CM PSI R Chabot

Statistique descriptive univariée
Bases de R
Statistique descriptive multivariée
Notions sur les tests statistiques
Traitement de données avec R

initiation aux méthodes exploratoires
Simon Chabot
chabotsi@unice.fr
Université Côte d’Azur
24 janvier 2017
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Bases de R
Plan
Bases de R
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Bases de R
Plan
Bases de R
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Bases de R
Objectifs
I Définir le ou les groupes étudiés ;

I Définir le codage des observations ;
I Définir la présentation des données ;
I Réduire les données à l’aide de quelques indicateurs statistiques.
4 / 43
Bases de R
Définir le groupe étudié
En théorie une population entière. (toutes les personnes atteintes de la

maladie X).
En pratique un échantillon. (100 personnes atteintes de la maladie X).
Taille de l’échantillon
Pour étendre les résultats observés sur l’échantillon à la population totale,
la taille de l’échantillon doit être représentatif !
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Bases de R

maladie X).
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Bases de R

maladie X).
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Bases de R
Définir le codage des observations
Type de variables
qualitative non-mesurable :
I sexe
I présence ou absence d’un marqueur
I etc
quantitative mesurable :
I taille
I poids
I durée
I etc
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Bases de R
Lancé d’un dé à 6 faces
I Je fais n lancés.
I Je compte le nombre d’apparitions de chaque face.
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Bases de R
Présentation des résultats
Occurrences 1 2 3 4 5 6 total
Effectifs n1 n2 n3 n4 n5 n6 n
Fréquences f1 f2 f3 f4 f5 f6 1
6 6
X ni X
n= ni , fi = , fi = 1
n
i=1 i=1
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Bases de R
Présentation des résultats
Occurrences 1 2 3 4 5 6 total
Effectifs 0 0 3 3 3 1 10
Fréquences 0 0 0.3 0.3 0.3 0.1 1
6 6
X ni X
n= ni , fi = , fi = 1
n
i=1 i=1
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Bases de R
Histogramme (10 lancés)

0.30
0.25
0.20
Histogramme
Fréquence
0.15
Un histogramme représente la
fréquence d’apparition de
0.10
chaque observation.
0.05
0.00
0 1 2 3 4 5 6
Valeur du dé
9 / 43
Bases de R

0.25
0.20
Histogramme
0.15
Fréquence
0.10
chaque observation.
0.05
0.00
0 1 2 3 4 5 6
Valeur du dé
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Bases de R

0.15
Histogramme
0.10
Fréquence
0.05
chaque observation.
0.00
0 1 2 3 4 5 6
Valeur du dé
9 / 43
Bases de R

0.15
Observations
I Il faut “un grand
0.10
nombre” d’observations
Fréquence
pour conclure.
I Les fréquences semblent
0.05
converger (vers
1/6 ≈ 0.167. . .).
0.00
0 1 2 3 4 5 6
Valeur du dé
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Bases de R
Modélisation
Variable aléatoire
Une Variable Aléatoire X est une fonction définie sur l’ensemble des
éventualités Ω.
Pour le dé
I Ω = {1, 2, 3, 4, 5, 6},
I X : ω 7→ X(ω) ∈ Ω.
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Bases de R
Modélisation
Loi de probabilité
Une v.a. est décrite par une loi de probabilité, qui mesure, pour chaque
valeur possible de Ω, la probabilité que X prenne cette valeur.
Si le dé n’est pas biaisé

La loi est uniforme. La probabilité que X prenne une valeur donnée est de
1/6.
L’histogramme donne une idée de la loi de probabilité.
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Bases de R
Estimation de la loi, moyenne

I X = v.a. correspond à la valeur du dé
I pi = P(X = xi ) probabilité que X prenne la valeur xi .
I X1 , X2 , X3 , . . . sont des observations.
Moyennes
P
Moyenne théorique E[X] = xi p i
1 Pin
Moyenne empirique X̄n = n i Xi
Estimation de la moyenne
Dans le cas où la moyenne théorique n’est pas connue, la moyenne
empirique en donne une estimation, car :
lim X̄n = E[X]

n→∞
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Bases de R

Moyennes
P
1 Pin
lim X̄n = E[X]

n→∞
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Bases de R

Moyennes
P
1 Pin
lim X̄n = E[X]

n→∞
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Bases de R
Nouvelle expérience
Description
I Je lance 100 dés non biaisés.

