From c670f3d2f2c3cefd9209fb09cc5ff15e05b9b312 Mon Sep 17 00:00:00 2001 From: Nima Hejazi Date: Thu, 5 Mar 2020 16:56:08 -0800 Subject: [PATCH] update after CRAN release --- CRAN-RELEASE | 2 - README.Rmd | 18 ++++---- README.md | 34 +++++++------- docs/articles/intro_hal9001.html | 42 ++++++++--------- docs/authors.html | 4 +- docs/index.html | 79 +++++++++++++++----------------- docs/news/index.html | 3 +- inst/CITATION | 2 +- 8 files changed, 90 insertions(+), 94 deletions(-) delete mode 100644 CRAN-RELEASE diff --git a/CRAN-RELEASE b/CRAN-RELEASE deleted file mode 100644 index f384ad9f..00000000 --- a/CRAN-RELEASE +++ /dev/null @@ -1,2 +0,0 @@ -This package was submitted to CRAN on 2020-02-26. -Once it is accepted, delete this file and tag the release (commit 30933d3fbc). diff --git a/README.Rmd b/README.Rmd index f38af78a..35e86b0b 100644 --- a/README.Rmd +++ b/README.Rmd @@ -19,9 +19,11 @@ knitr::opts_chunk$set( [![Travis-CI Build Status](https://travis-ci.org/tlverse/hal9001.svg?branch=master)](https://travis-ci.org/tlverse/hal9001) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/jeremyrcoyle/hal9001?branch=master&svg=true)](https://ci.appveyor.com/project/jeremyrcoyle/hal9001) [![Coverage Status](https://img.shields.io/codecov/c/github/tlverse/hal9001/master.svg)](https://codecov.io/github/tlverse/hal9001?branch=master) +[![CRAN](http://www.r-pkg.org/badges/version/hal9001)](http://www.r-pkg.org/pkg/hal9001) +[![CRAN downloads](https://cranlogs.r-pkg.org/badges/hal9001)](https://CRAN.R-project.org/package=hal9001) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0) -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3558314.svg)](https://doi.org/10.5281/zenodo.3558314) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3558313.svg)](https://doi.org/10.5281/zenodo.3558313) > The _Scalable_ Highly Adaptive Lasso @@ -53,20 +55,18 @@ recent works. ## Installation - To contribute, install the _development version_ of `hal9001` from GitHub via [`remotes`](https://CRAN.R-project.org/package=remotes): ```{r gh-master-installation, eval = FALSE} -remotes::install_github("tlverse/hal9001", build_vignettes = FALSE) +remotes::install_github("tlverse/hal9001") ``` --- @@ -85,11 +85,11 @@ the Highly Adaptive Lasso. For details on the properties of the estimator, the interested reader is referred to @benkeser2016hal and @vdl2017generally. ```{r example} -# load the hal9001 package +# load the package and set a seed library(hal9001) +set.seed(385971) # simulate data -set.seed(385971) n <- 100 p <- 3 x <- xmat <- matrix(rnorm(n * p), n, p) @@ -126,8 +126,8 @@ After using the `hal9001` R package, please cite the following: year = {2019}, howpublished = {\url{https://github.com/tlverse/hal9001}}, note = {{R} package version 0.2.5}, - url = {https://doi.org/10.5281/zenodo.3558314}, - doi = {10.5281/zenodo.3558314} + url = {https://doi.org/10.5281/zenodo.3558313}, + doi = {10.5281/zenodo.3558313} } --- diff --git a/README.md b/README.md index 5868a22f..7ffee9b3 100644 --- a/README.md +++ b/README.md @@ -9,12 +9,15 @@ Status](https://travis-ci.org/tlverse/hal9001.svg?branch=master)](https://travis Status](https://ci.appveyor.com/api/projects/status/github/jeremyrcoyle/hal9001?branch=master&svg=true)](https://ci.appveyor.com/project/jeremyrcoyle/hal9001) [![Coverage Status](https://img.shields.io/codecov/c/github/tlverse/hal9001/master.svg)](https://codecov.io/github/tlverse/hal9001?branch=master) +[![CRAN](http://www.r-pkg.org/badges/version/hal9001)](http://www.r-pkg.org/pkg/hal9001) +[![CRAN +downloads](https://cranlogs.r-pkg.org/badges/hal9001)](https://CRAN.R-project.org/package=hal9001) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0) -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3558314.svg)](https://doi.org/10.5281/zenodo.3558314) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3558313.svg)](https://doi.org/10.5281/zenodo.3558313) > The *Scalable* Highly Adaptive Lasso @@ -47,21 +50,18 @@ consider consulting Benkeser and van der Laan (2016), van der Laan ## Installation - To contribute, install the *development version* of `hal9001` from GitHub via [`remotes`](https://CRAN.R-project.org/package=remotes): ``` r -remotes::install_github("tlverse/hal9001", build_vignettes = FALSE) +remotes::install_github("tlverse/hal9001") ``` ----- @@ -81,13 +81,13 @@ estimator, the interested reader is referred to Benkeser and van der Laan (2016) and van der Laan (2017a). ``` r -# load the hal9001 package +# load the package and set a seed library(hal9001) #> Loading required package: Rcpp #> hal9001 v0.2.5: The Scalable Highly Adaptive Lasso +set.seed(385971) # simulate data -set.seed(385971) n <- 100 p <- 3 x <- xmat <- matrix(rnorm(n * p), n, p) @@ -98,12 +98,12 @@ hal_fit <- fit_hal(X = x, Y = y) #> [1] "I'm sorry, Dave. I'm afraid I can't do that." hal_fit$times #> user.self sys.self elapsed user.child sys.child -#> enumerate_basis 0.002 0.00 0.001 0 0 -#> design_matrix 0.001 0.00 0.002 0 0 -#> remove_duplicates 0.005 0.00 0.004 0 0 -#> reduce_basis 0.000 0.00 0.000 0 0 -#> lasso 0.226 0.02 0.247 0 0 -#> total 0.234 0.02 0.254 0 0 +#> enumerate_basis 0.005 0.000 0.006 0 0 +#> design_matrix 0.005 0.000 0.005 0 0 +#> remove_duplicates 0.017 0.000 0.017 0 0 +#> reduce_basis 0.000 0.000 0.000 0 0 +#> lasso 0.261 0.005 0.270 0 0 +#> total 0.288 0.005 0.298 0 0 # training sample prediction preds <- predict(hal_fit, new_data = x) @@ -134,8 +134,8 @@ After using the `hal9001` R package, please cite the following: year = {2019}, howpublished = {\url{https://github.com/tlverse/hal9001}}, note = {{R} package version 0.2.5}, - url = {https://doi.org/10.5281/zenodo.3558314}, - doi = {10.5281/zenodo.3558314} + url = {https://doi.org/10.5281/zenodo.3558313}, + doi = {10.5281/zenodo.3558313} } ``` diff --git a/docs/articles/intro_hal9001.html b/docs/articles/intro_hal9001.html index e6bf8c62..aa2eef9b 100644 --- a/docs/articles/intro_hal9001.html +++ b/docs/articles/intro_hal9001.html @@ -82,7 +82,7 @@

