R for Beginners

Emmanuel
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6 Programming with R in pratice 64
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 2 A few concepts before starting

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> ?lm

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Arithmetic
$(OOL#): help(lm)package:base
L#) help("lm") ;LF. >;. :LO. R Documentation
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> help("*")
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Error: syntax error
> ?*
 > help("bs")
No documentation for bs in specified packages and libraries:
you could try help.search("bs")
> help("bs", try.all.packages = TRUE)
Help for topic bs is not in any loaded package but
can be found in the following packages:

Package Library
splines /usr/lib/R/library

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> help("bs", package = "splines")

bs package:splines R Documentation

B-Spline Basis for Polynomial Splines

Description:

Generate the B-spline basis matrix for a polynomial spline.

...

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 3 Data with R

3.1 Objects

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> x
[1] Inf
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[1] Inf
> exp(-x)
[1] 0
> x - x
[1] NaN

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> qnorm(0.025)
[1] -1.959964
> qnorm(0.975)
[1] 1.959964

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[1] 1 10

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> x <- 0.5
> 0 < x < 1
[1] FALSE

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[1] 3
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> x
[1] 1 2 20 4 5

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> i <- c(1, 3)

> x[i]
[1] 1 20

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[1] "c" "d"

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> A <- array(1:8, dim = c(2, 2, 2))

> A
, , 1

[,1] [,2]
[1,] 1 3
[2,] 2 45.7963 0 Td (1)4

, , 2

[,1] [,2]
[1,] 5 45.7963 0 Td (1)7
[2,] 6 45.7963 0 Td (1)8

> dimnames(A) <- list(c("a", "b"), c("c", "d"), c("e", "f"))

> A
, , e

c d
a 1 3
b 2 4

, , f

c d
a 5 7
b 6 8

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> x <- 1:4

> a <- 10
8zzz
> z <- a * x
log(x, base) computes the logarithm of x with base base
scaleTf ) if x is a matrix, cenlogarithmdata; 0 Td5.540ith
 [1,] 1 1 2 2
[2,] 1 1 2 2

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m2) %*% cbind(m1,
m2)
[,1] [,2] [,3] [,4]
[1,] 2 2 4 4
[2,] 2 2 4 4
[3,] 4 4 8 8
[4,] 4 4 8 8
> cbind(m1,
m2) %*% rbind(m1,
m2)

10 10
10 10

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 4 Graphics with R

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X11 X11 pdf
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 > layout(matrix(1:4, 2, 2))

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)?F?).)h

> mat <- matrix(1:4, 2, 2)

> mat
[,1] [,2]
[1,] 1 3
[2,] 2 4
> layout(mat)
4.2 Graphical functions

A.6. ?: L# (F.6F?.J (3 >;. ;?7;dK.F.K 76L-;?$LK 3B#$>?(#: ?# <g

plot(x) plot of the values of x (on the

symbols(x, y, ...) draws, at the coordinates given by x and y, symy
rect(x1, y1, x2, draws a rectangle which left, right, bottom, and top limits are
y2) x1, x2, y1, and y2, respectively
polygon(x, y)
4.4 Graphical parameters

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 How to customize a plot with R

2 1 0 1 2

Ten random values

lat

long
Petal.Length
o o
o o o o
o o o
o o o o
o o o
o o o
o
o
o

Petal.Width
8
7 8

Sepal.Length 6
oo o
oo o o o
oo
o o
5 o ooo
o
ooooo
oo
oo o o
o oo o o
5 6 oo
oo
Sepal
Length

Scatter Plot Matrix

 5 Statistical analyses with R

5F.# O(6. >;L#

> aov.spray <- aov(sqrt(InsectSprays[, 1]) ~ InsectSprays[, 2])

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1.52.53.5
 Partial for spray

3 2 1 0 1 2
0
1
2
3

spray
4
5
6
>?(#: J;?$; $L# P. B:.) >( .N>6L$>
> str(summary(aov.spray))
List of 1
$ :Classes anova and data.frame: 2 obs. of 5 variables:
..$ Df : num [1:2] 5 66
..$ Sum Sq : num [1:2] 88.4 26.1
..$ Mean Sq: num [1:2] 17.688 0.395
..$ F value: num [1:2] 44.8 NA
..$ Pr(>F) : num [1:2] 0 NA
- attr(*, "class")= chr [1:2] "summary.Td (num)Tjn avar Td (2)j 34.
>;?: KL>>.6 (PC.$>_ PB> ?# :(O. $L:.: L 3B6>;.6 L67BO.#> ?: #.$.::L6" K?G. 3(6
predict (6 updateg

add1 tests successively all the terms that can be added to a model
drop1 aom successively all the terms that can be removed from a model
tests
step selects a model with AIC (calls add1 and

757.elect12.4701 0 Td (del)Tj 14.87sq 4.8 0 0 -110.4 4752 Td 6872.28 cm644 /IM true /W 1 /H 1
 6 Programming with R in pratice

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(Intercept) x
31.683 5.377

[[2]]

Call:
FUN(formula = X[[2]])

Coefficients:
(Intercept) poly(x, 2)1 poly(x, 2)2
4.9330 1 mf5.o330
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> layout(matrix(1:3, 3, 1))

> ricker(0.1, 1); title("r = 1")
> ricker(0.1, 2); title("r = 2")
> ricker(0.1, 3); title("r = 3")

^l
 7 Literature on R

Manuals. @.F.6LK OL#BLK: L6. )?:>6?PB>.) J?>; < ?# < A0%5i)($iOL#BLKih

An Introduction to R Z<d?#>6(g-)3b_
R Instal
withnto
R