I Je somme les faces.
I Je recommence l’expérience n fois.
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Bases de R
Histogramme après 10000 lancés (des 100 dés)

I Une idée de la moyenne
empirique ?
0.020
1000
1 X
X̄1000 = Xi = 350.1
1000
0.015
i=1
Fréquence
I Quelle confiance
0.010
accorder à la moyenne
empirique ?
0.005
I Quelle erreur
0.000
faisons-nous par rapport

300 320 340 360 380 400 420 à la moyenne théorique ?
Somme des 100 dés
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Bases de R
Histogramme après 10000 lancés (des 100 dés)

I Une idée de la moyenne
empirique ?
0.020
1000
1 X
X̄1000 = Xi = 350.1
1000
0.015
i=1
Fréquence
I Quelle confiance
0.010
accorder à la moyenne
empirique ?
0.005
I Quelle erreur
0.000
faisons-nous par rapport

300 320 340 360 380 400 420 à la moyenne théorique ?
Somme des 100 dés
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Bases de R
Dispersion d’une V.A. autour de sa moyenne
Définition de la variance
Variance théorique Var(x) = E[X 2 ] − E[X]2
1 Pn
Variance empirique Sn2 = n−1 i=1 (Xi − X̄n )
2
Définition de l’écart-type
p
Écart-type théorique Var(x)
Écart-type empirique Sn
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Bases de R
Dispersion d’une V.A. autour de sa moyenne
Définition de la variance
Variance théorique Var(x) = E[X 2 ] − E[X]2
1 Pn
Variance empirique Sn2 = n−1 i=1 (Xi − X̄n )
2
Définition de l’écart-type
p
Écart-type théorique Var(x)
Écart-type empirique Sn
15 / 43
Bases de R
Loi normale, ou Loi Gaussienne
Loi normale
I Permet de modéliser de nombreux
Histogramme (1000 lancés) phénomènes aléatoires naturels ;
I Caractérisée entièrement par la moyenne µ
0.020
et l’écart-type σ.
0.015
Fréquence
I Densité :
0.010
1 − 1 ( x−µ )2
0.005
f (x) = e 2 σ
2πσ
0.000
300 320 340 360 380 400 420
Somme des 100 dés
I Notation :
X ∼ N (µ, σ 2 )
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Bases de R
Loi normale, ou Loi Gaussienne
Figure – Loi normale, par Nusha à Slovenian Wikipedia (GFDL)

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Bases de R
Intervalle de confiance pour la moyenne
Définition d’un intervalle de confiance

L’Intervalle de Confiance (IC) de niveau α est tel que :
I il est centré autour de la moyenne empirique ;
I il contient la moyenne théorique avec une probabilité α.
L’IC de niveau α est défini par :

Sn Sn
IC = X̄n − tα √ ; X̄n + tα √
n n
où :
I tα est un réel qui dépend de α. Des tables reliant tα et α existent
dans la littérature. Par exemple, pour α = 95%, on a tα = 1.96 1
1. si n suffisamment grand
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Bases de R


Sn Sn
IC = X̄n − tα √ ; X̄n + tα √
n n
où :
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Bases de R


Sn Sn
IC = X̄n − tα √ ; X̄n + tα √
n n
où :
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Bases de R
Intervalle de confiance pour la somme des 1000 dés
Soit n le nombre de lancés.
n 100 1000
X̄n 351.4 350.1
Sn 17.1 16.5
IC à 95% [348.1, 354.8] [349.1, 351.1]
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Bases de R
Boite à moustache
Boite à moustache (1000 lancés)
420
● I maximum
400
I 2e quartile
380
I médiane
1er quartile
360
I minimum
340
Les cercles représentent les

320
valeurs exclues, car trop

●
extrêmes, ou atypiques.
300
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Somme des 100 dés
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Bases de R
Plan
Bases de R
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Bases de R
I R est un logiciel libre.

I R est un langage dédié aux statistiques et à la représentation des
données.
I Disponible sur toutes les plateformes : http://www.r-project.org
I Langage matriciel de la même famille que Matlab ou Scilab.
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Bases de R
Aide
I Documentation riche (livres, forum, etc.)

