Nothing
## ----load-library, message=FALSE----------------------------------------------
library("TreeSearch")
## ----rng-version--------------------------------------------------------------
# Set a random seed so that random functions in this document are reproducible
suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
set.seed(888)
## ----load-longrich-data-------------------------------------------------------
data(congreveLamsdellMatrices)
myMatrix <- congreveLamsdellMatrices[[10]]
## ----addition-tree------------------------------------------------------------
additionTree <- AdditionTree(myMatrix, concavity = "profile")
TreeLength(additionTree, myMatrix, "profile")
par(mar = rep(0.25, 4), cex = 0.75) # make plot easier to read
plot(additionTree)
## ----random-tree--------------------------------------------------------------
randomTree <- TreeTools::RandomTree(myMatrix, root = TRUE)
TreeLength(randomTree, myMatrix, "profile")
njTree <- TreeTools::NJTree(myMatrix)
TreeLength(njTree, myMatrix, "profile")
## ----starting-score, message = FALSE------------------------------------------
betterTrees <- MaximizeParsimony(myMatrix, additionTree, concavity = "profile",
ratchIter = 3, tbrIter = 3, maxHits = 8)
## ----ratchet-search-results---------------------------------------------------
TreeLength(betterTrees[[1]], myMatrix, "profile")
par(mar = rep(0.25, 4), cex = 0.75) # make plot easier to read
plot(ape::consensus(betterTrees))
## ----suboptimal-sampling, message = FALSE-------------------------------------
suboptimals <- MaximizeParsimony(myMatrix, betterTrees, tolerance = 3,
ratchIter = 2, tbrIter = 3,
maxHits = 25,
concavity = "profile")
## ----plot-suboptimal-consensus------------------------------------------------
par(mar = rep(0.25, 4), cex = 0.75)
table(signif(TreeLength(suboptimals, myMatrix, "profile")))
plot(ape::consensus(suboptimals))
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.