add copyright to all R files

merliseclyde · Oct 23, 2024 · 73c4ffd · 73c4ffd
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -25,6 +25,9 @@ cran-comments.md
 ^CRAN-RELEASE$
 ^codecov\.yml$
 CONTRIBUTING.md
+.htaccess
+R/copyright.txt
+src/copyright.txt
 
 ^cran-comments\.md$
 ^doc$

diff --git a/.gitignore b/.gitignore
@@ -19,3 +19,6 @@ docs
 tests/testthat/Rplots.pdf
 R/gordy.R
 inst/doc
+R/copyright.txt
+src/copyright.txt
+
diff --git a/.htaccess b/.htaccess
@@ -0,0 +1,6 @@
+# Extra Security Headers
+<IfModule mod_headers.c>
+    Header set X-XSS-Protection "1; mode=block"
+    Header always append X-Frame-Options SAMEORIGIN
+    Header set X-Content-Type-Options nosniff
+</IfModule>
diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,8 @@
 # BAS 1.7.4
 
 * added hexagon sticker
+* add copyright to source files to satistfy OpenSSF Best Practices
+
 
 # BAS 1.7.3
 

diff --git a/R/BAS-package.R b/R/BAS-package.R
@@ -1,3 +1,6 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
 #' _PACKAGE
 #' @name BAS
 #'

diff --git a/R/EB_global.R b/R/EB_global.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Find the global Empirical Bayes estimates for BMA
 #'
 #' Finds the global Empirical Bayes estimates of g in Zellner's g-prior and

diff --git a/R/as_matrix.R b/R/as_matrix.R
@@ -1,3 +1,6 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
 #' Coerce a BAS list object into a matrix.
 #'
 #' Models, coefficients, and standard errors in objects of class 'bas' are

diff --git a/R/bas_glm.R b/R/bas_glm.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Bayesian Adaptive Sampling Without Replacement for Variable Selection in
 #' Generalized Linear Models
 #'

diff --git a/R/bas_lm.R b/R/bas_lm.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 normalize.initprobs.lm <- function(initprobs, p) {
   if (length(initprobs) != p) {
     stop(paste(

diff --git a/R/beta_priors.R b/R/beta_priors.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Empirical Bayes Prior Distribution for Coefficients in BMA Model
 #'
 #' Creates an object representing the EB prior for BAS GLM.

diff --git a/R/cch.R b/R/cch.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Compound Confluent hypergeometric function of two variables
 #'
 #' Compute the Confluent Hypergeometric function of two variables, also know as

diff --git a/R/coefficients.R b/R/coefficients.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Coefficients of a Bayesian Model Average object
 #'
 #' Extract conditional posterior means and standard deviations, marginal

diff --git a/R/confint.R b/R/confint.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Compute Credible Intervals for BAS regression coefficients from BAS objects
 #'
 #' Uses Monte Carlo simulations using posterior means and standard deviations

diff --git a/R/cv_summary.R b/R/cv_summary.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Summaries for Out of Sample Prediction
 #'
 #' Compute average prediction error from out of sample predictions

diff --git a/R/data.R b/R/data.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Bodyfat Data
 #'
 #' Lists estimates of the percentage of body fat determined by underwater

diff --git a/R/diagnostics.R b/R/diagnostics.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' BAS MCMC diagnostic plot
 #'
 #' Function to help assess convergence of MCMC sampling for bas objects.

diff --git a/R/eplogprob.R b/R/eplogprob.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' eplogprob - Compute approximate marginal inclusion probabilities from
 #' pvalues
 #'

diff --git a/R/glm_fit.R b/R/glm_fit.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Fitting Generalized Linear Models and Bayesian marginal likelihood
 #' evaluation
 #'

diff --git a/R/hypergeometric1F1.R b/R/hypergeometric1F1.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Confluent hypergeometric1F1 function
 #'
 #' Compute the Confluent Hypergeometric function: 1F1(a,b,c,t) =

diff --git a/R/hypergeometric2F1.R b/R/hypergeometric2F1.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Gaussian hypergeometric2F1 function
 #'
 #' Compute the Gaussian Hypergeometric2F1 function: 2F1(a,b,c,z) = Gamma(b-c)

diff --git a/R/image.R b/R/image.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Images of models used in Bayesian model averaging
 #'
 #' Creates an image of the models selected using \code{\link{bas}}.

diff --git a/R/interactions.R b/R/interactions.R
@@ -1,4 +1,7 @@
-
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 
 make.parents.of.interactions <-
   function(mf, data) {

diff --git a/R/model_priors.R b/R/model_priors.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Uniform Prior Distribution for Models
 #'
 #' Creates an object representing the prior distribution on models for BAS.

diff --git a/R/outliers.R b/R/outliers.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 ########## Functions for Chaloner and Brant ###############
 #' Bayesian Outlier Detection
 #'

diff --git a/R/plot.R b/R/plot.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Plot Diagnostics for an BAS Object
 #'
 #' Four plots (selectable by 'which') are currently available: a plot of

diff --git a/R/plot_coef.R b/R/plot_coef.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Plots the posterior distributions of coefficients derived from Bayesian
 #' model averaging
 #'

diff --git a/R/predict.R b/R/predict.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Prediction Method for an Object of Class basglm
 #' @description Predictions under model averaging from a BMA (BAS) object for GLMs
 #' under different loss functions.

diff --git a/R/summary.R b/R/summary.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Print a Summary of Bayesian Model Averaging objects from BAS
 #'
 #' \code{summary} and \code{print} methods for Bayesian model averaging objects

diff --git a/R/update.R b/R/update.R
@@ -1,3 +1,7 @@
+# Copyright (c) 2024 Merlise Clyde and contributors to BAS. All rights reserved.
+# This work is licensed under a GNU GENERAL PUBLIC LICENSE Version 3.0
+# License text is available at https://www.gnu.org/licenses/gpl-3.0.html
+#
 #' Update BAS object using a new prior
 #'
 #' Update a BMA object using a new prior distribution on the coefficients.