I http://www.duclert.org/Aide-memoire-R/Le-langage/
Introduction.php
I help(mean) ou bien ?mean
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Bases de R
Environnement
I top-level
I écrire des scripts : source(’mon_script.r’)
Démo de R
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Bases de R
Environnement
I top-level
I écrire des scripts : source(’mon_script.r’)
Démo de R
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Bases de R
Plan
Bases de R
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Bases de R
Jeu de données “crabs” (Leptograpsus variegatus)
200 crabes ont été ramassés en Australie.

Pour chaque crabe, l’équipe de scientifique a relevé :
I sa couleur (Orange ou Bleu)
I son sexe (F ou M)
I la taille du lobe frontal (FL, frontal lobe)
I la taille de l’arrière train (RW, rear width)
I la longueur de la carapace (CL, carapace length)
I la largeur de la carapace (CW, carapace width)
I l’épaisseur du corps (BD, body depth)
Nous allons décrire une partie de cet ensemble de données, à l’aide du

logiciel R.
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Bases de R

I son sexe (F ou M)

logiciel R.
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Bases de R

I son sexe (F ou M)

logiciel R.
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Bases de R

I son sexe (F ou M)

logiciel R.
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Bases de R

I son sexe (F ou M)

logiciel R.
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Bases de R

I son sexe (F ou M)

logiciel R.
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Bases de R

I son sexe (F ou M)

logiciel R.
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Bases de R

I son sexe (F ou M)

logiciel R.
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Bases de R
Résumé des données
5 enregistrements pris au hasard : crabs[sample(200, 5), ]
sp sex index FL RW CL CW BD
103 O M 3 10.7 8.6 20.7 22.7 9.2
151 O F 1 10.7 9.7 21.4 24.0 9.8
4 B M 4 9.6 7.9 20.1 23.1 8.2
192 O F 42 20.5 17.5 40.0 45.5 19.2
157 O F 7 14.0 12.8 28.8 32.4 12.7
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Bases de R
Résumé des données

Données statistiques par variables : summary(crabs)
sp sex index FL RW
B:100 F:100 Min. : 1.0 Min. : 7.20 Min. : 6.50
O:100 M:100 1st Qu.:13.0 1st Qu.:12.90 1st Qu.:11.00
Median :25.5 Median :15.55 Median :12.80
Mean :25.5 Mean :15.58 Mean :12.74
3rd Qu.:38.0 3rd Qu.:18.05 3rd Qu.:14.30
Max. :50.0 Max. :23.10 Max. :20.20
CW BD
Min. :17.10 Min. : 6.10
1st Qu.:31.50 1st Qu.:11.40
Median :36.80 Median :13.90
Mean :36.41 Mean :14.03
3rd Qu.:42.00 3rd Qu.:16.60
Max. :54.60 Max. :21.60 27 / 43
Bases de R
Chercher les liens entre les différentes variables
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Interprétation ? 28 / 43
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Interprétation ?
Comment interpréter ce que l’on voit ?
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Interprétation ?
Comment interpréter ce que l’on voit ? 29 / 43
Bases de R
Régression linéaire
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Le nuage de points (xi , yi ) est
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15 20 25 30 35 40 45

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30 / 43
Bases de R
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15 20 25 30 35 40 45

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30 / 43
Bases de R
Ajustement du modèle
f (x) = ax + b
I Trouver a et b de sorte à minimiser l’erreur quadratique :

