From 77401b12ec2e441584c7eba0543e23dccacede2c Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 20 Aug 2024 16:47:00 +0200
Subject: [PATCH 1/2] Added validation for `nlambda <= maxgrid` (closes #54)

---
 R/MADMMplasso.R                  |  3 ++
 tests/testthat/test-validation.R | 80 ++++++++++++++++++++++++++++++++
 2 files changed, 83 insertions(+)
 create mode 100644 tests/testthat/test-validation.R

diff --git a/R/MADMMplasso.R b/R/MADMMplasso.R
index 970ab59..05fe31a 100644
--- a/R/MADMMplasso.R
+++ b/R/MADMMplasso.R
@@ -49,6 +49,9 @@
 #' @example inst/examples/MADMMplasso_example.R
 #' @export
 MADMMplasso <- function(X, Z, y, alpha, my_lambda = NULL, lambda_min = 0.001, max_it = 50000, e.abs = 1E-3, e.rel = 1E-3, maxgrid, nlambda, rho = 5, my_print = FALSE, alph = 1.8, tree, pal = cl == 1L, gg = NULL, tol = 1E-4, cl = 1L, legacy = FALSE) {
+  # Validation
+  stopifnot(nlambda <= maxgrid)
+
   # Recalculating the number of CPUs
   if (pal && cl > 1L) {
     cl <- 1L
diff --git a/tests/testthat/test-validation.R b/tests/testthat/test-validation.R
new file mode 100644
index 0000000..6ff5962
--- /dev/null
+++ b/tests/testthat/test-validation.R
@@ -0,0 +1,80 @@
+
+# Setting up objects =========================================================
+N <- 100
+p <- 50
+nz <- 4
+K <- nz
+X <- matrix(rnorm(n = N * p), nrow = N, ncol = p)
+mx <- colMeans(X)
+sx <- sqrt(apply(X, 2, var))
+X <- scale(X, mx, sx)
+X <- matrix(as.numeric(X), N, p)
+Z <- matrix(rnorm(N * nz), N, nz)
+mz <- colMeans(Z)
+sz <- sqrt(apply(Z, 2, var))
+Z <- scale(Z, mz, sz)
+beta_1 <- rep(x = 0, times = p)
+beta_2 <- rep(x = 0, times = p)
+beta_3 <- rep(x = 0, times = p)
+beta_4 <- rep(x = 0, times = p)
+beta_5 <- rep(x = 0, times = p)
+beta_6 <- rep(x = 0, times = p)
+
+beta_1[1:5] <- c(2, 2, 2, 2, 2)
+beta_2[1:5] <- c(2, 2, 2, 2, 2)
+beta_3[6:10] <- c(2, 2, 2, -2, -2)
+beta_4[6:10] <- c(2, 2, 2, -2, -2)
+beta_5[11:15] <- c(-2, -2, -2, -2, -2)
+beta_6[11:15] <- c(-2, -2, -2, -2, -2)
+
+Beta <- cbind(beta_1, beta_2, beta_3, beta_4, beta_5, beta_6)
+colnames(Beta) <- 1:6
+
+theta <- array(0, c(p, K, 6))
+theta[1, 1, 1] <- 2
+theta[3, 2, 1] <- 2
+theta[4, 3, 1] <- -2
+theta[5, 4, 1] <- -2
+theta[1, 1, 2] <- 2
+theta[3, 2, 2] <- 2
+theta[4, 3, 2] <- -2
+theta[5, 4, 2] <- -2
+theta[6, 1, 3] <- 2
+theta[8, 2, 3] <- 2
+theta[9, 3, 3] <- -2
+theta[10, 4, 3] <- -2
+theta[6, 1, 4] <- 2
+theta[8, 2, 4] <- 2
+theta[9, 3, 4] <- -2
+theta[10, 4, 4] <- -2
+theta[11, 1, 5] <- 2
+theta[13, 2, 5] <- 2
+theta[14, 3, 5] <- -2
+theta[15, 4, 5] <- -2
+theta[11, 1, 6] <- 2
+theta[13, 2, 6] <- 2
+theta[14, 3, 6] <- -2
+theta[15, 4, 6] <- -2
+
+pliable <- matrix(0, N, 6)
+for (e in 1:6) {
+  pliable[, e] <- compute_pliable(X, Z, theta[, , e])
+}
+
+esd <- diag(6)
+e <- MASS::mvrnorm(N, mu = rep(0, 6), Sigma = esd)
+y_train <- X %*% Beta + pliable + e
+y <- y_train
+
+colnames(y) <- c(paste0("y", seq_len(ncol(y))))
+TT <- tree_parms(y)
+gg1 <- matrix(0, 2, 2)
+gg1[1, ] <- c(0.02, 0.02)
+gg1[2, ] <- c(0.02, 0.02)
+
+# Running MADMMplasso ========================================================
+test_that("MADMMplasso() prevents silly arguments", {
+  expect_error(
+    MADMMplasso(X, Z, y, 0.2, maxgrid = 1, nlambda = 2, tree = TT, gg = gg1)
+  )
+})

From 195122cf5de2bdb7211f887468a6ded4645e1c3a Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Tue, 20 Aug 2024 16:47:05 +0200
Subject: [PATCH 2/2] Increment version number to 0.0.0.9023

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 81c007a..c0fe5fd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MADMMplasso
 Title: Multi Variate Multi Response 'ADMM' with Interaction Effects
-Version: 0.0.0.9022
+Version: 0.0.0.9023
 Authors@R:
     c(
         person(