1.3.6 when the variance of error is 0, stop the null model fitting

Author: weizhouUMICH

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SAIGE
 Type: Package
 Title: Efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE+) 
-Version: 1.3.5
-Date: 2024-04-23
+Version: 1.3.6
+Date: 2024-05-27
 Author: Wei Zhou, Zhangchen Zhao, Wenjian Bi, Seunggeun Lee, Cristen Willer
 Maintainer: SAIGE team <saige.genetics@gmail.com> 
 Description:an R package that implements the Scalable and Accurate Implementation of Generalized mixed model that uses the saddlepoint approximation (SPA)(mhof, J. P. , 1961; Kuonen, D. 1999; Dey, R. et.al 2017) and large scale optimization techniques to calibrate case-control ratios in logistic mixed model score tests (Chen, H. et al. 2016) in large PheWAS. It conducts both single-variant association tests and set-based tests for rare variants.  
@@ -15,4 +15,4 @@ SystemRequirements: GNU make
 RoxygenNote: 7.1.2
 NeedsCompilation: yes
 Encoding: UTF-8
-Packaged: 2024-02-06 EST
+Packaged: 2024-05-27 EST

R/SAIGE_fitGLMM_fast.R

@@ -446,11 +446,11 @@ glmmkin.ai_PCG_Rcpp_Quantitative = function(bedFile, bimFile, famFile, Xorig, is
     #Y = eta - offset + (y - mu)/mu.eta
     #sqrtW = mu.eta/sqrt(family$variance(mu))
 
-    if(tau[1]<=0){
-      stop("ERROR! The first variance component parameter estimate is 0\n")
-    }
+    #if(tau[1]<=0){
+    #  stop("ERROR! The first variance component parameter estimate is 0\n")
+    #}
 
-    if(tau[2] <= 0) break	
+    if(tau[1]<=0 | tau[2] <= 0) break	
 
 
     if(max(abs(tau - tau0)/(abs(tau) + abs(tau0) + tol)) < tol) break