n
1X
M SE = (f (xi ) − yi )2
n
i=1
I Fonction R : lm(y~x)
31 / 43
Bases de R
Régression linéaire sur CW et CL
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32 / 43
Bases de R
Corrélation linéaire entre deux variables
Corrélation linéaire
On voit que CL et CW sont fortement liées. On dit que ces variables sont
corrélées.
On quantifie la corrélation entre deux variables X et Y par un réel compris
entre -1 et 1.
Forte corrélation |Cor(X, Y )| > 0.8
Faible corrélation |Cor(X, Y )| < 0.3
33 / 43
Bases de R
corrélées.
entre -1 et 1.
33 / 43
Bases de R
corrélées.
entre -1 et 1.
33 / 43
Bases de R
Corrélation linéaire pour le jeu de données Crabs
> cor(crabs[,4:8])
FL RW CL CW BD
FL 1.0000000 0.9069876 0.9788418 0.9649558 0.9876272
RW 0.9069876 1.0000000 0.8927430 0.9004021 0.8892054
CL 0.9788418 0.8927430 1.0000000 0.9950225 0.9832038
CW 0.9649558 0.9004021 0.9950225 1.0000000 0.9678117
BD 0.9876272 0.8892054 0.9832038 0.9678117 1.0000000
34 / 43
Bases de R
Attention au coefficient de corrélation !
Figure – By Denis Boigelot, [CC0], via Wikimedia Commons
35 / 43
Bases de R
Attention au coefficient de corrélation !
Figure – By Denis Boigelot, [CC0], via Wikimedia Commons
35 / 43
Bases de R
Visualiser rapidement les relations entre les variables
6 10 14 18 20 30 40 50
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36 / 43
Bases de R
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●●●●● ●●● ●●● ●
●
●●●
●●
●● ●●
●●●● ●●
●●
●●●
● ●●
●● ● ●●
●
●●
● ● ●●●
● ●●●● ● ●●●
●●●
● ●●
●●
● ●
●● ●●●
B O
●● ●
● ●● ●
●
●● ● ●
●● ●●
● ● ●●
6
● ● ●
●● ●●
● ● ●●
● ● ●●●
45
●●
● ●
●
●● ● ●●
●
● ●● ●● ● ●● ●●
●●
●●● ●● ●● ●●
● ● ●●● ● ●●
● ●●●
●●
●●● ●● ●●● ● ●
● ● ● ●
●
●
●
●●● ●●●●
●● ●
●●
●
●
●● ●●
●●●●●
●
● ● ●●
●●
●
●
●●●●
● ●
●●
●
●
●●●●
●●●●●● ●
●
●●●●
●
F rouge bleu
●●●●●●● ●
●
● ● ●●●●
● ●
●●
●●
●● ●
●●
●
●
●● ●
●●●
●●
● ●
●
●
●●●
●
●
●
●● ●● ●●
●●
●
●
●●●● ●
●●●●●
●●
●●
● ●
35
●●● ●
●● ●
● ●● ●● ●●●
●●●
●
●●● ●●
● ● ●●●●
●
● ●
●
●
●●
●
●●
●●●
● ●●●
●
●
●
●
●
●
●
● ●
●●●
●●
●●
●
●
●●●
●●
● ●● ● ●●●● ●●
● ●
●●●
●●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●●●●
●
●
●
●
●
●
●
●
●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●●
●
●●
●
●
●
●●
●
●●
●
●●●●●
●
●
●●
●
●
●●
●
●
CL ●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●●
● ● ● ●●●
● ●●
25
●●●● ●
●●●
●● ●●
● ●●●●●
●●●
●●● ●●
●● ●
● ● ●
●●● ●●●●
●
●
●●
● ●●●●
● ●
●●
●
●●● ● ●
●
●●
●●
●
●
●
●
●
●●
●● ●
●●●●●●
●●
●●●
●
●
●●
●
●
●●
●●
●●●
M vert noir
●
●
● ●●●
● ●● ●
● ● ●● ●
●
●● ●● ●
● ●●
15
● ● ● ●
● ● ● ●
●
● ●● ● ●● ●●
●● ●●
50
●●●
● ● ●●
● ●●●●
●
●
●●
●●● ● ●
●●●●● ●●●●●●●
●●●
●
●●●
●●● ●●●● ●●●
● ●
●●
●●
●
●
●
● ●●
●
●●●●●
●
● ● ●● ●●
●● ● ●
●●
●●●●●●●●
● ●●
●●● ●● ●
●● ●
●●
●●
● ●●●●
●●●●●●●
●
●
●
●●
●●●●
●
●●
●
●●
●
●●
●●
●
●●
●● ● ●●
●●●
●
●●
●
●
●
●
●
●
●●●
●●● ●●
●●●
●
● ●● ●●●
● ● ●●
40
●
●
●● ●●
●●
● ●
●●
●●
●●● ●●
● ●
●●
● ● ●● ●●● ●
●●
●
●
●
●
●●●●
●●● ●● ●
●● ●
●
●●
●●
●
●●
● ●●
●●●●
●
●
●
● ●
●●
●●●●
●●
●
●
●
●●●
●
●
●
●●
●●●
● ●
●● ●
● ●●
●● ●
●
●●
●
CW ●
●●
●
● ●●
Table – classes de crabes

