From add21d5379beeb4d35daea0d0e0476a414843e51 Mon Sep 17 00:00:00 2001
From: ryanchrist <ryan.christ7@gmail.com>
Date: Mon, 23 Sep 2024 12:14:11 -0500
Subject: [PATCH] Introducing tests for CladeMat

---
 tests/testthat/test-CladeMat.R | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 tests/testthat/test-CladeMat.R

diff --git a/tests/testthat/test-CladeMat.R b/tests/testthat/test-CladeMat.R
new file mode 100644
index 0000000..842bd2e
--- /dev/null
+++ b/tests/testthat/test-CladeMat.R
@@ -0,0 +1,22 @@
+test_that("CladeMat Matches GoldMaster CladeMat", {
+
+  CacheHaplotypes(SmallHaps)
+  map <- SmallMap
+
+  target.idx <- floor(L()/2)
+  pars <- Parameters(CalcRho(diff(map),s = 0.01),mu = 0.0001) # specify HMM parameters
+  fwd <- MakeForwardTable(pars)
+  bck <- MakeBackwardTable(pars)
+  Forward(fwd, pars, target.idx)
+  Backward(bck, pars, target.idx)
+
+  unit.dist <- -log(pars$pars$mu)
+  thresh <- 0.2
+
+  M <- matrix(0,N()/2,N()/2)
+  neigh <- CladeMat(fwd,bck,M,unit.dist = unit.dist, thresh = thresh ,max1var = TRUE)
+
+  M2 <- kalis:::CladeMat.GM(fwd,bck,unit.dist = unit.dist, thresh = thresh)
+
+  expect_equal(M, M2)
+})