From 8ee93cdd77ef3092aed411c3ce6db1f03a8b7d46 Mon Sep 17 00:00:00 2001
From: Christian Roever <christian.roever@med.uni-goettingen.de>
Date: Thu, 29 Sep 2022 12:50:07 +0200
Subject: [PATCH] adapted to new forestplot package version
---
DESCRIPTION | 4 ++--
R/bayesmeta.R | 9 ++++-----
R/bmr.R | 4 ++--
man/bayesmeta-package.Rd | 4 ++--
man/forestplot.bayesmeta.Rd | 2 +-
man/forestplot.bmr.Rd | 2 +-
man/forestplot.escalc.Rd | 4 ++--
7 files changed, 14 insertions(+), 15 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 87cb7a5..bf87954 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: bayesmeta
Type: Package
Title: Bayesian Random-Effects Meta-Analysis and Meta-Regression
-Version: 3.1
-Date: 2022-09-14
+Version: 3.2
+Date: 2022-09-29
Authors@R: c(person(given="Christian", family="Roever", role=c("aut","cre"),
email="christian.roever@med.uni-goettingen.de",
comment=c(ORCID="0000-0002-6911-698X")),
diff --git a/R/bayesmeta.R b/R/bayesmeta.R
index f5fac88..dfbf1f7 100644
--- a/R/bayesmeta.R
+++ b/R/bayesmeta.R
@@ -2213,7 +2213,7 @@ forestplot.bayesmeta <- function(x, labeltext,
heterogeneity = TRUE,
digits = 2,
plot = TRUE,
- fn.ci_norm, fn.ci_sum, col, legend, boxsize, ...)
+ fn.ci_norm, fn.ci_sum, col, legend=NULL, boxsize, ...)
#
# ARGUMENTS:
# x : a "bayesmeta" object.
@@ -2330,7 +2330,7 @@ forestplot.bayesmeta <- function(x, labeltext,
boxsize <- c(rep(0.25,x$k+1), 0.4)
if (prediction) boxsize <- c(boxsize, 0.2)
}
- if (shrinkage && missing(legend))
+ if (shrinkage && is.null(legend))
legend <- c("quoted estimate", "shrinkage estimate")
# specify data for plotting:
if (shrinkage) { # (show shrinkage intervals)
@@ -2387,7 +2387,7 @@ forestplot.escalc <- function(x, labeltext,
exponentiate = FALSE,
digits = 2,
plot = TRUE,
- fn.ci_norm, fn.ci_sum, col, legend, boxsize, ...)
+ fn.ci_norm, fn.ci_sum, col, boxsize, ...)
#
# ARGUMENTS:
# x : a "bayesmeta" object.
@@ -2516,8 +2516,7 @@ forestplot.escalc <- function(x, labeltext,
fn.ci_norm = fn.ci_norm,
fn.ci_sum = fn.ci_sum,
col = col,
- boxsize = boxsize,
- legend = legend, ...)
+ boxsize = boxsize, ...)
plot(fp)
}
invisible(list("data" = ma.dat[-1,],
diff --git a/R/bmr.R b/R/bmr.R
index 2695595..515f403 100644
--- a/R/bmr.R
+++ b/R/bmr.R
@@ -1960,7 +1960,7 @@ forestplot.bmr <- function(x,
digits = 2,
decplaces.X,
plot = TRUE,
- fn.ci_norm, fn.ci_sum, col, legend, boxsize, ...)
+ fn.ci_norm, fn.ci_sum, col, legend=NULL, boxsize, ...)
# ARGUMENTS:
# x : a "bmr" object.
# X.mean : regressor matrix for summary (mean) estimate(s)
@@ -2165,7 +2165,7 @@ forestplot.bmr <- function(x,
if (missing(boxsize)) {
boxsize <- c(rep(0.25,x$k+1), rep(0.4, meanNumber), rep(0.2, predNumber))
}
- if (shrinkage && missing(legend))
+ if (shrinkage && is.null(legend))
legend <- c("quoted estimate", "shrinkage estimate")
# specify data for plotting:
if (shrinkage) { # (show shrinkage intervals)
diff --git a/man/bayesmeta-package.Rd b/man/bayesmeta-package.Rd
index c691116..6e4725e 100644
--- a/man/bayesmeta-package.Rd
+++ b/man/bayesmeta-package.Rd
@@ -15,8 +15,8 @@
\tabular{ll}{
Package: \tab bayesmeta\cr
Type: \tab Package\cr
- Version: \tab 3.1\cr
- Date: \tab 2022-09-14\cr
+ Version: \tab 3.2\cr
+ Date: \tab 2022-09-29\cr
License: \tab GPL (>=2)
}
The main functionality is provided by the \code{\link{bayesmeta}()}
diff --git a/man/forestplot.bayesmeta.Rd b/man/forestplot.bayesmeta.Rd
index 48a3cd3..bdc0ce9 100644
--- a/man/forestplot.bayesmeta.Rd
+++ b/man/forestplot.bayesmeta.Rd
@@ -13,7 +13,7 @@
\method{forestplot}{bayesmeta}(x, labeltext, exponentiate=FALSE,
prediction=TRUE, shrinkage=TRUE, heterogeneity=TRUE,
digits=2, plot=TRUE,
- fn.ci_norm, fn.ci_sum, col, legend, boxsize, ...)
+ fn.ci_norm, fn.ci_sum, col, legend=NULL, boxsize, ...)
}
\arguments{
\item{x}{
diff --git a/man/forestplot.bmr.Rd b/man/forestplot.bmr.Rd
index 9bf2e38..baa9020 100644
--- a/man/forestplot.bmr.Rd
+++ b/man/forestplot.bmr.Rd
@@ -14,7 +14,7 @@
labeltext, exponentiate=FALSE,
shrinkage=TRUE, heterogeneity=TRUE,
digits=2, decplaces.X, plot=TRUE,
- fn.ci_norm, fn.ci_sum, col, legend, boxsize, ...)
+ fn.ci_norm, fn.ci_sum, col, legend=NULL, boxsize, ...)
}
\arguments{
\item{x}{
diff --git a/man/forestplot.escalc.Rd b/man/forestplot.escalc.Rd
index 388d576..721288b 100644
--- a/man/forestplot.escalc.Rd
+++ b/man/forestplot.escalc.Rd
@@ -11,7 +11,7 @@
\usage{
\method{forestplot}{escalc}(x, labeltext, exponentiate=FALSE,
digits=2, plot=TRUE,
- fn.ci_norm, fn.ci_sum, col, legend, boxsize, ...)
+ fn.ci_norm, fn.ci_sum, col, boxsize, ...)
}
\arguments{
\item{x}{
@@ -33,7 +33,7 @@
\item{plot}{
a logical flag indicating whether to actually generate a plot.
}
- \item{fn.ci_norm, fn.ci_sum, col, legend, boxsize, \ldots}{
+ \item{fn.ci_norm, fn.ci_sum, col, boxsize, \ldots}{
other arguments passed on to the
\pkg{forestplot} package's \code{\link[forestplot]{forestplot}}
function (see also the help there).
--
GitLab