●●
●● ●●
●● ●● ●●
●
●● ●●●
●
● ●●
●●
●●
●
●●
●●
● ●
●●
●●●
●● ●●●
●●●●●
●●●●
●● ●●●●
●●
●
● ●● ● ●●●
●●●●
●●●●
●●●
●
●
●●●
●
●●●
●
● ●
●
●●
●
●
●●
●
●
●●●
●
●
●
●
●●●
●●
●● ●●
●●
●
●
●
●
●
●
●
●●
●
●●
●●
●●
●
●●●●
●
30
● ●●● ●● ● ●●
●
●● ●●
● ●●
●
●
●●●
●●● ●●
●
●●
●●
●●● ●
●
●●● ●●●●●●
●
●● ●
●●●
●● ● ●●
●
●
● ●
●●●●
●●●● ● ●●
●
●●
● ●●
●
●
●
● ● ●●
● ●●
●
● ●●
● ●
●
● ●●●●
●
●●
●●●●●
● ● ●
●●
●●
●● ● ●
●
●●●
●
●
● ●●●●
●
● ●● ● ●
20
● ● ●
●● ●● ●● ●●
● ● ● ●
●●● ●
●● ● ●●●● ●
●
●
● ● ●●●
● ●●●
● ●
●● ● ●
20
●● ● ●●
●●●●●● ●● ●● ●
●
● ●●●●●
● ●
●● ● ●
●
●●● ●
● ●●●● ●
● ●●● ●●●●●
●
●●●
● ●
●●●
●● ●
●●
●●● ●● ●
●●
●
● ●●●●
●
●
●
●●
●
● ● ●●●●
●●●●●
● ●
●●●●
●●
●
● ●
●●
●●●●●●●● ● ●
●●●● ● ●
●●
●●
● ●
●●●● ●● ●
● ●●
●●
●
●● ●●
● ●●
● ● ●
● ●
●
●
●
●●
●
● ●
●● ●
●●
●
●
●
●●
● ●
●●●
●
●● ●● ●
● ● ●●● ●●
● ●●● ●
●●●●●
15
●
●●●
●● ● ●● ●● ● ●● ●
●●
●● ●
●●
●●●
●●●●●● ●
● ●●● ●
● ●● ●
●
● ●●●
●
●●●● ●● ●●● ●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
● ●
●
●
●
●
●●
●
●●
●
●
●●
●
●
●
● ●●
●
●●●●●●●●
●●●●●●●
● ●●
●●
●
●
●●
●
●
●
●
●●
●●●●
●●
●
●
●
●
●●
●
●●
●
●
●
●
●●
●
●
●
●
●●
●
●
●
●
●●
●●
●
●●●
●
●●
●
●
●
●
●
●
●
●
●
●●●
●
●
●
●●●
●
●●● ●
●
●
●
●
●●●
●●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●
BD
●●
●●
● ●● ●●
●●
●
●●● ●●
●●●
●
●●
●
● ●●●●●
●
●●●
●●
●● ●●●●●
●●● ●● ●● ●● ●● ●
●
10
●●
● ● ●
●●●
● ●
●
● ●
●●
●●●
● ●●●
●
● ●●
●●●
●● ●●●●●●
●
●●●
● ●●●●● ●●
●●● ●●●●●●
●●
●●● ●
● ●● ●●●● ●●●
●
●● ●●● ●
● ●
●●
● ●
●● ●
●●
● ●●● ●●● ●
●●●
● ● ● ●
10 15 20 15 25 35 45 10 15 20
36 / 43
Bases de R
Peut-on prédire l’espèce et le sexe d’un crabe ?
6 10 14 18 20 30 40 50
●● ● ●● ●
● ●
● ● ●● ● ● ● ● ●
●●● ●
● ● ●●
● ●●●● ●●●●● ●●●
●●
●
●● ●●●● ● ● ●●●● ●●●●● ● ● ●●● ●
●● ● ●
● ●
●
pairs(crabs[,4:8],
20
●● ●
● ●
●●● ●●
● ● ●
●●
●●
● ●●●● ● ●
● ●● ●
●●
● ●● ●●
●●
●●
●
●●● ● ●●● ●●
● ●●●●●
●● ● ●●
●●
●
●
● ●●●● ●●●●●●
●
●
●●
●●
●● ●
●●●●●
● ●●●
●
●
●●●
●●
●●●●●
●
●
●
●●
●
●●
●
●
●●●
●●
●
●●
●●●
●●
●
●●
●●
●●
●●● ●●
●
●● ● ●●
●●●●●
●●
●● ●
●●●
●
●● ●●●● ●●
●●●●
●
●●
●●●
●●● ● ● ● ● ●
●
●●●●
●●●
●●●● ●● ●
●
●●●●●
●●●● ●●●●●●
●●●
●●●●● ● ●
●●
●●
●
●● ●● ●
FL ● ●●●
●●
●
● ●●●
●●●
●● ●●
● ●●
●● ●●
●●
●●
● ●
15
●●
●●●●
●●
●●●●
●●● ●
●
● ●●
●●
●●
●●
● ●
●
●
● ●●
●●
●●
●●● ●●●●
●
●●
●
●
●●●●
●●●●●●●
● ●● ● ●● ●
●
●●
●●
●●● ●● ●
●●●●●
●●
● ● ●●
●●
● ●● ●●
●●
●
●●
●●
●
●●●●
●
●
●●
●●●●
●● ●
●●●
●
●
●
●●
● ●●
●●●●●●
● ●●
●
●
●
●●
●●
●
●●●●
●●● ●●
● ●●●●
●●●●●
●
●
●● ●●●●●
●● ●
●
● ●
●
●●●
●●
●
●●
●●● ●● ●
