From 8f037a1ad0ecd74a3fefc3d8bbc686805a006610 Mon Sep 17 00:00:00 2001
From: Klaus Holst <klaus@holst.it>
Date: Mon, 6 Jan 2025 13:05:19 +0100
Subject: [PATCH] fixing nosuggests msg

---
 R/matrices.R                    | 15 ++++++++++-----
 tests/testthat/test-influence.R | 21 ++++++++++++---------
 2 files changed, 22 insertions(+), 14 deletions(-)

diff --git a/R/matrices.R b/R/matrices.R
index 7c3fdd35..9781bb70 100644
--- a/R/matrices.R
+++ b/R/matrices.R
@@ -213,10 +213,16 @@ mat.lvm <- function(x,ii=index(x),...) {
 
     parBelongsTo <- lapply(parBelongsTo,function(x) sort(unique(x)))
 
-
-    return(list(mean=cbind(idxM,pidxM),
-                reg=cbind(idxA,pidxA),
-                cov=cbind(idxP,pidxP),
+    meanl <- idxM
+    if (!is.null(meanl)) meanl <- cbind(meanl, pidxM)
+    regl <- idxA
+    if (!is.null(regl)) regl <- cbind(regl, pidxA)
+    covl <- idxP
+    if (!is.null(covl)) covl <- cbind(covl, pidxP)
+
+    return(list(mean=meanl,
+                reg=regl,
+                cov=covl,
                 epar=ee,
                 parval=parval,
                 constrain.idx=constrain.idx,
@@ -225,7 +231,6 @@ mat.lvm <- function(x,ii=index(x),...) {
 }
 
 
-
 matrices.lvm <- function(x,pars,meanpar=NULL,epars=NULL,data=NULL,...) {
     ii <- index(x)
     pp <- c(rep(NA,ii$npar.mean),pars,epars)
diff --git a/tests/testthat/test-influence.R b/tests/testthat/test-influence.R
index 7fe3ebfa..bacf5a41 100644
--- a/tests/testthat/test-influence.R
+++ b/tests/testthat/test-influence.R
@@ -1,34 +1,35 @@
 context("Influence functions")
 
 test_that("GEE", {
-  require("geepack")
+  if (requireNamespace("geepack",quietly=TRUE)) {
   d <- lvm(y ~ x, ~ id) |>
     distribution(~id, uniform.lvm(value=seq(1:20))) |>
     sim(100, seed=1)
   d0 <- d[order(d$id), ]
-  g <- geeglm(y ~ x, data=d0, id=d0$id)
+  g <- geepack::geeglm(y ~ x, data=d0, id=d0$id)
   V <- summary(g)$cov.scaled
   g0 <- glm(y ~ x, data=d)
   V0 <- vcov(estimate(g0, id = d$id))
   testthat::expect_true(sum((V - V0)^2) < 1e-12)
+  }
 })
 
-
 test_that("merge, IC, estimate with 'id' argument", {
-  require("geepack")
   d <- data.frame(id=c("a","a","b","b","b","b","c","c","d"),
                 id1=c("a","a","b1","b1","b2","b2","c","c","d"),
                 y=rnorm(9), x=rnorm(9))
   d$id0 <- as.numeric(as.factor(d$id))
 
   l <- glm(y ~ x, data=d)
-  V <- summary(geeglm(y ~ x, id=d$id0, data=d))$cov.scaled
-  V0 <- vcov(estimate(l, id=d$id))
-  testthat::expect_true(sum((V - V0)^2) < 1e-12)
-
   e1 <- estimate(l, id=d$id1)
+  V0 <- vcov(e)
   V1 <- vcov(estimate(e1, id=c(1,2,2,3,4)))
-  testthat::expect_true(sum((V - V1)^2) < 1e-12)
+
+  if (requireNamespace("geepack",quietly=TRUE)) {
+    V <- summary(geepack::geeglm(y ~ x, id=d$id0, data=d))$cov.scaled
+    testthat::expect_true(sum((V - V0)^2) < 1e-12)
+    testthat::expect_true(sum((V - V1)^2) < 1e-12)
+  }
 
   e <- merge(estimate(l), estimate(l), id=list(d$id, d$id1))
   testthat::expect_true(sum((vcov(e1) - vcov(e)[3:4,3:4])^2) < 1e-12)
@@ -47,6 +48,7 @@ test_that("negative binomial regression (glm.nb)", {
   x <- rnorm(n)
   lam <- z * exp(x)
   y <- rpois(n, lam)
+  if (requireNamespace("MASS",quietly=TRUE)) {
   m <- MASS::glm.nb(y ~ x)
   testthat::expect_true(abs(lava:::logL.glm(m) - logLik(m)) < 1e-6)
   p <- coef(m)+1
@@ -57,6 +59,7 @@ test_that("negative binomial regression (glm.nb)", {
   u1 <- as.vector(numDeriv::jacobian(function(p) lava:::logL.glm(m, p = p), p))
   u2 <- score(m, p = p)
   testthat::expect_true(sum((u1 - u2)^2) < 1e-6)
+  }
 })