From d9011222fa393682056d295ed38e277b297d4d99 Mon Sep 17 00:00:00 2001
From: MikeDMorgan <michael.morgan@abdn.ac.uk>
Date: Mon, 3 Jun 2024 16:13:32 +0100
Subject: [PATCH] add warning if glmm.solver is NULL and using GLMM

---
 R/testNhoods.R | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/R/testNhoods.R b/R/testNhoods.R
index 71b1ac8..239595c 100644
--- a/R/testNhoods.R
+++ b/R/testNhoods.R
@@ -419,6 +419,13 @@ testNhoods <- function(x, design, design.df, kinship=NULL,
 
         # I think these need to be logged
         offsets <- log(dge$samples$norm.factors)
+
+        # if glmm.solver isn't set but is running GLMM
+        if(is.null(glmm.solver) & isTRUE(is.lmm)){
+            warning("NULL value for glmm.solver - setting to Fisher. Please set glmm.solver")
+            glmm.solver <- "Fisher"
+        }
+
         glmm.cont <- list(theta.tol=max.tol, max.iter=max.iters, solver=glmm.solver)
 
         #wrapper function is the same for all analyses