
install.packages("phonTools")


library(phonTools)

# Load audio file
sound <- loadsound("Mono_XC386310__Northern_Goshawk__Accipiter_gentilis.wav")

# Make 3 spectrograms
par(mfrow = c(3,1), mar = c(4,4,1,1))
spectrogram(sound)
spectrogram(sound, color = 'alternate')
spectrogram(sound, color = FALSE)


# This is a Comment because it is preceded by a # (hashtag)
x <- 5

# Lets print our variables to screen
print(x) # Note that comments can be written after a statement (but not before)

[1] 5


# This function returns the computer's current date and time 
Sys.time()

[1] "2020-12-28 16:47:33 AST"


# This function prints-to-screen its input
print("Hello world!")

[1] "Hello world!"


# This function prints-to-screen its input (i.e. first argument), but also rounds the output to "3" significant digits
print(2.797337826, digits=3)

[1] 2.8


builtins() # List all built-in functions
options()  # Set options to control how R computes & displays results

# General
print()      # Print to screen
?NA          # Help page on handling of missing data values
abs(x)       # The absolute value of "x"
append()     # Add elements to a vector
cat(x)       # Prints the arguments
cbind()      # Combine vectors by row/column (cf. "paste" in Unix)
diff(x)      # Returns suitably lagged and iterated differences
gl()         # Generate factors with the pattern of their levels
grep()       # Pattern matching
identical()  # Test if 2 objects are *exactly* equal
jitter()     # Add a small amount of noise to a numeric vector
julian()     # Return Julian date
length(x)    # Return no. of elements in vector x
mat.or.vec() # Create a matrix or vector
paste(x)     # Concatenate vectors after converting to character
range(x)     # Returns the minimum and maximum of x
rep(1,5)     # Repeat the number 1 five times
rev(x)       # List the elements of "x" in reverse order
seq(1,10,0.4)  # Generate a sequence (1 -> 10, spaced by 0.4)
sequence()     # Create a vector of sequences
sign(x)        # Returns the signs of the elements of x
sort(x)        # Sort the vector x
order(x)       # list sorted element numbers of x
tolower(),toupper()  # Convert string to lower/upper case letters
unique(x)      # Remove duplicate entries from vector
system("cmd")  # Execute "cmd" in operating system (outside of R)
floor(x), ceiling(x), round(x), signif(x), trunc(x)   # rounding functions
# Container objects
c(x)         # Combine values into a vector or List
vector()     # Produces a vector of given length and mode
matrix()     # Makes a matrix
data.frame() # Makes data frame

# Environment and working directory
ls()         # List objects in current environment
getwd()        # Return working directory
setwd()        # Set working directory
Sys.getenv(x)  # Get the value of the environment variable "x"
Sys.putenv(x)  # Set the value of the environment variable "x"
Sys.time()     # Return system time
Sys.Date()     # Return system date
?files         # Help on low-level interface to file system
list.files()   # List files in a give directory
file.info()    # Get information about files


log(x),logb(),log10(),log2(),exp(),expm1(),log1p(),sqrt()   # Fairly obvious
cos(),sin(),tan(),acos(),asin(),atan(),atan2()       # Usual stuff
cosh(),sinh(),tanh(),acosh(),asinh(),atanh()         # Hyperbolic functions
union(),intersect(),setdiff(),setequal()             # Set operations
eigen() # Computes eigenvalues and eigenvectors
sqrt()  # Square root
sum()   # Sum

pi      # Pi constant

deriv()      # Symbolic and algorithmic derivatives of simple expressions
integrate()  # Adaptive quadrature over a finite or infinite interval.

?Control     # Help on control flow statements (e.g. if, for, while)
?Extract     # Help on operators acting to extract or replace subsets of vectors
?Logic       # Help on logical operators
?regex       # Help on regular expressions used in R
?Syntax      # Help on R syntax and giving the precedence of operators


help(package=graphics) # List all graphics functions

plot()                # Generic function for plotting of R objects
par()                 # Set or query graphical parameters
curve(5*x^3,add=T)    # Plot an equation as a curve
points(x,y)           # Add another set of points to an existing graph
arrows()              # Draw arrows [see errorbar script]
abline()              # Adds a straight line to an existing graph
lines()               # Join specified points with line segments
segments()            # Draw line segments between pairs of points
hist(x)               # Plot a histogram of x
pairs()               # Plot matrix of scatter plots
matplot()             # Plot columns of matrices

?device               # Help page on available graphical devices
postscript()          # Plot to postscript file
pdf()                 # Plot to pdf file
png()                 # Plot to PNG file
jpeg()                # Plot to JPEG file
persp()               # Draws perspective plot
contour()             # Contour plot
image()               # Plot an image


help(package=stats)   # List all stats functions

?Chisquare            # Help on chi-squared distribution functions
?Poisson              # Help on Poisson distribution functions
help(package=survival) # Survival analysis

cor.test()            # Perform correlation test
cumsum(); cumprod(); cummin(); cummax()   # Cumuluative functions for vectors
density(x)            # Compute kernel density estimates
ks.test()             # Performs one or two sample Kolmogorov-Smirnov tests
loess(), lowess()     # Scatter plot smoothing
mad()                 # Calculate median absolute deviation
mean(x), weighted.mean(x), median(x), min(x), max(x), quantile(x)
rnorm(), runif()  # Generate random data with Gaussian/uniform distribution
splinefun()           # Perform spline interpolation
smooth.spline()       # Fits a cubic smoothing spline
sd()                  # Calculate standard deviation
summary(x)            # Returns a summary of x: mean, min, max etc.
t.test()              # Student's t-test
var()                 # Calculate variance
sample()              # Random samples & permutations
ecdf()                # Empirical Cumulative Distribution Function
qqplot()              # quantile-quantile plot

lm      # Fit liner model


?print


help(print)


x <- 5 # Example 1

5 -> x # Example 2

x = 5  # Example 3


x <- 5

x


y <- 3000

y


a = 0

a

my_cute_variable <- 35

my_cute_variable


x <- Sys.time()

print(x)

