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Fix bug when kernel has only one positive eigenvalues #79

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Fix bug when kernel has only one positive eigenvalues #79

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f66823d
Fix bug when kernel has only one positive eigenvalues
fmorgante Oct 10, 2024
93d80a4
Compute covariance matrix with flashier
fmorgante Mar 5, 2025
4143214
Handle rows with all missing values
fmorgante Mar 5, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
Package: BGLR
Version: 1.1.3
Version: 1.1.4
Title: Bayesian Generalized Linear Regression
Authors@R: c(person(given = "Gustavo",
family = "de los Campos",
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2 changes: 1 addition & 1 deletion R/BGLR.R
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Expand Up @@ -548,7 +548,7 @@ setLT.RKHS=function(LT,y,n,j,weights,saveAt,R2,nLT,rmExistingFiles,verbose)
tmp= LT$d > LT$tolD
LT$levelsU = sum(tmp)
LT$d = LT$d[tmp]
LT$V = LT$V[, tmp]
LT$V = LT$V[, tmp, drop=FALSE]

#Default degrees of freedom and scale parameter associated with the variance component for marker effect
if (is.null(LT$df0))
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4 changes: 2 additions & 2 deletions R/Multitrait.R
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Expand Up @@ -1284,8 +1284,8 @@ Multitrait<-function(y,

n<-nrow(y)

#Compute sample variance covariance matrix
Sy<-cov(y,use="pairwise.complete.obs")
#Compute sample variance covariance matrix using flashier (removing rows that have all NAs)
Sy <- mr.mash.alpha:::compute_cov_flash(y[rowSums(is.na(y)) != ncol(y), ])
Sy[is.na(Sy)]=0

#Deep copy of y, DO NOT REPLACE with y.back<-y, it does not work, both objects
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