Fixed column and row names for many varbvs outputs; R CMD check --as-…

…cran returns OK.
pcarbo · Nov 3, 2017 · a7b6bd5 · a7b6bd5
1 parent e84b225
commit a7b6bd5
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Showing 4 changed files with 14 additions and 12 deletions.
diff --git a/varbvs-R/R/confint.varbvs.R b/varbvs-R/R/confint.varbvs.R
@@ -74,7 +74,7 @@ get.confint.matrix <- function (fit, i, level) {
 
     # Set up the data structure for storing the output.
     out           <- matrix(0,ns + 1,2)
-    rownames(out) <- c(paste0("theta_",1:ns),"averaged")
+    rownames(out) <- c(colnames(fit$alpha),"averaged")
 
     # Compute the credible interval for each hyperparameter setting.
     for (j in 1:ns)

diff --git a/varbvs-R/R/predict.varbvs.R b/varbvs-R/R/predict.varbvs.R
@@ -88,6 +88,5 @@ predict.varbvs <-
 varbvs.linear.predictors <- function (X, Z, family, mu.cov, alpha, mu) {
   ns <- ncol(alpha)
   Y  <- Z %*% mu.cov + X %*% (alpha*mu)
-  colnames(Y) <- paste0("theta_",1:ns)
   return(Y)
 }
diff --git a/varbvs-R/R/varbvs.R b/varbvs-R/R/varbvs.R
@@ -425,6 +425,7 @@ varbvs <- function (X, Z, y, family = c("gaussian","binomial"), sigma, sa,
   }
 
   # Add names to some of the outputs.
+  hyper.labels                <- paste("theta",1:ns,sep = "_")
   rownames(fit$alpha)         <- colnames(X)
   rownames(fit$mu)            <- colnames(X)
   rownames(fit$s)             <- colnames(X)
@@ -433,18 +434,22 @@ varbvs <- function (X, Z, y, family = c("gaussian","binomial"), sigma, sa,
   rownames(fit$mu.cov)        <- colnames(Z)
   names(fit$beta.cov)         <- colnames(Z)
   rownames(fit$fitted.values) <- rownames(X)
-  colnames(fit$mu.cov)        <- paste("theta",1:ns,sep = "_")
-  colnames(fit$alpha)         <- paste("theta",1:ns,sep = "_")
-  colnames(fit$mu)            <- paste("theta",1:ns,sep = "_")
-  colnames(fit$s)             <- paste("theta",1:ns,sep = "_")
+  colnames(fit$mu.cov)        <- hyper.labels
+  colnames(fit$alpha)         <- hyper.labels
+  colnames(fit$mu)            <- hyper.labels
+  colnames(fit$s)             <- hyper.labels
+  colnames(fit$fitted.values) <- hyper.labels
   if (family == "gaussian") {
     rownames(fit$residuals) <- rownames(X)
-    colnames(fit$pve)       <- paste("theta",1:ns,sep = "_")
+    colnames(fit$residuals) <- hyper.labels
+    colnames(fit$pve)       <- hyper.labels
   } else {
-    rownames(fit$eta) <- rownames(X)
-    colnames(fit$eta) <- paste("theta",1:ns,sep = "_")
+    rownames(fit$eta)                <- rownames(X)
+    colnames(fit$eta)                <- hyper.labels
     rownames(fit$residuals$deviance) <- rownames(X)
     rownames(fit$residuals$response) <- rownames(X)
+    colnames(fit$residuals$deviance) <- hyper.labels
+    colnames(fit$residuals$response) <- hyper.labels
   }
   if (prior.same)
     fit$logodds <- c(fit$logodds)

diff --git a/varbvs-R/R/varbvs.properties.R b/varbvs-R/R/varbvs.properties.R
@@ -45,11 +45,9 @@ coef.varbvs <- function (object, ...) {
   ns <- length(object$w)
   if (ns == 1)
     out <- with(object,rbind(mu.cov,alpha*mu))
-  else {
+  else
     out <- with(object,rbind(cbind(mu.cov,beta.cov),
                              cbind(alpha*mu,beta)))
-    colnames(out) <- c(paste0("theta_",1:ns),"averaged")
-  }
   return(out)
 }