From 366204dc5ed4883a81ef7efbde528b5b4c5fd31e Mon Sep 17 00:00:00 2001
From: Gleb Tikhonov <gleb.tikhonov@helsinki.fi>
Date: Wed, 10 Apr 2024 19:10:08 +0300
Subject: [PATCH] Fixes for LFix and LRan summations.

---
 R/computeInitialParameters.R | 5 +----
 R/computeWAIC.R              | 5 +----
 R/predict.R                  | 4 ++--
 R/updateBetaSel.R            | 2 +-
 R/updateEta.R                | 2 +-
 R/updateInvSigma.R           | 2 +-
 R/updateZ.R                  | 2 +-
 R/updatewRRR.R               | 2 +-
 8 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/R/computeInitialParameters.R b/R/computeInitialParameters.R
index 8adfec0..a7a6f34 100644
--- a/R/computeInitialParameters.R
+++ b/R/computeInitialParameters.R
@@ -249,10 +249,7 @@ computeInitialParameters = function(hM, initPar, computeZ=TRUE){
             LRan[[r]] = LRan[[r]] + (Eta[[r]][hM$Pi[,r],,drop=FALSE]*hM$rL[[r]]$x[as.character(hM$dfPi[,r]),r]) %*% Lambda[[r]][,,k]
       }
    }
-   if(hM$nr > 0){
-      Z = LFix + Reduce("+", LRan)
-   } else
-      Z = LFix
+   Z = Reduce("+", c(list(LFix), LRan))
 
    if(computeZ){
       Z = updateZ(Y=hM$Y,Z=Z,Beta=Beta,iSigma=sigma^-1,Eta=Eta,Lambda=Lambda, Loff=hM$Loff,X=XScaled,Pi=hM$Pi,dfPi=hM$dfPi,distr=hM$distr,rL=hM$rL)
diff --git a/R/computeWAIC.R b/R/computeWAIC.R
index e28fae9..9b4b271 100644
--- a/R/computeWAIC.R
+++ b/R/computeWAIC.R
@@ -72,10 +72,7 @@ computeWAIC = function(hM, ghN=11, byColumn=FALSE){
                LRan[[r]] = LRan[[r]] + (Eta[[r]][Pi[,r],]*rL[[r]]$x[as.character(dfPi[,r]),k]) %*% Lambda[[r]][,,k]
          }
       }
-      if(nr > 0){
-         E = LFix + Reduce("+", LRan)
-      } else
-         E = LFix
+      E = Reduce("+", c(list(LFix), LRan))
 
       indNA = is.na(Y)
       std = matrix(sigma^-0.5,ny,ns,byrow=TRUE)
diff --git a/R/predict.R b/R/predict.R
index 3cba9a7..0761830 100644
--- a/R/predict.R
+++ b/R/predict.R
@@ -262,7 +262,7 @@ get1prediction <-
                 LRan[[r]] = LRan[[r]] + (Eta[[r]][as.character(dfPiNew[,r]),]*rL[[r]]$x[as.character(dfPiNew[,r]),k]) %*% sam$Lambda[[r]][,,k]
         }
     }
-    L = Reduce("+", c(LFix, LRan))
+    L = Reduce("+", c(list(LFix), LRan))
     if(!is.null(Loff)) L = L + Loff
 
     ## predict can be slow with Yc and especially with high mcmcStep
@@ -294,7 +294,7 @@ get1prediction <-
                         sam$Lambda[[r]][,,k]
             }
         }
-        if(object$nr > 0){L = LFix + Reduce("+", LRan)} else L = LFix
+        L = Reduce("+", c(list(LFix), LRan))
     }
     if(!expected){
         Z = L + matrix(sqrt(sam$sigma),nrow(L),object$ns,byrow=TRUE) * matrix(rnorm(nrow(L)*object$ns),nrow(L),object$ns)
diff --git a/R/updateBetaSel.R b/R/updateBetaSel.R
index 3bdf086..8b134db 100644
--- a/R/updateBetaSel.R
+++ b/R/updateBetaSel.R
@@ -42,7 +42,7 @@ updateBetaSel = function(Z,XSelect, BetaSel, Beta, iSigma,
    LFix = matrix(NA,ny,ns)
    for(j in 1:ns)
       LFix[,j] = X[[j]]%*%Beta[,j]
-   E = Reduce("+", c(LFix,LRan))
+   E = Reduce("+", c(list(LFix), LRan))
    if(!is.null(Loff)) E = E + Loff
 
