ANOVA y Tukey

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Cargar paquetes

library(ggplot2)
library(dplyr)

##
## Attaching package: ’dplyr’

## The following objects are masked from ’package:stats’:

##
## filter, lag

## The following objects are masked from ’package:base’:

##
## intersect, setdiff, setequal, union

library(agricolae)
library(car)

## Loading required package: carData

##
## Attaching package: ’car’

## The following object is masked from ’package:dplyr’:

##
## recode

library(FSA)

## ## FSA v0.8.32. See citation(’FSA’) if used in publication.

## ## Run fishR() for related website and fishR(’IFAR’) for related book.

##
## Attaching package: ’FSA’

1
## The following object is masked from ’package:car’:
##
## bootCase

Cargar la base de datos

data(PlantGrowth)

PlantGrowth

## weight group
## 1 4.17 ctrl
## 2 5.58 ctrl
## 3 5.18 ctrl
## 4 6.11 ctrl
## 5 4.50 ctrl
## 6 4.61 ctrl
## 7 5.17 ctrl
## 8 4.53 ctrl
## 9 5.33 ctrl
## 10 5.14 ctrl
## 11 4.81 trt1
## 12 4.17 trt1
## 13 4.41 trt1
## 14 3.59 trt1
## 15 5.87 trt1
## 16 3.83 trt1
## 17 6.03 trt1
## 18 4.89 trt1
## 19 4.32 trt1
## 20 4.69 trt1
## 21 6.31 trt2
## 22 5.12 trt2
## 23 5.54 trt2
## 24 5.50 trt2
## 25 5.37 trt2
## 26 5.29 trt2
## 27 4.92 trt2
## 28 6.15 trt2
## 29 5.80 trt2
## 30 5.26 trt2

Prueba de Normalidad

hist(PlantGrowth$weight)

2
 Histogram of PlantGrowth$weight
8
6
Frequency

4
2
0

3.5 4.0 4.5 5.0 5.5 6.0 6.5

PlantGrowth$weight

shapiro.test(PlantGrowth$weight)

##
## Shapiro-Wilk normality test
##
## data: PlantGrowth$weight
## W = 0.98268, p-value = 0.8915

qqPlot(PlantGrowth$weight)

3
 6.0
PlantGrowth$weight

5.5
5.0
4.5
4.0

16
14
3.5

−2 −1 0 1 2

norm quantiles

## [1] 14 16

Prueba de homocedasticidad, se pueden utilizar la prueba de Levene y la prueba de Bartlett para conocer si
nuestros datos presentan homocedasticidad.
Si nuestros datos presentan normalidad lo mas recomendable es utilizar la prueba de Bartlett.
Test de Bartlett

bartlett.test(weight ~ group, PlantGrowth)

##
## Bartlett test of homogeneity of variances
##
## data: weight by group
## Bartlett’s K-squared = 2.8786, df = 2, p-value = 0.2371

Test de Levene

leveneTest(y=PlantGrowth$weight, group = PlantGrowth$group, center = "mean")

## Levene’s Test for Homogeneity of Variance (center = "mean")

## Df F value Pr(>F)
## group 2 1.237 0.3062
## 27

4
Prueba de ANOVA, realizamos la prueba de anova para conocer si exiten diferencias significativas del peso
de las plantas de acuerdo al tratamiento.

planta_modelo<-aov(weight~group,PlantGrowth)

summary(planta_modelo)

## Df Sum Sq Mean Sq F value Pr(>F)

## group 2 3.766 1.8832 4.846 0.0159 *
## Residuals 27 10.492 0.3886
## ---
## Signif. codes: 0 ’***’ 0.001 ’**’ 0.01 ’*’ 0.05 ’.’ 0.1 ’ ’ 1

Prueba de Tukey, realizamos la prueba post hoc para conocer entre cuales grupos hay diferencias significativas

TukeyHSD(planta_modelo,"group")

## Tukey multiple comparisons of means

## 95% family-wise confidence level
##
## Fit: aov(formula = weight ~ group, data = PlantGrowth)
##
## $group
## diff lwr upr p adj
## trt1-ctrl -0.371 -1.0622161 0.3202161 0.3908711
## trt2-ctrl 0.494 -0.1972161 1.1852161 0.1979960
## trt2-trt1 0.865 0.1737839 1.5562161 0.0120064

Prueba de Duncan, realizamos la prueba post hoc (lternativa a la prueba de Tukey) para conocer entre cuales
grupos hay diferencias significativas

Plantas_ducan<-duncan.test(planta_modelo,"group",alpha=0.01,console=TRUE)

##
## Study: planta_modelo ~ "group"
##
## Duncan’s new multiple range test
## for weight
##
## Mean Square Error: 0.3885959
##
## group, means
##
## weight std r Min Max
## ctrl 5.032 0.5830914 10 4.17 6.11
## trt1 4.661 0.7936757 10 3.59 6.03
## trt2 5.526 0.4425733 10 4.92 6.31
##
## Alpha: 0.01 ; DF Error: 27
##
## Critical Range
## 2 3

5
## 0.7724154 0.8055987
##
## Means with the same letter are not significantly different.
##
## weight groups
## trt2 5.526 a
## ctrl 5.032 ab
## trt1 4.661 b

plot(Plantas_ducan)

Groups and Range

7

a
ab b
6
5
4
3

trt2 ctrl trt1

Realizamos un grafico ilustrando las diferencias registradas.

Preparamos los datos con dplyr

resumen_data <- PlantGrowth %>%

group_by(group)%>%
summarise(pesoMedio = mean(weight),
sd = sd(weight),
es = sd/sqrt(n()))

Preparamos los datos con FSA

TablaRes <- Summarize(weight ~ group, data= PlantGrowth)

TablaRes$ES <- TablaRes$sd / sqrt(TablaRes$n)

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Realizamos el grafico con ggplot

ggplot(resumen_data, aes(x=group, y=pesoMedio)) +

geom_bar(stat="identity", width=.5) +
labs(title="diferencia por grupo",
subtitle="Sub titulo",
caption="source: mpg") +
theme(axis.text.x = element_text(angle=0, vjust=0.6))+
ylab("peso")+
geom_errorbar(aes(ymin = pesoMedio - es,
ymax = pesoMedio + es),
width = 0.5,
size = 0.5)

diferencia por grupo

Sub titulo

4
peso

ctrl trt1 trt2

group
source: mpg

Grafico con colores y leyenda

ggplot(resumen_data, aes(x=group, y=pesoMedio)) +

geom_bar(stat="identity", width=.5, aes(fill= group)) +
labs(title="diferencia por grupo",
subtitle="Sub titulo",
caption="source: mpg") +
theme(axis.text.x = element_text(angle=0, vjust=0.6))+
ylab("peso")+
geom_errorbar(aes(ymin = pesoMedio - es,
ymax = pesoMedio + es,
color= group),

7
 width = 0.5,
size = 0.5)

diferencia por grupo

Sub titulo

4
group
ctrl
peso

trt1
trt2
2

ctrl trt1 trt2

group
source: mpg

ggplot(resumen_data, aes(x=group, y=pesoMedio)) +

geom_bar(fill= "yellow", stat="identity", width=.5) +
labs(title="diferencia por grupo",
subtitle="Sub titulo",
caption="source: mpg") +
theme(axis.text.x = element_text(angle=0, vjust=0.6))+
ylab("peso")+
geom_errorbar(aes(ymin = pesoMedio - es,
ymax = pesoMedio + es),
width = 0.5,
size = 0.5,
color= "red")

8
 diferencia por grupo
Sub titulo

4
peso

ctrl trt1 trt2

group
source: mpg