fixes #77

UW-GAC · Nov 8, 2023 · 25933a8 · 25933a8
1 parent 44503b2
commit 25933a8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,8 +3,8 @@ Type: Package
 Title: GENetic EStimation and Inference in Structured samples
         (GENESIS): Statistical methods for analyzing genetic data from
         samples with population structure and/or relatedness
-Version: 2.33.0
-Date: 2021-08-23
+Version: 2.33.1
+Date: 2023-11-07
 Author: Matthew P. Conomos, Stephanie M. Gogarten,
 	Lisa Brown, Han Chen, Thomas Lumley, Kenneth Rice, Tamar Sofer, Adrienne Stilp, Timothy Thornton, Chaoyu Yu
 Maintainer: Stephanie M. Gogarten <[email protected]>

diff --git a/R/spa.R b/R/spa.R
@@ -21,7 +21,7 @@ SPA_pval <- function(score.result, nullmod, G, pval.thresh = 1){
 		# calculate the fitted values  from the null model;
                 # expit(eta) = expit(X\beta + Zb)
                 if (nullmod$model$family$mixedmodel) {
-                    mu <- as.vector(expit(nullmod$fit$linear.predictor))
+                    mu <- as.vector(plogis(nullmod$fit$linear.predictor))
                 } else {
                     # fitted.values from glm models are already the expit.
                     mu <- as.vector(nullmod$fit$fitted.values)