[Genabel-commits] r1565 - pkg/MetABEL/R

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2014-01-26 23:31:35 +0100 (Sun, 26 Jan 2014)
New Revision: 1565

Modified:
   pkg/MetABEL/R/forestplot.R
Log:
Fix NOTEs when running R CMD check (lower=F in call to pchisq() should be lower.tail=FALSE).
Also a few minor other fixes of arguments and two error messages.


Modified: pkg/MetABEL/R/forestplot.R
===================================================================
--- pkg/MetABEL/R/forestplot.R	2014-01-26 22:28:08 UTC (rev 1564)
+++ pkg/MetABEL/R/forestplot.R	2014-01-26 22:31:35 UTC (rev 1565)
@@ -14,11 +14,11 @@
         mse       <- sqrt(invsumw2)
         npop      <- length(estimate)
         estimate[npop+1] <- mestimate
-        se[npop+1]     <- mse
-        labels[npop+1] <- "Pooled"
+        se[npop+1]       <- mse
+        labels[npop+1]   <- "Pooled"
         chi2 <- round(estimate * estimate / (se * se), 2)
         p <- sprintf("%5.1e", pchisq(estimate * estimate / (se * se),
-                                     1, lower=F))
+                                     1, lower.tail=FALSE))
         ##	p[as.numeric(p)<0] <- "<1.e-16"
 
         if (CI > 1 || CI < 0) {
@@ -44,17 +44,17 @@
         maxv <- max(upper)
         maxv <- maxv + abs(maxv / 10)
         maxv <- max(rbnd, maxv)
-        hgt <- (length(estimate) + 1) * del
+        hgt  <- (length(estimate) + 1) * del
 
-        if (any(is.na(estimate))) stop("estimate got NAs")
-        if (any(is.na(se))) stop("se got NAs")
+        if (any(is.na(estimate))) stop("estimate contains NAs")
+        if (any(is.na(se))) stop("se contains NAs")
 
         plot(x=c(cntr, cntr), y=c(0, hgt), xlim=c(minv, maxv),
-             ylim=c(0, hgt), typ="l", lwd=2, xlab="Beta", ...)
+             ylim=c(0, hgt), type="l", lwd=2, xlab="Beta", ...)
 
         for (i in c(1:(length(estimate)-1))) {
             points(x=c(lower[i], upper[i]), y=c((i) * del, (i) * del),
-                   typ="l", lwd=2)
+                   type="l", lwd=2)
             points(x=c(estimate[i]), y=c((i) * del), pch=19, cex=1)
             text(estimate[i], i * del + 1,
                  paste(labels[i], " (Chi2=", chi2[i], ", P=", p[i],
@@ -65,16 +65,16 @@
         for (i in c(length(estimate))) {
             points(x=c(lower[i], estimate[i]),
                    y=c((i) * del, (i) * del + hoff),
-                   typ="l", lwd=2)
+                   type="l", lwd=2)
             points(x=c(estimate[i], upper[i]),
                    y=c((i) * del + hoff, (i) * del),
-                   typ="l", lwd=2)
+                   type="l", lwd=2)
             points(x=c(upper[i], estimate[i]),
                    y=c((i) * del, (i) * del - hoff),
-                   typ="l", lwd=2)
+                   type="l", lwd=2)
             points(x=c(lower[i], estimate[i]),
                    y=c((i) * del, (i) * del - hoff),
-                   typ="l", lwd=2)
+                   type="l", lwd=2)
             text(estimate[i], i * del + 5,
                  paste(labels[i], " (Chi2=", chi2[i], ", P=", p[i],
                        ")", sep=""),