From: Benjamin Auder <benjamin.auder@somewhere>
Date: Wed, 4 Mar 2020 17:14:01 +0000 (+0100)
Subject: Rename main function into runValse, remove testthat folder since nobody's gonna write... 
X-Git-Url: https://git.auder.net/variants/Chakart/pieces/doc/current/img/%7B%7B%20pkg.url%20%7D%7D?a=commitdiff_plain;h=859c30ec72871f923da0498c14a94e67b0219875;p=valse.git

Rename main function into runValse, remove testthat folder since nobody's gonna write tests
---

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index b620b65..8dd0fcb 100644
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -23,8 +23,7 @@ Imports:
 Suggests:
     capushe,
     methods,
-    roxygen2,
-    testthat
+    roxygen2
 URL: http://git.auder.net/?p=valse.git
 License: MIT + file LICENSE
 RoxygenNote: 7.0.2
diff --git a/pkg/R/initSmallEM.R b/pkg/R/initSmallEM.R
index 937ea73..fccd51d 100644
--- a/pkg/R/initSmallEM.R
+++ b/pkg/R/initSmallEM.R
@@ -5,9 +5,10 @@
 #' @param Y matrix of responses (of size n*m)
 #'
 #' @return a list with phiInit, rhoInit, piInit, gamInit
-#' @export
+#'
 #' @importFrom methods new
 #' @importFrom stats cutree dist hclust runif
+#' @export
 initSmallEM <- function(k, X, Y, fast)
 {
   n <- nrow(X)
diff --git a/pkg/R/main.R b/pkg/R/main.R
index 8649342..85a41b7 100644
--- a/pkg/R/main.R
+++ b/pkg/R/main.R
@@ -1,4 +1,4 @@
-#' valse
+#' runValse
 #'
 #' Main function
 #'
@@ -26,8 +26,9 @@
 #'
 #' @examples
 #' #TODO: a few examples
+#'
 #' @export
-valse <- function(X, Y, procedure = "LassoMLE", selecMod = "DDSE", gamma = 1, mini = 10,
+runValse <- function(X, Y, procedure = "LassoMLE", selecMod = "DDSE", gamma = 1, mini = 10,
   maxi = 50, eps = 1e-04, kmin = 2, kmax = 3, rank.min = 1, rank.max = 5, ncores_outer = 1,
   ncores_inner = 1, thresh = 1e-08, grid_lambda = numeric(0), size_coll_mod = 10,
   fast = TRUE, verbose = FALSE, plot = TRUE)
diff --git a/pkg/R/plot_valse.R b/pkg/R/plot_valse.R
index 83316dc..3160067 100644
--- a/pkg/R/plot_valse.R
+++ b/pkg/R/plot_valse.R
@@ -8,10 +8,7 @@
 #' @param n sample size
 #' @return several plots
 #'
-#' @examples TODO
-#'
 #' @export
-#'
 plot_valse <- function(X, Y, model, n, comp = FALSE, k1 = NA, k2 = NA)
 {
   require("gridExtra")
diff --git a/pkg/R/selectVariables.R b/pkg/R/selectVariables.R
index a4bc0f4..0c18c67 100644
--- a/pkg/R/selectVariables.R
+++ b/pkg/R/selectVariables.R
@@ -18,10 +18,7 @@
 #'
 #' @return a list of outputs, for each lambda in grid: selected,Rho,Pi
 #'
-#' @examples TODO
-#'
 #' @export
-#'
 selectVariables <- function(phiInit, rhoInit, piInit, gamInit, mini, maxi, gamma,
   glambda, X, Y, thresh = 1e-08, eps, ncores = 3, fast)
 {
diff --git a/pkg/inst/testdata/TODO.csv b/pkg/inst/testdata/TODO.csv
deleted file mode 100644
index d679966..0000000
--- a/pkg/inst/testdata/TODO.csv
+++ /dev/null
@@ -1 +0,0 @@
-ou alors data_test.RData, possible aussi
diff --git a/pkg/man/valse-package.Rd b/pkg/man/valse-package.Rd
index 534375b..377891d 100644
--- a/pkg/man/valse-package.Rd
+++ b/pkg/man/valse-package.Rd
@@ -12,14 +12,12 @@
 }
 
 \details{
-	The package devtools should be useful in development stage, since we rely on testthat for
-	unit tests, and roxygen2 for documentation. knitr is used to generate the package vignette.
-	Concerning the other suggested packages:
-	\itemize{
-		\item{parallel (generally) permits to run the bootstrap method faster.}
-	}
-
-	The three main functions are ...
+  Two methods are implemented to cluster data with finite mixture
+  regression models. Those procedures deal with high-dimensional covariates and
+  responses through a variable selection procedure based on the Lasso estimator.
+  
+  The main function is runValse(), which calls all other functions.
+  See also plot_valse() which plots the relevant parameters after a run.
 }
 
 \author{
diff --git a/pkg/tests/testthat.R b/pkg/tests/testthat.R
deleted file mode 100644
index 88e5631..0000000
--- a/pkg/tests/testthat.R
+++ /dev/null
@@ -1,4 +0,0 @@
-library(testthat)
-library(valse) #ou load_all()
-
-test_check("valse")
diff --git a/pkg/tests/testthat/helper-context1.R b/pkg/tests/testthat/helper-context1.R
deleted file mode 100644
index b40f358..0000000
--- a/pkg/tests/testthat/helper-context1.R
+++ /dev/null
@@ -1,5 +0,0 @@
-# Potential helpers for context 1
-help <- function()
-{
-	#...
-}
diff --git a/pkg/tests/testthat/test-context1.R b/pkg/tests/testthat/test-context1.R
deleted file mode 100644
index 17c633f..0000000
--- a/pkg/tests/testthat/test-context1.R
+++ /dev/null
@@ -1,11 +0,0 @@
-context("Context1")
-
-test_that("function 1...",
-{
-	#expect_lte( ..., ...)
-})
-
-test_that("function 2...",
-{
-	#expect_equal(..., ...)
-})
diff --git a/pkg/vignettes/.gitignore b/pkg/vignettes/.gitignore
deleted file mode 100644
index e6493d4..0000000
--- a/pkg/vignettes/.gitignore
+++ /dev/null
@@ -1,14 +0,0 @@
-#ignore jupyter generated file (ipynb, HTML)
-*.html
-*.ipynb
-
-#and various (pdf)LaTeX files, in case of
-*.tex
-*.pdf
-*.aux
-*.dvi
-*.log
-*.out
-*.toc
-*.synctex.gz
-/figure/
diff --git a/test/script_data.R b/test/script_data.R
index da319da..1635746 100644
--- a/test/script_data.R
+++ b/test/script_data.R
@@ -10,6 +10,6 @@ Beta[1:4,1:4,1] = 3*diag(4)
 Beta[1:4,1:4,2] = -2*diag(4)
 
 Data = generateXY(200, c(0.5,0.5), rep(0,p), Beta, diag(p), covY)
-#  
+
 Res = valse(Data$X,Data$Y, fast=TRUE, plot=FALSE, verbose = TRUE, kmax=3, size_coll_mod = 50, selecMod = "DDSE", mini = 50, maxi=100)
 plot(Res$tableau[,3], -Res$tableau[,4])