README and NEWS corr

NEWS.md

@@ -1,126 +1,126 @@
-## 1.0.1
+# 1.0.1
 
-### New features
+## New features
 - New `vcov` method
 
-### Bug fixes
+## Bug fixes
 - Adapts `smooth_scam` function to new version of package `gratia`
 - Fixes names in confidence intervals from `confint.cgaim`
 
-## 1.0.0
+# 1.0.0
 
-### Changes
+## Changes
 - Expanded documentation
 - Merged all control parameters into a single one. Added function `control.cgaim`
 
-### Bug fixes
+## Bug fixes
 - Fixed bug with select in `predict.cgaim` and `plot.cgaim`
 - Fixed reporting active constraints from `osqp`
 - Changed derivative function for `gam` (previous was deprecated)
 - Bug in the use of `foreach` in `boot.cgaim`
 - The main function now checks for irreducibility of the constraint matrix.
 - Fixed crash when a wrong argument is given in `acons`.
 
-## 0.4.00 - 2022-05-28
+# 0.4.00 - 2022-05-28
 
-### New features
+## New features
 - Confidence intervals through normal approximation.
 - New function dedicated to bootstrap resampling. Result can be used in other functions such as `confint`.
 
-### Changes
+## Changes
 - Changes in bootstrap confidence intervals. Evaluated at index values.
 - Parallel through the `doParallel` package, made easier.
 - QR decomposition for alpha updating to stabilize it.
 - Internal change in function organization.
 
-## 0.3.05
+# 0.3.05
 
-### Bug fixes
+## Bug fixes
 - Fixed bug related to model frame with covariates
 
-## 0.3.04
+# 0.3.04
 
-### Changes
+## Changes
 - Changed default solver to `osqp`.
 
-### Bug fixes
+## Bug fixes
 - Fixed bug in replication of `bvec` when `Cmat` is passed through alpha_control.
 
-## 0.3.03
+# 0.3.03
 
-### Bug fixes
+## Bug fixes
 - Fixed issue in the finding of active constraints in `quadprog` for `edf` (yes, again).
 
-## 0.3.02
+# 0.3.02
 
-### Bug fixes
+## Bug fixes
 - Fixed issue in the finding of active constraints in `quadprog` for `edf`.
 
-## 0.3.01
+# 0.3.01
 
-### Changes
+## Changes
 - Slight change in convergence handling: now possibility to choose between convergence in RSS or coefficients.
 
-### Bug fixes
+## Bug fixes
 - Fixed bug caused by naming variables in `g`.
 
-## 0.3.00
+# 0.3.00
 
-### New features
+## New features
 - Add computation of effective degrees of freedom.
 - Add GCV computation.
 - Add `ctol` parameter to add a small margin to constraints.
 
-### Changes
+## Changes
 - Names of algorithm controlling arguments changed with specific help pages added.
 - Internal reorganization of functions.
 
-## 0.2.04
+# 0.2.04
 
-### Bug fixes
+## Bug fixes
 - Bug for the predict function when some data come from matrices.
 
-## 0.2.03
+# 0.2.03
 
-### Bug fixes
+## Bug fixes
 - Fixed computation of bootstrap confidence intervals for ridge functions `g`.
 - Got back to new form of documentation.
 
-## 0.2.02
+# 0.2.02
 
-### Changes
+## Changes
 - Restricted the computation of confidence intervals to percentile bootstrap. The others need a proper implementation.
 
-### Bug fixes
+## Bug fixes
 - Removed the computation of all standard errors from the main function `cgaim`. They were half-baked and caused more problems than were useful.
 - Fixed issues on the documentation
 
-## 0.2.01
+# 0.2.01
 
-### Changes
+## Changes
 - Now uses `mgcv::gam` instead of `scam` when no smoothing constraints are given. Doesn't apply to `scar` and `cgam` yet.
 
-## 0.2.0
+# 0.2.0
 
-### New features
+## New features
 - Custom function `s` for non-index smooth terms. Maps to the right function depending on the function used at the GAM step.
 - Possibility to use package `cgam` for constrained smooths.
 
-### Changes
+## Changes
 - Change of argument names in `g`.
 - Warning messages for convergence failures.
 
-### Bug fixes
+## Bug fixes
 - Fixes a bug related to argument `select` in `plot.cgaim`
 - Fixes a bug related to the computation of covariance matrices after estimation
 - Fixes bug occurring for single-index models without covariate
 
-## 0.1.1
+# 0.1.1
 
-### Function 'g'
+## Function 'g'
 - argument 'label' now defaults to the name of the first variable given
 - now takes list of matrices to facilitate calling the function
 - smarter attribution of names inside each index
 
-### Bug fixes
+## Bug fixes
 - fixes the mixing of names in elements `gfit` and `beta` from the output

README.md

@@ -1,16 +1,19 @@
 # cgaim
 
-Constrained groupwise additive index models
+[![](https://www.r-pkg.org/badges/version/cgaim?color=green)](https://cran.r-project.org/package=cgaim)
+[![](http://cranlogs.r-pkg.org/badges/grand-total/cgaim?color=green)](https://cran.r-project.org/package=cgaim)
+
+Constrained Groupwise Additive Index Models
 
 ## Description
 
-The `cgaim` package provide allows fitting groupwise additive index models with constraints on both the ridge functions and indices coefficients. Methods to plot the ridge functions, predict new data and compute confidence intervals are also included in the package.
+The `cgaim` package allows fitting Groupwise Additive Index Models with constraints (CGAIM) on both the ridge functions and indices coefficients. Methods to plot the ridge functions, predict new data and compute confidence intervals are also included in the package.
 
-The statistical model is detailed in the following publication
+The model and fitting are described in:
 
 -----
 
-Pierre Masselot, Fateh Chebana, Céline Campagna, Éric Lavigne, Taha B M J Ouarda, Pierre Gosselin (2022). **Constrained groupwise additive index models.** *Biostatistics*, 00(00), 1-19. https://doi.org/10.1093/biostatistics/kxac023.
+Pierre Masselot, Fateh Chebana, Céline Campagna, Éric Lavigne, Taha B M J Ouarda, Pierre Gosselin (2022). **Constrained groupwise additive index models.** *Biostatistics*, 24(04), 1066–1084. https://doi.org/10.1093/biostatistics/kxac023.
 
 -----