Nima Hejazi and Jeremy Coyle

-

2020-02-26

+

2020-03-05

Source: vignettes/intro_hal9001.Rmd @@ -152,12 +152,12 @@ 

## [1] "Without your space helmet, Dave. You're going to find that rather difficult."
##                   user.self sys.self elapsed user.child sys.child
-## enumerate_basis       0.004    0.001   0.005          0         0
-## design_matrix         0.017    0.000   0.017          0         0
+## enumerate_basis       0.016    0.000   0.016          0         0
+## design_matrix         0.033    0.000   0.033          0         0
 ## remove_duplicates     0.010    0.000   0.010          0         0
 ## reduce_basis          0.000    0.000   0.000          0         0
-## lasso                 0.672    0.000   0.672          0         0
-## total                 0.703    0.001   0.704          0         0
+## lasso 0.619 0.016 0.635 0 0 +## total 0.678 0.016 0.694 0 0 
## $call
 ## fit_hal(X = x, Y = y, fit_type = "glmnet")
@@ -16416,12 +16416,12 @@ 

 ## 
 ## $times
 ##                   user.self sys.self elapsed user.child sys.child
-## enumerate_basis       0.004    0.001   0.005          0         0
-## design_matrix         0.017    0.000   0.017          0         0
+## enumerate_basis       0.016    0.000   0.016          0         0
+## design_matrix         0.033    0.000   0.033          0         0
 ## remove_duplicates     0.010    0.000   0.010          0         0
 ## reduce_basis          0.000    0.000   0.000          0         0
-## lasso                 0.672    0.000   0.672          0         0
-## total                 0.703    0.001   0.704          0         0
+## lasso                 0.619    0.016   0.635          0         0
+## total                 0.678    0.016   0.694          0         0
 ## 
 ## $lambda_star
 ## [1] 0.01537728
@@ -16565,12 +16565,12 @@ 

 
## 'lassi' is experimental: fit_type='glmnet' is recommended in nearly all cases.

 
 
