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### R BASICS WORKSHOP                                                        ###
### EXERCISE 4.1: Opening and Saving Data Tables                             ###
###                                                                          ###
### Center for Conservation and Sustainable Development                      ###
### Missouri Botanical Garden                                                ###
### Website: rbasicsworkshop.weebly.com                                      ###
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## OBJECTIVE:
## In this exercise, you will practice data tables in R, and saving them into
## files.


getwd()
# With this command, you find what is the current working directory. This is the
# folder in your computer that R uses for default to read and write files.

# This means that if you do not provide an folder address to the opening/saving
# functions, R will assume the files are or need to be in the working directory.


# To change the working directory, you can use the "file" tab in PCs,
# the "Session" tab in Rstudio or the "some other place" in Macs.

# Alternatively, you can use the function 'setwd'. To give an address to this
# (and other functions), you must provide a character string similar to this:
# "Folder1/folder2/folder3"


## TASK 1. Change the working directory in your R session to a folder you want
## to use.


# The main function to open a data table in R is read.table. The files that can
# be opened by this function must text files, typically of extensions '.txt',
# '.csv' or '.dat'.


## TASK 2. Using the function read.table, open the files
## 'NeotropicoOccidente_COL.txt' and 'NeotropicoOccidente_IGM2.txt'.
## Name the resulting objects "col" and "igm2". Note that these are
## comma-separated text files, and that the first row represents column names.


## TASK 3. Check the number of columns and rows of the objects that you just
## created with the contents of the files. Also, check what type of object
## "col" and "igm2" are.

## If you see that there is only one column, then you opened the file
## incorrectly.


plot(igm2$PETmin, igm2$TOPOG)
# Now that the files are open, you can do things with them. For example, this
# Makes a plot of minimum potential evapo-transpiration (PETmin) against
# topography in the Neotropics.

plot(igm2$Lat, igm2$PETmin)
# This one makes a figure showing the latitudinal variation in PETmin.


# Now, lets suppose that you want to extract the residuals of a regression
# between PETmin and latitude, and save them into a file.

lm.results <- lm(igm2$PETmin~igm2$Lat+I(igm2$Lat^2))
lm.residuals <- residuals(lm.results)
# This runs a polynomial regression, and then extracts the residuals into an
# object named "lm.residuals"


## TASK 4. Use the function 'write.table' to save the object 'lm.residuals' into
## a tab-separated text file in your working directory. Name the file
## 'RegressionResiduals.txt".


## TASK 5. Open the file 'AdultLiteracy.xslx'. Save the contents of the
## file in an object of any name. Note here that the original files is an excel
## file. This means you first need to open it with excel, then save it as a text
## file, then use 'read.table' to open it in R.


## TASK 6. Open any other data table you have in your computer, maybe one with
## your own data.






















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### TASK SOLUTIONS #############################################################
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## TASK 1 ##
setwd('Address/goes/here') # Numeric vector


## TASK 2 ##
## There are three main ways to do this:

## 1
col <- read.table(file="NeotropicoOccidente_COL.txt", header=TRUE, sep=",")
igm2 <- read.table(file="NeotropicoOccidente_IGM2.txt", header=TRUE, sep=",")

## 2
col <- read.table(file=file.choose(), header=TRUE, sep=",")
igm2 <- read.table(file=file.choose(), header=TRUE, sep=",")

## 3
col <- read.table(file="folder1/folder2/folder3/NeotropicoOccidente_COL.txt",
  header=TRUE, sep=",")
igm2 <- read.table(file="folder1/folder2/folder3/NeotropicoOccidente_IGM2.txt",
  header=TRUE, sep=",")


## TASK 3 ##
dim(col)
dim(igm2)

class(col)
class(igm2)


## TASK 4 ##
## There are two main ways to do this:

## 1
write.table(x=lm.residuals, file="RegressionResiduals.txt", sep="\t")

## 2
write.table(x=lm.residuals, file="folder1/folder2/RegressionResiduals.txt", sep="\t")


## TASK 5 ##
## No solution here, sorry! :)


## TASK 6 ##
## No solution here, sorry! :)