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### R BASICS WORKSHOP                                                        ###
### EXERCISE 6.3: Object manipulation, indexing a phylogeny                  ### 
###                                                                          ###
### Center for Conservation and Sustainable Development                      ###
### Missouri Botanical Garden                                                ###
### Website: rbasicsworkshop.weebly.com                                      ### 
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### INTRODUCTION ############################################## ##################
# In this exercise you will explore the structure of objects of class "phylo",
# used to represent phylogenies in R. You will manipulate these objects and produce
# phylogeny graphs.

# TASK 1 ##
# Install package "ape" if you haven't already
install.packages("ape")
# Load "ape"
library(ape)

## TASK 2 ##
# Read the file "tree_central_ages.new" (available on the workshop page); this file contains
# a dated phylogeny (timeline) of all plant families (in "Newick" format). Make sure
# to set your working directory to indicate where the "tree_central_ages.new" file is.
setwd("C:/_transfer/R_Basics_Workshop/St_Louis_June_2023/DataSets") #Ivan's working directory
phylo.fam.world <- read.tree("tree_central_ages.new")

## TASK 3 ##
# plot the phylogeny
plot(phylo.fam.world, type="fan", cex=0.2)

## TASK 4 ##
# Examine the properties of object "phylo.fam.world"
class(phylo.fam.world)
attributes(phylo.fam.world)
str(phylo.fam.world) #note that objects of class "phylo" are lists

## TASK 5 ##
# Read the section on objects of class "phylo" on page 30 of Paradis (2012, Analysis
# of phylogenetics and evolution with R", available on the workshop page:
# http://rbasicsworkshop.weebly.com/books.html).
# Use the "$" operator to explore the components of the phylo class: "edge",
# "edge.length", "tip.label", "Nnode", "node.lable", "root.edge". For example:
phylo.fam.world$edge
# note that you can use numeric indexing on each component, for example:
phylo.fam.world$edge[1:7,]

## TASK 6 ##
# Examine the object classes returned by indexing with single and double square brackets:
class(phylo.fam.world[1])
class(phylo.fam.world[[1]])
class(phylo.fam.world[2])
class(phylo.fam.world[[2]])
class(phylo.fam.world[3])
class(phylo.fam.world[[3]])

## TASK 7 ##
# Examine the names of the phylogeny tips
phylo.fam.world$tip.label
# study the following code, it is used to edit the names of the phylogeny tips,
# changing the first letter from lowercase to uppercase; to understand the code, visit the help
# pages for functions "paste", "toupper", and "substring":
phylo.fam.world$tip.label <- paste(toupper(substring(phylo.fam.world$tip.label, 1, 1)), substring(phylo.fam.world$tip.label, 2), sep= "")
#examine the result
phylo.fam.world$tip.label

## TASK 8 ##
# Study the following code carefully. Visit the help page for function "drop.tip".
# Use this function to plot a selection of phylogeny tips, for example:
phylo.fam.world.1 <- drop.tip(phylo.fam.world, 25:476, subtree=TRUE)
plot(phylo.fam.world.1, type="p", cex=0.8, show.node.label=F)
axisPhylo(1)
phylo.fam.world.2 <- drop.tip(phylo.fam.world, c(1:24,51:476), subtree=TRUE)
plot(as.phylo(phylo.fam.world.2), type="p", cex=0.8,show.node.label=F)
axisPhylo(1)
phylo.fam.world.3 <- drop.tip(phylo.fam.world, c(1:50,70:476), subtree=TRUE)
plot(as.phylo(phylo.fam.world.3), type="p", cex=0.8,show.node.label=F)
axisPhylo(1)
# Write your own code for other similar cases