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### library(metafor); library(testthat); Sys.setenv(NOT_CRAN="true")
context("Checking misc: funnel() functions")
source("settings.r")
test_that("funnel() works correctly.", {
expect_equivalent(TRUE, TRUE) # avoid 'Empty test' message
skip_on_cran()
### simulate a large meta-analytic dataset (correlations with rho = 0.0)
### with no heterogeneity or publication bias; then try out different
### versions of the funnel plot
gencor <- function(rhoi, ni) {
x1 <- rnorm(ni, mean=0, sd=1)
x2 <- rnorm(ni, mean=0, sd=1)
x3 <- rhoi*x1 + sqrt(1-rhoi^2)*x2
cor(x1, x3)
}
set.seed(78123)
k <- 200 ### number of studies to simulate
ni <- round(rchisq(k, df=2) * 20 + 20) ### simulate sample sizes (skewed distribution)
ri <- mapply(gencor, rep(0.0,k), ni) ### simulate correlations
dat <- escalc(measure="ZCOR", ri=ri, ni=ni) ### compute r-to-z transformed correlations
res <- rma(yi, vi, data=dat, method="EE")
png(filename="images/test_misc_funnel_1_test.png", res=200, width=1800, height=2000, type="cairo")
par(mfrow=c(5,2), mar=c(5,4,1,1), cex=0.5)
funnel(res, yaxis="sei")
funnel(res, yaxis="vi")
funnel(res, yaxis="seinv")
funnel(res, yaxis="vinv")
funnel(res, yaxis="ni")
funnel(res, yaxis="ninv")
funnel(res, yaxis="sqrtni")
funnel(res, yaxis="sqrtninv")
funnel(res, yaxis="lni")
funnel(res, yaxis="wi")
dev.off()
expect_true(.vistest("images/test_misc_funnel_1_test.png", "images/test_misc_funnel_1.png"))
png(filename="images/test_misc_funnel_2_test.png", res=200, width=1800, height=2000, type="cairo")
par(mfrow=c(5,2), mar=c(5,4,1,1), cex=0.5)
funnel(dat$yi, dat$vi, yaxis="sei")
funnel(dat$yi, dat$vi, yaxis="vi")
funnel(dat$yi, dat$vi, yaxis="seinv")
funnel(dat$yi, dat$vi, yaxis="vinv")
funnel(dat$yi, dat$vi, yaxis="ni")
funnel(dat$yi, dat$vi, yaxis="ninv")
funnel(dat$yi, dat$vi, yaxis="sqrtni")
funnel(dat$yi, dat$vi, yaxis="sqrtninv")
funnel(dat$yi, dat$vi, yaxis="lni")
funnel(dat$yi, dat$vi, yaxis="wi")
dev.off()
expect_true(.vistest("images/test_misc_funnel_2_test.png", "images/test_misc_funnel_2.png"))
})
rm(list=ls())
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