From 772c04c7d8f92ee284d68e5d002e951dd8efba54 Mon Sep 17 00:00:00 2001
From: Christian Roever <christian.roever@med.uni-goettingen.de>
Date: Wed, 14 Sep 2022 09:20:22 +0200
Subject: [PATCH] fixed 'class()' calls
---
R/bayesmeta.R | 4 ++--
R/bmr.R | 56 +++++++++++++++++++++++++++++++++++++--------------
2 files changed, 43 insertions(+), 17 deletions(-)
diff --git a/R/bayesmeta.R b/R/bayesmeta.R
index c2e4d4e..f5fac88 100644
--- a/R/bayesmeta.R
+++ b/R/bayesmeta.R
@@ -792,7 +792,7 @@ bayesmeta.default <- function(y, sigma, labels=names(y),
c("tau","mu","theta")))
expectation <- try(integrate(function(x)return(dposterior(x)*x), lower=0, upper=Inf,
rel.tol=rel.tol.integrate, abs.tol=abs.tol.integrate)$value, silent=TRUE)
- if (class(expectation)=="try-error") {
+ if (inherits(expectation, "try-error")) {
expectation <- NA
variance <- NA
}
@@ -800,7 +800,7 @@ bayesmeta.default <- function(y, sigma, labels=names(y),
variance <- try(integrate(function(x)return(dposterior(x)*(x-expectation)^2), lower=0, upper=Inf,
rel.tol=rel.tol.integrate, abs.tol=abs.tol.integrate)$value,
silent=TRUE)
- if (class(variance)=="try-error")
+ if (inherits(variance, "try-error"))
variance <- NA
}
sumstats[c("mean","sd"),"tau"] <- c(expectation, sqrt(variance))
diff --git a/R/bmr.R b/R/bmr.R
index 4fab5fc..2695595 100644
--- a/R/bmr.R
+++ b/R/bmr.R
@@ -63,9 +63,15 @@ beta.convert <- function(beta, which.beta, d, betanames)
if (missing(which.beta)) { # default "which.beta"
betaIdx <- 1:d
} else { # try to make sense of "which.beta" argument; general sanity checks:
+ #if (!is.vector(which.beta)
+ # || (!is.element(class(which.beta),
+ # c("numeric", "integer", "logical", "character"))
+ # | (length(which.beta) > d))) {
+ # warning("Cannot make sense of \"which.beta\" argument (1).")
+ #}
if (!is.vector(which.beta)
- || (!is.element(class(which.beta),
- c("numeric", "integer", "logical", "character"))
+ || (!inherits(which.beta,
+ c("numeric", "integer", "logical", "character"))
| (length(which.beta) > d))) {
warning("Cannot make sense of \"which.beta\" argument (1).")
}
@@ -430,13 +436,23 @@ bmr.default <- function(y, sigma, labels = names(y),
missing(beta) || (is.matrix(beta) | is.data.frame(beta) | is.vector(beta)))
if (!missing(beta)) {
if (!missing(which.beta)) { # general sanity checks
+ #if (!is.vector(which.beta)
+ # || (!is.element(class(which.beta),
+ # c("numeric", "integer", "logical", "character"))
+ # | ((class(which.beta)=="logical")
+ # && ((length(which.beta) != d) | (sum(which.beta)!=1)))
+ # | ((is.element(class(which.beta),
+ # c("numeric", "integer", "character"))
+ # & (length(which.beta) != 1))))) {
+ # warning("Cannot make sense of \"which.beta\" argument (1).")
+ #}
if (!is.vector(which.beta)
- || (!is.element(class(which.beta),
- c("numeric", "integer", "logical", "character"))
- | ((class(which.beta)=="logical")
+ || (!inherits(which.beta,
+ c("numeric", "integer", "logical", "character"))
+ | (inherits(which.beta, "logical")
&& ((length(which.beta) != d) | (sum(which.beta)!=1)))
- | ((is.element(class(which.beta),
- c("numeric", "integer", "character"))
+ | ((inherits(which.beta,
+ c("numeric", "integer", "character"))
& (length(which.beta) != 1))))) {
warning("Cannot make sense of \"which.beta\" argument (1).")
}
@@ -517,13 +533,23 @@ bmr.default <- function(y, sigma, labels = names(y),
missing(beta.p) || (is.matrix(beta.p) | is.data.frame(beta.p) | is.vector(beta.p)))
if (!missing(beta.p)) {
if (!missing(which.beta)) { # general sanity checks
+ #if (!is.vector(which.beta)
+ # || (!is.element(class(which.beta),
+ # c("numeric", "integer", "logical", "character"))
+ # | ((class(which.beta)=="logical")
+ # & ((length(which.beta) != d) | (sum(which.beta) != 1)))
+ # | ((is.element(class(which.beta),
+ # c("numeric", "integer", "character"))
+ # & (length(which.beta) != 1))))) {
+ # warning("Cannot make sense of \"which.beta\" argument (1).")
+ #}
if (!is.vector(which.beta)
- || (!is.element(class(which.beta),
- c("numeric", "integer", "logical", "character"))
- | ((class(which.beta)=="logical")
- & ((length(which.beta) != d) | (sum(which.beta) != 1)))
- | ((is.element(class(which.beta),
- c("numeric", "integer", "character"))
+ || (!inherits(which.beta,
+ c("numeric", "integer", "logical", "character"))
+ | (inherits(which.beta,"logical")
+ & ((length(which.beta) != d) | (sum(which.beta) != 1)))
+ | ((inherits(which.beta,
+ c("numeric", "integer", "character"))
& (length(which.beta) != 1))))) {
warning("Cannot make sense of \"which.beta\" argument (1).")
}
@@ -1248,7 +1274,7 @@ bmr.default <- function(y, sigma, labels = names(y),
lower=0, upper=Inf,
rel.tol=rel.tol.integrate,
abs.tol=abs.tol.integrate)$value, silent=TRUE)
- if (class(expectation)=="try-error") {
+ if (inherits(expectation,"try-error")) {
expectation <- NA
variance <- NA
} else {
@@ -1256,7 +1282,7 @@ bmr.default <- function(y, sigma, labels = names(y),
lower=0, upper=Inf,
rel.tol=rel.tol.integrate,
abs.tol=abs.tol.integrate)$value, silent=TRUE)
- if (class(variance)=="try-error")
+ if (inherits(variance, "try-error"))
variance <- NA
}
sumstats[c("mean","sd"), "tau"] <- c(expectation, sqrt(variance))
--
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