●●
●
●
●●
●●●
●
●
●
●
●●●
●●
●●
●
●●
●●
●●
●●
●
●
●
●
●● ●
●
●●
●
●●●●
●●
●
●
●●
●
●●
●
●
●
●●
●
●
●●
●●
col=crabs$class)
10
●● ●
●● ● ●
● ●
●●
●
●●● ●●
● ●●● ●●●
●
●●●
●● ●
●●
●● ● ●●
●● ●
●●
● ● ● ●
● ● ● ●
● ● ● ●
18
● ● ● ●
●●● ●●
●●
●
●
●● ●●●
● ●●● ● ●●
● ● ● ●●
● ●
●
● ● ●● ●
●● ●●●●●
●
●●
● ●●●
●
●●●
●
● ● ● ● ●● ●●
●●
●
●● ●
●
● ● ●● ●●● ●●
●
●● ● ●● ●●●
● ●●●●
●
●● ●● ●● ● ●●
●●
● ●●●
●● ● ● ●● ●
●●●●● ●●● ● ●●● ●
●● ●●● ● ●
● ● ●●
B O
● ●●● ● ●
● ●●
●● ●●● ●● ●
●
●●● ●● ● ●●
● ● ●●
●●●●
●
14
● ● ● ●● ● ● ●● ●
● ● ●● ● ● ●●●● ●● ●●●
● ● ●● ●● ●
● ●
●● ●●
●
●●
●
●
●●
●
●
●
●
●●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●●
●
●●
●
●
●
●
●
●
●
●
●
●
●●
●
●●
●
●
●
●
●●●
●
●
●
●●
●●●
●
●● ●
RW ●
●●
●●
●
●
●●
●
●
●●
●
●
●●
●
●●●●
●●●●
●
●
●
●●●
●
●
●
●
●
●●
●
● ●
●
●●
●
●
●●
●
●
●
●●
●
●
●
●
●
●●
●
●
●●
●
●
●
●
●●●●
●●
●●
●
●
●●
●
●
●
●
●●
●
●
●
●
●
●
●
●
●●●
●●
● ●●
●
●
●
●
●●
●●
● ●●
●
●●
●
●
●●
●
●
●
●
●
●● ●
● ●
●●
●●
●
●●
●●
●●
●
●
●●
●●
●
●
●
●●
●
●
● ●●
●●●
●
●
●
●●
●
●●
●●●
●●
●●
●●
●●
● ●●
●● ●
●●
●●
●●
●
●
●●●
●●●● ● ●●●●
●
●●●
●
●●
●●● ●●●
● ●
●
●●
●●●
● ● ●●●
●●●●●
●●●●●●
●
●●
● ● ●●● ● ●● ●● ●● ●●●●●
10
● ●
●●● ● ●● ●
●●● ● ●● ●
● ● ●
● ●● ●
●●●● ●●●
●●●● ●●● ●●● ●
●
●●●
●●
●● ●●
●●
●● ●●
●●
●●●
● ●●
●● ● ●●
●
●●
● ● ●●●
● ●●●● ● ●●●
●●
●●●
● ●
●
●
●
●●
● ●
●
●●● ●●●
●
●
●● ● ●
●● ●●
● ● ●●
F rouge bleu
6
● ● ●
●● ●●
● ● ●●
● ● ●●●
45
●●
● ●
●
●● ● ●●
●
● ●
● ●● ● ●● ●●
●●
●●● ●● ●● ●●
● ● ●● ● ●●
● ●●
●
●●●●●
●
●●
●●
●
●●●● ●●● ● ●
● ●●●
●
●
●
●● ●
●●
●
●
●
●
●●●● ●●●●
●●
●●
●
●●
●
● ●●● ● ●
●● ●●
●● ●
●●
●● ●●● ●
●●
●●●
M vert noir
●●
● ●●
● ● ●
●
● ● ●●●●● ●
●●
●●
●● ●
●●
●
●
●●
●●●●
●●
● ●
●
●
●●●
●
●
●
●● ●●●● ●●
●●
●
●
●●●● ●
●●●●●
●●
●●
● ●
35
●●● ●● ●
● ● ●
●●●
●
●●●● ●
●●
● ● ●●●●
●
● ●
●
●
●●
●
●●
●●●
● ●●●
●
●
●
●
●
●
●
●
● ●
●●
●
●
●●
●
●
●
●
●
●●●
●●
● ● ● ● ●● ●●
● ●
●●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●●
●
●
●
●
●
●●
●
●
●
●
●
●
●
●●●●
●
●
●
●
●
●
●
●
●
●●
●●
●
●
●
●
●
●
●
●
●
●
●
●
●●●
●
●
●●●
●●
●●
●
●●
●●
●●
●
●
●
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10 15 20 15 25 35 45 10 15 20
37 / 43
Bases de R
6 10 14 18 20 30 40 50
pairs(crabs[,4:8],
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col=crabs$class)
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F rouge bleu
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M vert noir
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Table – classes de crabes

