+#>  Median :15.0   Median : 36.00  
+#>  Mean   :15.4   Mean   : 42.98  
+#>  3rd Qu.:19.0   3rd Qu.: 56.00  
+#>  Max.   :25.0   Max.   :120.00
+```
+
+You’ll still need to render `README.Rmd` regularly, to keep `README.md`
+up-to-date. `devtools::build_readme()` is handy for this. You could also
+use GitHub Actions to re-render `README.Rmd` every time you push. An
+example workflow can be found here:
+<https://github.com/r-lib/actions/tree/v1/examples>.
+
+You can also embed plots, for example:
+
+<img src="man/figures/README-pressure-1.png" width="100%" />
+
+In that case, don’t forget to commit and push the resulting figure
+files, so they display on GitHub and CRAN.

src/.gitignore

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+*.o
+*.so
+*.dll

src/RcppExports.cpp

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+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include <Rcpp.h>
+
+using namespace Rcpp;
+
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
+// coord_desc
+NumericVector coord_desc(NumericMatrix X, NumericVector y, double lambda, double thresh, int maxit);
+RcppExport SEXP _ImbLassoRcpp_coord_desc(SEXP XSEXP, SEXP ySEXP, SEXP lambdaSEXP, SEXP threshSEXP, SEXP maxitSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< NumericMatrix >::type X(XSEXP);
+    Rcpp::traits::input_parameter< NumericVector >::type y(ySEXP);
+    Rcpp::traits::input_parameter< double >::type lambda(lambdaSEXP);
+    Rcpp::traits::input_parameter< double >::type thresh(threshSEXP);
+    Rcpp::traits::input_parameter< int >::type maxit(maxitSEXP);
+    rcpp_result_gen = Rcpp::wrap(coord_desc(X, y, lambda, thresh, maxit));
+    return rcpp_result_gen;
+END_RCPP
+}
+// logit_i
+NumericVector logit_i(NumericMatrix X, double b0, NumericVector b);
+RcppExport SEXP _ImbLassoRcpp_logit_i(SEXP XSEXP, SEXP b0SEXP, SEXP bSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< NumericMatrix >::type X(XSEXP);
+    Rcpp::traits::input_parameter< double >::type b0(b0SEXP);
+    Rcpp::traits::input_parameter< NumericVector >::type b(bSEXP);
+    rcpp_result_gen = Rcpp::wrap(logit_i(X, b0, b));
+    return rcpp_result_gen;
+END_RCPP
+}
+// betamat
+mat betamat(NumericMatrix X, NumericVector y, double lambda, double thresh, int maxit);
+RcppExport SEXP _ImbLassoRcpp_betamat(SEXP XSEXP, SEXP ySEXP, SEXP lambdaSEXP, SEXP threshSEXP, SEXP maxitSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< NumericMatrix >::type X(XSEXP);
+    Rcpp::traits::input_parameter< NumericVector >::type y(ySEXP);
+    Rcpp::traits::input_parameter< double >::type lambda(lambdaSEXP);
+    Rcpp::traits::input_parameter< double >::type thresh(threshSEXP);
+    Rcpp::traits::input_parameter< int >::type maxit(maxitSEXP);
+    rcpp_result_gen = Rcpp::wrap(betamat(X, y, lambda, thresh, maxit));
+    return rcpp_result_gen;
+END_RCPP
+}
+// prob_i
+NumericVector prob_i(NumericVector logit);
+RcppExport SEXP _ImbLassoRcpp_prob_i(SEXP logitSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< NumericVector >::type logit(logitSEXP);
+    rcpp_result_gen = Rcpp::wrap(prob_i(logit));
+    return rcpp_result_gen;
+END_RCPP
+}
+// smoteCpp
+NumericMatrix smoteCpp(const NumericMatrix& X, const IntegerVector& y, const int k, const int m);
+RcppExport SEXP _ImbLassoRcpp_smoteCpp(SEXP XSEXP, SEXP ySEXP, SEXP kSEXP, SEXP mSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const NumericMatrix& >::type X(XSEXP);
+    Rcpp::traits::input_parameter< const IntegerVector& >::type y(ySEXP);
+    Rcpp::traits::input_parameter< const int >::type k(kSEXP);
+    Rcpp::traits::input_parameter< const int >::type m(mSEXP);
+    rcpp_result_gen = Rcpp::wrap(smoteCpp(X, y, k, m));
+    return rcpp_result_gen;
+END_RCPP
+}
+// soft_thresh
+double soft_thresh(double z, double gamma);
+RcppExport SEXP _ImbLassoRcpp_soft_thresh(SEXP zSEXP, SEXP gammaSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< double >::type z(zSEXP);
+    Rcpp::traits::input_parameter< double >::type gamma(gammaSEXP);
+    rcpp_result_gen = Rcpp::wrap(soft_thresh(z, gamma));
+    return rcpp_result_gen;
+END_RCPP
+}
+// stratifiedCpp
+List stratifiedCpp(const NumericMatrix& X, const IntegerVector& y, const int size);
+RcppExport SEXP _ImbLassoRcpp_stratifiedCpp(SEXP XSEXP, SEXP ySEXP, SEXP sizeSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const NumericMatrix& >::type X(XSEXP);
+    Rcpp::traits::input_parameter< const IntegerVector& >::type y(ySEXP);
+    Rcpp::traits::input_parameter< const int >::type size(sizeSEXP);
+    rcpp_result_gen = Rcpp::wrap(stratifiedCpp(X, y, size));
+    return rcpp_result_gen;
+END_RCPP
+}
+// weight_i
+NumericVector weight_i(NumericVector prob);
+RcppExport SEXP _ImbLassoRcpp_weight_i(SEXP probSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< NumericVector >::type prob(probSEXP);
+    rcpp_result_gen = Rcpp::wrap(weight_i(prob));
+    return rcpp_result_gen;
+END_RCPP
+}
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_ImbLassoRcpp_coord_desc", (DL_FUNC) &_ImbLassoRcpp_coord_desc, 5},
+    {"_ImbLassoRcpp_logit_i", (DL_FUNC) &_ImbLassoRcpp_logit_i, 3},
+    {"_ImbLassoRcpp_betamat", (DL_FUNC) &_ImbLassoRcpp_betamat, 5},
+    {"_ImbLassoRcpp_prob_i", (DL_FUNC) &_ImbLassoRcpp_prob_i, 1},
+    {"_ImbLassoRcpp_smoteCpp", (DL_FUNC) &_ImbLassoRcpp_smoteCpp, 4},
+    {"_ImbLassoRcpp_soft_thresh", (DL_FUNC) &_ImbLassoRcpp_soft_thresh, 2},
+    {"_ImbLassoRcpp_stratifiedCpp", (DL_FUNC) &_ImbLassoRcpp_stratifiedCpp, 3},
+    {"_ImbLassoRcpp_weight_i", (DL_FUNC) &_ImbLassoRcpp_weight_i, 1},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_ImbLassoRcpp(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}