##                   user.self sys.self elapsed user.child sys.child
-## enumerate_basis       0.004    0.000   0.004          0         0
-## design_matrix         0.014    0.000   0.014          0         0
-## remove_duplicates     0.005    0.000   0.005          0         0
-## reduce_basis          0.004    0.000   0.005          0         0
-## lasso                 1.784    0.001   1.785          0         0
-## total                 1.807    0.001   1.808          0         0

+## enumerate_basis       0.005        0   0.005          0         0
+## design_matrix         0.020        0   0.020          0         0
+## remove_duplicates     0.009        0   0.009          0         0
+## reduce_basis          0.007        0   0.007          0         0
+## lasso                 1.975        0   1.977          0         0
+## total                 2.009        0   2.011          0         0

In the above, all basis functions with fewer than 7.0710678% of observations meeting the criterion imposed are automatically removed prior to the Lasso step of fitting the HAL regression. The results appear below

## $call
@@ -32663,12 +32663,12 @@ 

 ## 
 ## $times
 ##                   user.self sys.self elapsed user.child sys.child
-## enumerate_basis       0.004    0.000   0.004          0         0
-## design_matrix         0.014    0.000   0.014          0         0
-## remove_duplicates     0.005    0.000   0.005          0         0
-## reduce_basis          0.004    0.000   0.005          0         0
-## lasso                 1.784    0.001   1.785          0         0
-## total                 1.807    0.001   1.808          0         0
+## enumerate_basis       0.005        0   0.005          0         0
+## design_matrix         0.020        0   0.020          0         0
+## remove_duplicates     0.009        0   0.009          0         0
+## reduce_basis          0.007        0   0.007          0         0
+## lasso                 1.975        0   1.977          0         0
+## total                 2.009        0   2.011          0         0
 ## 
 ## $lambda_star
 ## [1] 0.01073374
diff --git a/docs/authors.html b/docs/authors.html
index 0d24e4e7..9eb64cdd 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -122,14 +122,14 @@ 
Citation

 
     
Coyle JR, Hejazi NS, van der Laan MJ (2020).
 hal9001: The scalable highly adaptive lasso.
-doi: 10.5281/zenodo.3558314, R package version 0.2.5, https://github.com/tlverse/hal9001. 
+doi: 10.5281/zenodo.3558313, R package version 0.2.5, https://github.com/tlverse/hal9001. 
 

     
@Manual{,
   title = {{hal9001}: The scalable highly adaptive lasso},
   author = {Jeremy R Coyle and Nima S Hejazi and Mark J {van der Laan}},
   year = {2020},
   note = {R package version 0.2.5},
-  doi = {10.5281/zenodo.3558314},
+  doi = {10.5281/zenodo.3558313},
   url = {https://github.com/tlverse/hal9001},
 }

 
diff --git a/docs/index.html b/docs/index.html
index 8f58c742..3aa71dd3 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -103,17 +103,10 @@ 

 

 

 Installation

-
+
For standard use, we recommend installing the package from CRAN via

+
install.packages("hal9001")

 
To contribute, install the development version of hal9001 from GitHub via remotes:

-
remotes::install_github("tlverse/hal9001", build_vignettes = FALSE)

+
remotes::install_github("tlverse/hal9001")

 

 

 

@@ -126,34 +119,34 @@ 

 

 Example

 
This minimal example shows how to use hal9001 to obtain predictions based on the Highly Adaptive Lasso. For details on the properties of the estimator, the interested reader is referred to Benkeser and van der Laan (2016) and van der Laan (2017a).

-
+
 

 

 

@@ -173,8 +166,8 @@ 

       year  = {2019},
       howpublished = {\url{https://github.com/tlverse/hal9001}},
       note = {{R} package version 0.2.5},
-      url = {https://doi.org/10.5281/zenodo.3558314},
-      doi = {10.5281/zenodo.3558314}
+      url = {https://doi.org/10.5281/zenodo.3558313},
+      doi = {10.5281/zenodo.3558313}
     }
@@ -226,6 +219,8 @@

Links

diff --git a/docs/news/index.html b/docs/news/index.html index 6bf868ef..57f208a3 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -122,7 +122,8 @@

Changelog

-hal9001 0.2.5

+hal9001 0.2.5 2020-03-05 + diff --git a/inst/CITATION b/inst/CITATION index c7240236..70e8ce60 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -12,5 +12,5 @@ bibentry(bibtype = "Manual", person("Mark", "van der Laan", "J")), year = year, note = note, - doi = "10.5281/zenodo.3558314", + doi = "10.5281/zenodo.3558313", url = "https://github.com/tlverse/hal9001")