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37 / 43
Bases de R
0.28 0.32 0.36 0.40 0.6 1.0 1.4

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0.38 0.42 0.46 0.84 0.88 0.92 0.32 0.36 0.40
37 / 43
Bases de R
BF BM ●
OF OM
0.48
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On voit apparaitre quatre groupes
0.42
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distinct, un par classe.
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●
0.38
0.28 0.30 0.32 0.34 0.36 0.38 0.40
crabs$RW/crabs$CW
37 / 43
Bases de R
Plan
Bases de R
38 / 43
Bases de R
Objectif
Démarche consistant à rejeter ou ne pas rejeter une hypothèse statistique 2 ,
en fonction d’un échantillon.
Il s’agit d’émettre des conclusions sur une population, en leur rattachant

des risques de se tromper.
Exemple
Hypothèse H0 : Les observations suivent une loi normale
2. Appelée hypothèse nulle H0 .

39 / 43
Bases de R
Objectif
Démarche consistant à rejeter ou ne pas rejeter une hypothèse statistique 2 ,
en fonction d’un échantillon.
Il s’agit d’émettre des conclusions sur une population, en leur rattachant

des risques de se tromper.
Exemple
Hypothèse H0 : Les observations suivent une loi normale
2. Appelée hypothèse nulle H0 .

