Nothing
context("PRESENT");
var.cov <- c("sodium", "lvef", "any.vasodilator.use");
var.resp <- "y";
var.trt <- "trt";
var.censor <- "censor";
resptype <- "survival";
var.cov <- c("sodium", "lvef", "any.vasodilator.use");
var.estvar <- c("Estimate", "Variance");
subgrp.effect <- bzGetSubgrpRaw(solvd.sub,
var.resp = var.resp,
var.trt = var.trt,
var.cov = var.cov,
var.censor = var.censor,
resptype = resptype);
rst.sr <- bzCallStan("sr",
dat.sub=subgrp.effect,
var.estvar = var.estvar,
var.cov = var.cov,
par.pri = c(B=1000, C=1000),
chains=4,
iter=40,
warmup=20, seed=1000);
rst.nse <- bzCallStan("nse",
dat.sub=subgrp.effect,
var.estvar = var.estvar,
var.cov = var.cov,
par.pri = c(B=1000),
chains=4,
iter=40,
warmup=20, seed=1000);
test_that("select subgroup", {
mus <- array(1:100, dim=c(20,5));
expect_identical(get.sel.subgrp(mus), as.numeric(1:5));
expect_identical(get.sel.subgrp(mus, "A"), as.numeric(1:5));
expect_identical(get.sel.subgrp(mus, 1:10), as.numeric(1:5));
expect_identical(get.sel.subgrp(mus, 7:9), as.numeric(1:5));
})
test_that("get all mus", {
mus.1 <- get.all.mus(rst.sr);
mus.2 <- get.all.mus(rst.sr, sel.grps = 1:2);
mus.3 <- get.all.mus(rst.sr, sel.grps = 1:2, ref.stan.rst = rst.nse);
mus.4 <- get.all.mus(rst.sr, sel.grps = 1:2,
ref.stan.rst = rst.nse, ref.sel.grps = 3:4);
expect_equal(nrow(mus.1), 80);
expect_equal(ncol(mus.1), 8);
expect_equal(nrow(mus.2), 80);
expect_equal(ncol(mus.2), 2);
expect_identical(colnames(mus.2), c("Subgroup 1", "Subgroup 2"));
expect_equal(nrow(mus.3), 80);
expect_equal(ncol(mus.3), 3);
expect_identical(colnames(mus.3), c("Subgroup 1", "Subgroup 2", "No subgroup effect(1)"));
expect_equal(nrow(mus.4), 80);
expect_equal(ncol(mus.4), 4);
expect_identical(colnames(mus.4),
c("Subgroup 1", "Subgroup 2", "No subgroup effect(3)", "No subgroup effect(4)"));
})
test_that("beanz comparison", {
bz.1 <- bzSummaryComp(rst.sr, sel.grps=NULL, cut=0, digits=3);
bz.2 <- bzSummaryComp(rst.sr, sel.grps=c(1:3), cut=0, digits=3);
bz.3 <- bzSummaryComp(rst.sr, sel.grps=c(1:3), cut=0.1, digits=3);
expect_equal(nrow(bz.1), 28);
expect_equal(nrow(bz.2), 3);
expect_equal(colnames(bz.3)[9], "ProbLT0.1");
expect_true(is.data.frame(bz.3));
})
test_that("beanz summary", {
bz.1 <- bzSummary(rst.sr, sel.grps=NULL, cut=0, digits=3);
bz.2 <- bzSummary(rst.sr, sel.grps=c(1:3), cut=0.1, digits=3);
bz.3 <- bzSummary(rst.sr, sel.grps=c(1:3), ref.stan.rst = rst.nse);
expect_equal(nrow(bz.1), 8);
expect_equal(ncol(bz.1), 9);
expect_equal(nrow(bz.2), 3);
expect_equal(colnames(bz.2)[9], "ProbLT0.1");
expect_true(is.data.frame(bz.2));
expect_equal(nrow(bz.3), 4);
})
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