inst/informal_test.R

In ms609/inapplicable: Inapplicable data in parsimony analysis

setwd('../R')
dyn.load('../src/fitch.dll')
library('phangorn')
source('prepare_data.R')
source('fitch.R')
library('testthat')
test_dir('../tests/testthat')

library(devtools)
#install_github("TGuillerme/Inapp")
library(Inapp)
tree <- read.tree(text='((((((a, b), c), d), e), f), (g, (h, (i, (j, (k, l))))));')
mp <- morphyData <- StringToMorphy((data_string<-'1??--??--100'), tree$tip)
plot.states.matrix(apply.reconstruction(tree, data_string, passes = 4, 'NA'),counts=c(1,2), show.labels = c(1,2))

result <- InapplicableFitch(tree, mp)
result
nodes <- (length(tree$tip) + 1):(2 * length(tree$tip) - 1)

dyn.unload('../src/fitch.dll')



#load('../data/SigSut.RData')

#phy <- SigSut.phy
#tree <- rtree(length(phy), tip.label = names(phy), br=NULL)