39 / 43
Bases de R
p-value
Elle représente la probabilité qui mesure le degré de certitude avec lequel il
est possible d’invalider l’hypothèse nulle.
Des probabilités faibles permettent d’invalider l’hypothèse nulle avec plus
de certitude.
En pratique
I p ≤ 0.01 : très forte présomption contre l’hypothèse nulle

I 0.01 < p ≤ 0.05 : forte présomption contre l’hypothèse nulle
I 0.05 < p ≤ 0.1 : faible présomption contre l’hypothèse nulle
I 0.1 < p : pas de présomption contre l’hypothèse nulle
40 / 43
Bases de R
p-value
Elle représente la probabilité qui mesure le degré de certitude avec lequel il
est possible d’invalider l’hypothèse nulle.
Des probabilités faibles permettent d’invalider l’hypothèse nulle avec plus
de certitude.
En pratique
I p ≤ 0.01 : très forte présomption contre l’hypothèse nulle

I 0.01 < p ≤ 0.05 : forte présomption contre l’hypothèse nulle
I 0.05 < p ≤ 0.1 : faible présomption contre l’hypothèse nulle
I 0.1 < p : pas de présomption contre l’hypothèse nulle
40 / 43
Bases de R
Quelques exemples de tests
normalité H0 : Les observations suivent une loi normale

I Test de Kolmogorov-Smirnov : ks.test(x, "pnorm",
0, 1)
I Test de Shapiro-Wilks : shapiro.test(x)
comparaison H0 : Les moyennes observées sont égales

I Test t de Student : t.test(v1, v2) (si v1 et v2
suivent des lois normales.)
I Test de Mann-Whitneya-Wilcoxon : wilcox.test(v1,
v2) (sinon).
Plus d’exemples sur :
https://fr.wikipedia.org/wiki/Test_(statistique)
41 / 43
Bases de R

0, 1)

v2) (sinon).
41 / 43
Bases de R

0, 1)

v2) (sinon).
41 / 43
Bases de R
42 / 43
Bases de R
Merci !
42 / 43

CM PSI R Chabot

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Statistique descriptive univariée

Traitement de données avec R

Université Côte d’Azur

Statistique descriptive univariée

Statistique descriptive multivariée

Notions sur les tests statistiques

Statistique descriptive univariée

Statistique descriptive multivariée

Notions sur les tests statistiques

I Définir le ou les groupes étudiés ;

Définir le groupe étudié

En théorie une population entière. (toutes les personnes atteintes de la

Définir le groupe étudié

En théorie une population entière. (toutes les personnes atteintes de la

Définir le groupe étudié

En théorie une population entière. (toutes les personnes atteintes de la

Définir le codage des observations

Lancé d’un dé à 6 faces

Présentation des résultats

Présentation des résultats

Histogramme (10 lancés)

Histogramme (50 lancés)

Histogramme (1000 lancés)

Histogramme (10000 lancés)

Si le dé n’est pas biaisé

L’histogramme donne une idée de la loi de probabilité.

Estimation de la loi, moyenne

lim X̄n = E[X]

Estimation de la loi, moyenne

lim X̄n = E[X]

Estimation de la loi, moyenne

lim X̄n = E[X]

I Je lance 100 dés non biaisés.

Histogramme après 10000 lancés (des 100 dés)

faisons-nous par rapport

Histogramme après 10000 lancés (des 100 dés)

faisons-nous par rapport

Dispersion d’une V.A. autour de sa moyenne

Dispersion d’une V.A. autour de sa moyenne

Loi normale, ou Loi Gaussienne

300 320 340 360 380 400 420

Somme des 100 dés

Loi normale, ou Loi Gaussienne

Figure – Loi normale, par Nusha à Slovenian Wikipedia (GFDL)

Intervalle de confiance pour la moyenne

Définition d’un intervalle de confiance

Intervalle de confiance pour la moyenne

Définition d’un intervalle de confiance

Intervalle de confiance pour la moyenne

Définition d’un intervalle de confiance

Intervalle de confiance pour la somme des 1000 dés

Soit n le nombre de lancés.

Les cercles représentent les

valeurs exclues, car trop

Somme des 100 dés

Statistique descriptive univariée

Statistique descriptive multivariée

Notions sur les tests statistiques

I R est un logiciel libre.

I Documentation riche (livres, forum, etc.)

Statistique descriptive univariée

Statistique descriptive multivariée

Notions sur les tests statistiques