To read data in R you need to specify the working directory
The working directory (wd) can be set with the function setwd()
The way you do this depends on the operating system (windows, mac, ubuntu)
08/04/2015
To read data in R you need to specify the working directory
The working directory (wd) can be set with the function setwd()
The way you do this depends on the operating system (windows, mac, ubuntu)
To find the location you can look at the properties of a file in that folder and copy it
Make sure you have forward-slash (/) between folder names
Do not include any file name in the folder directory name
The path to the folder should be quoted ("")
It is always better to copy/paste (less typos)
In windows it should be something like this
setwd("C:/location")
You can also do this (ONLY WINDOWS!)
setwd(choose.dir())
That should pop-up a window where you can choose the location
Should be something like this
setwd("/Users/yourname/..")
do not include whatever you have before "users" (like macintosh… )
setwd("~/Dropbox/2015 La Selva REU")
The example file name is "acoustic parameters song-cognition aug-15.csv"
download it from here http://marceloarayasalas.weebly.com/uploads/2/5/5/2/25524573/acoustic_parameters_song-cognition_aug-15.csv
First look at the files in the working directory to make sure you got the right name
list.files()
That should return a list of file names
If your working directory is "2015 La Selva REU" you should be able to see the .csv file in the list
To read the csv file:
ap<-read.csv("acoustic parameters song-cognition aug-15.csv")
Make sure the name is quoted
The name matches exactly (better to copy/paste)
Include the extension name (.csv or whatever it is)
We need to install the package "readxl"
install.packages(pkgs = "readxl")
Then we load the package (otherwise it is not available in you R environment)
library(readxl)
Now we can use the function read_excel() to read the file
First download this file: http://marceloarayasalas.weebly.com/uploads/2/5/5/2/25524573/acoustic_parameters_song-cognition_aug-15.xlsx
ap<-read_excel("acoustic parameters song-cognition aug-15.xlsx",
sheet = "Sheet1")
Notice that you need to specify the file name (including extension) and the excel sheet name
We should make sure that R is reading the data in the right format
To check the data we can use the function str()
str(ap)
That should return something like this:
## Classes 'tbl_df', 'tbl' and 'data.frame': 409 obs. of 24 variables: ## $ sound.files: chr "203.SUR.2014.4.10.8.10.WAV" "203.SUR.2014.4.10.8.10.WAV" "203.SUR.2014.4.10.8.10.WAV" "203.SUR.2014.4.10.8.10.WAV" ... ## $ selec : chr "1-1" "1-2" "1-3" "1-4" ... ## $ duration : num NA 0.128 0.133 0.124 0.131 ... ## $ meanfreq : num 6.36 6.5 6.57 6.56 6.57 ... ## $ sd : num 1.24 1.13 1.09 1.16 1.12 ... ## $ median : num 6.59 6.68 6.68 6.77 6.74 ... ## $ Q25 : num 5.95 6.09 6.14 6.21 6.12 ... ## $ Q75 : num 7.21 7.22 7.29 7.34 7.31 ... ## $ IQR : num 1.26 1.13 1.15 1.13 1.19 ... ## $ skew : num 2.43 2.47 2.16 2.63 1.97 ... ## $ kurt : num 9.26 10.24 8.03 11.58 6.5 ... ## $ sp.ent : num 0.898 0.886 0.889 0.893 0.891 ... ## $ sfm : num 0.445 0.388 0.378 0.421 0.394 ... ## $ mode : num 6.82 6.37 6.1 7.1 6.11 ... ## $ centroid : num 6.36 6.5 6.57 6.56 6.57 ... ## $ peakf : num 6.21 6.21 6.35 6.39 6.07 ... ## $ meanfun : num 5.37 5.91 5.92 6.11 5.77 ... ## $ minfun : num 2.286 2.182 1.116 2.286 0.262 ... ## $ maxfun : num 8 8 8 8 8 8 8 8 8 8 ... ## $ meandom : num 6.68 6.77 6.99 6.92 6.9 ... ## $ mindom : num 5.28 5.6 5.92 5.92 5.92 5.76 5.76 5.44 5.92 5.92 ... ## $ maxdom : num 7.84 7.84 7.68 8 8 7.68 7.84 8 7.68 7.84 ... ## $ dfrange : num 2.56 2.24 1.76 2.08 2.08 1.92 2.08 2.56 1.76 1.92 ... ## $ modindx : num 0.226 0.25 0.321 0.285 0.267 ...
The output tells you the type of object (data frame), the number of rows and columns and the name of the columns
On that ouput look at the type of vector for each column
Continuous variables should be read as numeric vectors
You can also look at the entire data frame with the function View()
View(ap)
For most plots and test you need to have continuous variables identified as numeric in R
If not, you will get lots of errors
For the sake of the example I am going to make a factor the variable "duration"
dur<-as.factor(ap$duration)
To convert that variable back to a numeric one you need to do this
dur<-as.numeric(as.character(dur))
You can have numeric variables read as factors if you add any text to one of the cells
For instance, if you add NODATA to empty cells
Is better to leave them empty
Now you can start graphing your data
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