    ll = matrix(NA,ny,ns)
diff --git a/R/updateEta.R b/R/updateEta.R
index 63de714..fb3d769 100644
--- a/R/updateEta.R
+++ b/R/updateEta.R
@@ -30,7 +30,7 @@ updateEta = function(Y,Z,Beta,iSigma,Eta,Lambda,Alpha, rLPar, Loff,X,Pi,dfPi,rL)
    }
    for(r in seq_len(nr)){
       rnames=rownames(Eta[[r]])
-      S = Z - Reduce("+", c(LFix,LRan[setdiff(1:nr, r)]))
+      S = Z - Reduce("+", c(list(LFix), LRan[setdiff(1:nr,r)]))
       if(!is.null(Loff)) S = S - Loff
 
       lambda = Lambda[[r]]
diff --git a/R/updateInvSigma.R b/R/updateInvSigma.R
index 5e2894d..2060b9c 100644
--- a/R/updateInvSigma.R
+++ b/R/updateInvSigma.R
@@ -27,7 +27,7 @@ updateInvSigma = function(Y,Z,Beta,iSigma,Eta,Lambda, distr,Loff,X,Pi,dfPi,rL, a
                LRan[[r]] = LRan[[r]] + (Eta[[r]][Pi[,r],]*rL[[r]]$x[as.character(dfPi[,r]),k]) %*% Lambda[[r]][,,k]
          }
       }
-      Eps = Z - Reduce("+", c(LFix,LRan))
+      Eps = Z - Reduce("+", c(list(LFix), LRan))
       if(!is.null(Loff)) Eps = Eps - Loff
 
       Yx = !is.na(Y)
diff --git a/R/updateZ.R b/R/updateZ.R
index 61351f6..7be3afa 100644
--- a/R/updateZ.R
+++ b/R/updateZ.R
@@ -28,7 +28,7 @@ updateZ = function(Y,Z,Beta,iSigma,Eta,Lambda, Loff,X,Pi,dfPi,distr,rL, ind){
             LRan[[r]] = LRan[[r]] + (Eta[[r]][Pi[,r],]*rL[[r]]$x[as.character(dfPi[,r]),k]) %*% Lambda[[r]][,,k]
       }
    }
-   E = Reduce("+", c(LFix,LRan))
+   E = Reduce("+", c(list(LFix), LRan))
    if(!is.null(Loff)) E = E + Loff
 
    Z = matrix(NA,ny,ns)
diff --git a/R/updatewRRR.R b/R/updatewRRR.R
index 808465a..dd1febd 100644
--- a/R/updatewRRR.R
+++ b/R/updatewRRR.R
@@ -40,7 +40,7 @@ updatewRRR = function(Z,Beta,iSigma,Eta,Lambda, Loff,X1A,XRRR,Pi,dfPi,rL,PsiRRR,
             LRan[[r]] = LRan[[r]] + (Eta[[r]][Pi[,r],]*rL[[r]]$x[as.character(dfPi[,r]),r]) %*% Lambda[[r]][,,k]
       }
    }
-   S = Z - Reduce("+", c(LFix,LRan))
+   S = Z - Reduce("+", c(list(LFix), LRan))
    if(!is.null(Loff)) S = S - Loff
 
    A1 = BetaRRR%*%diag(iSigma,nrow = length(iSigma))%*%t(BetaRRR)