Tarea 01

Manuel SpÃà fÆ’Ãïà¿Ã ½nola

Ejercicio 1
Con el set de datos “butterfat” del paquete “GLMsData” realizar un anÃÃ ¡lisis del
contenido de grasa en porcentaje de vacas de 2 aÃÃ ±os y mayores de 4 aÃÃ ±os de 5
razas diferentes.
1. QuÃÃ © razas tiene el mÃÃ ¡s alto y el mÃÃ ¡s bajo contenido de grasa en su leche?
Muestra un grÃÃ ¡fico para el modelo resultante y los valores medios para ambas
razas.

2. Cuanto mÃÃ ¡s contenido de grasa en porcentaje tiene la raza Jersey con respecto
a la raza Holstein-Fresian? Muestra el tamaÃÃ ±o del efecto.

3. Cual es la diferencia del contenido de grasa en procentaje para vacas de 2 aÃÃ ±os
y mayores de 4 aÃÃ ±os? Muestra un grÃÃ ¡fico y el tamaÃÃ ±o del efecto.
library(tidyverse)

## -- Attaching packages -----------------------------------------

tidyverse 1.2.1 --

## v ggplot2 3.1.0 v purrr 0.3.2

## v tibble 2.1.1 v dplyr 0.8.0.1
## v tidyr 0.8.3 v stringr 1.4.0
## v readr 1.3.1 v forcats 0.4.0

## -- Conflicts --------------------------------------------
tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()

library(carData)
library(visdat)
library(ggplot2)
library(dplyr)
library(psycho)

## Warning: replacing previous import 'loo::kfold' by 'rstanarm::kfold'

when
## loading 'psycho'

library(tidyverse)
library(visreg)
library(sjPlot)
## Warning in checkMatrixPackageVersion(): Package version
inconsistency detected.
## TMB was built with Matrix version 1.2.17
## Current Matrix version is 1.2.15
## Please re-install 'TMB' from source using install.packages('TMB',
type = 'source') or ask CRAN for a binary version of 'TMB' matching
CRAN's 'Matrix' package

library(jtools)

##
## Attaching package: 'jtools'

## The following objects are masked from 'package:psycho':

##
## get_data, standardize

library(bbmle)

## Loading required package: stats4

##
## Attaching package: 'bbmle'

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

##
## slice

library(readxl)
library(visdat)
library(readr)
library(emmeans)
library(GLMsData)

data(butterfat)