[1] "2020-12-29 17:35:31 AST"


ls()


x <- 4 # Assign value of 4 to variable "a"
print(x) # Check the value of "a"

# Lets change the value of "a"
x <- 2986 # Assign value 4
print(x) # Check again the value of "a"

[1] 4
[1] 2986


a <- 4 # Make variable "a"
ls() # Check which variables exist in memory


rm(a) # Remove variable "a"
ls() # Check again which variables exist in memory


ls() # Check which variables exist in memory


rm(list = ls()) # Remove ALL variables

ls() # Check again which variables exist in memory


x <- 4.67

typeof(x)


y <- 4L

typeof(y)


a <- "hello" # Example 1
b <- "2.3"   # Example 2

typeof(a)
typeof(b)


x <- FALSE

typeof(x)


# Arithmetic Operators -------
+   # Addition
-   # Subtraction
*   # Multiplication
/   # Division
^   # Exponent
%%  # Modulus (Remainder from division)
%/% # Integer Division

# Relational Operators --------
<  # Less than
>  # Greater than
<= # Less than or equal to
>= # Greater than or equal to
== # Equal to
!= # Not equal to

# Logical Operators -----------
!  # Logical NOT
&  # Element-wise logical AND
&& # Logical AND
|  # Element-wise logical OR
|| # Logical OR

# Assignment Operators ---------
<-, <<-, = # Leftwards assignment
->, ->> # Rightwards assignment


7 * 2


x <- 8 - 3

x

2^3


7 > 2


9 >= 18


x <- c(5, 2, 7, 4)

x

class(x)


x <- c("a", "b", "c", "d")

x

class(x)


x <- c("a", "b", 7, "d")

x

class(x)


x <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12), nrow=4, ncol=3)

x

class(x)


x <- list(1L, "a", 4, 6.87, TRUE, "hello")

x

class(x)


# Example of lists within a list
y <- list(4, "world", x, 3.67)

y

class(y)


x <- data.frame(id = 1:10, x = 11:20, y = 21:30)

x

class(x)


data = c("beluga", "dolphin", "narwhal", "dolphin", "dolphin", "narwhal", "beluga", "beluga")

fdata = factor(data)

fdata


levels(fdata)


nlevels(fdata)


x <- c(5, 2, 7, 4)

y <- list(6, "hello", FALSE, x, 3.67, "world", 8L)


x[1]


y[2]


y[2]
class(y[2])

y[[2]]
class(y[[2]])


y[[1]] + y[[5]]


x[1:3]


y[5:7]


# Here is the list stored in element 3
y[4]

# Here is the 3rd element of the list stored inside element 3 of list 'y'
y[[4]][3]


# To retrieve the last element of x
x[length(x)]


# To retrieve the last 3 elements of x
x[(length(x)-2):length(x)]


x[x > 3]


x[x <= 4]


m <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12), nrow=4, ncol=3)

m


m[1,2]


m[6]


m[1:2,2:3]


m[, 1]


m[1,]


class(m)

class(m[, 1])


d <- data.frame(id = 1:10, x = 11:20, y = 21:30)

d


d[,2]


d[2]


d[,"x"]

d$x


d["x"]


class(d[,"x"]) # This drops the data.frame and returns a vector
class(d$x)     # This drops the data.frame and returns a vector
class(d["x"])  # This preserves the data.frame


d[["x"]][2]


d$x[2]


d$x[2:4]


cssFile <- '../css/custom.css'
IRdisplay::display_html(readChar(cssFile, file.info(cssFile)$size))

IRdisplay::display_html("<style>.Q::before {counter-increment: question_num;
    content: 'QUESTION ' counter(question_num) ': '; white-space: pre; }.T::before {counter-increment: task_num;
    content: 'Task ' counter(task_num) ': ';</style>")

How to get Help¶

Comments and statements¶

"Commenting out" code¶

Functions and their arguments¶

Arguments¶

"Ordered" arguments¶

"Named" arguments¶

How to find Functions¶

General use functions¶

Math functions¶

Graphical functions¶

Statistical functions¶

Help files (i.e. Function manuals)¶

Variables¶

Using "Variables" and "Functions" together¶

Check "Variables" loaded in memory¶

Overwriting "Variables" values¶

Deleting "Variables"¶

Deleting ONE variable¶

Deleting ALL variables¶

Basic data types¶

Double (or numeric)¶

Integers¶

Character¶

Logical¶

R Operators¶

Data Structures (i.e. "Container" objects)¶

Vector¶

Matrix¶

List¶

Data Frame¶

Factors¶

Indexing (slicing)¶

Navigating within a vectors and lists¶

Navigating within Matrices¶

Navigating within Data Frames¶