bf <- butterfat

bf

## Butterfat Breed Age

## 1 3.74 Ayrshire Mature
## 2 4.01 Ayrshire 2year
## 3 3.77 Ayrshire Mature
## 4 3.78 Ayrshire 2year
## 5 4.10 Ayrshire Mature
## 6 4.06 Ayrshire 2year
## 7 4.27 Ayrshire Mature
## 8 3.94 Ayrshire 2year
## 9 4.11 Ayrshire Mature
## 10 4.25 Ayrshire 2year
## 11 4.44 Ayrshire Mature
## 12 4.37 Ayrshire 2year
## 13 4.25 Ayrshire Mature
## 14 3.71 Ayrshire 2year
## 15 4.08 Ayrshire Mature
## 16 3.90 Ayrshire 2year
## 17 4.41 Ayrshire Mature
## 18 4.11 Ayrshire 2year
## 19 4.37 Ayrshire Mature
## 20 3.53 Ayrshire 2year
## 21 3.92 Canadian Mature
## 22 4.95 Canadian 2year
## 23 4.47 Canadian Mature
## 24 4.28 Canadian 2year
## 25 4.07 Canadian Mature
## 26 4.10 Canadian 2year
## 27 4.38 Canadian Mature
## 28 3.98 Canadian 2year
## 29 4.46 Canadian Mature
## 30 5.05 Canadian 2year
## 31 4.29 Canadian Mature
## 32 5.24 Canadian 2year
## 33 4.43 Canadian Mature
## 34 4.00 Canadian 2year
## 35 4.62 Canadian Mature
## 36 4.29 Canadian 2year
## 37 4.85 Canadian Mature
## 38 4.66 Canadian 2year
## 39 4.40 Canadian Mature
## 40 4.33 Canadian 2year
## 41 4.54 Guernsey Mature
## 42 5.18 Guernsey 2year
## 43 5.75 Guernsey Mature
## 44 5.04 Guernsey 2year
## 45 4.64 Guernsey Mature
## 46 4.79 Guernsey 2year
## 47 4.72 Guernsey Mature
## 48 3.88 Guernsey 2year
## 49 5.28 Guernsey Mature
## 50 4.66 Guernsey 2year
## 51 5.30 Guernsey Mature
## 52 4.50 Guernsey 2year
## 53 4.59 Guernsey Mature
## 54 5.04 Guernsey 2year
## 55 4.83 Guernsey Mature
## 56 4.55 Guernsey 2year
## 57 4.97 Guernsey Mature
## 58 5.38 Guernsey 2year
## 59 5.39 Guernsey Mature
## 60 5.97 Guernsey 2year
## 61 3.40 Holstein-Fresian Mature
## 62 3.55 Holstein-Fresian 2year
## 63 3.83 Holstein-Fresian Mature
## 64 3.95 Holstein-Fresian 2year
## 65 4.43 Holstein-Fresian Mature
## 66 3.70 Holstein-Fresian 2year
## 67 3.30 Holstein-Fresian Mature
## 68 3.93 Holstein-Fresian 2year
## 69 3.58 Holstein-Fresian Mature
## 70 3.54 Holstein-Fresian 2year
## 71 3.79 Holstein-Fresian Mature
## 72 3.66 Holstein-Fresian 2year
## 73 3.58 Holstein-Fresian Mature
## 74 3.38 Holstein-Fresian 2year
## 75 3.71 Holstein-Fresian Mature
## 76 3.94 Holstein-Fresian 2year
## 77 3.59 Holstein-Fresian Mature
## 78 3.55 Holstein-Fresian 2year
## 79 3.55 Holstein-Fresian Mature
## 80 3.43 Holstein-Fresian 2year
## 81 4.80 Jersey Mature
## 82 6.45 Jersey 2year
## 83 5.18 Jersey Mature
## 84 4.49 Jersey 2year
## 85 5.24 Jersey Mature
## 86 5.70 Jersey 2year
## 87 5.41 Jersey Mature
## 88 4.77 Jersey 2year
## 89 5.18 Jersey Mature
## 90 5.23 Jersey 2year
## 91 5.75 Jersey Mature
## 92 5.14 Jersey 2year
## 93 5.25 Jersey Mature
## 94 4.76 Jersey 2year
## 95 5.18 Jersey Mature
## 96 4.22 Jersey 2year
## 97 5.98 Jersey Mature
## 98 4.85 Jersey 2year
## 99 6.55 Jersey Mature
## 100 5.72 Jersey 2year

arrange(bf, - Butterfat, Breed)

## Butterfat Breed Age

## 1 6.55 Jersey Mature
## 2 6.45 Jersey 2year
## 3 5.98 Jersey Mature
## 4 5.97 Guernsey 2year
## 5 5.75 Guernsey Mature
## 6 5.75 Jersey Mature
## 7 5.72 Jersey 2year
## 8 5.70 Jersey 2year
## 9 5.41 Jersey Mature
## 10 5.39 Guernsey Mature
## 11 5.38 Guernsey 2year
## 12 5.30 Guernsey Mature
## 13 5.28 Guernsey Mature
## 14 5.25 Jersey Mature
## 15 5.24 Canadian 2year
## 16 5.24 Jersey Mature
## 17 5.23 Jersey 2year
## 18 5.18 Guernsey 2year
## 19 5.18 Jersey Mature
## 20 5.18 Jersey Mature
## 21 5.18 Jersey Mature
## 22 5.14 Jersey 2year
## 23 5.05 Canadian 2year
## 24 5.04 Guernsey 2year
## 25 5.04 Guernsey 2year
## 26 4.97 Guernsey Mature
## 27 4.95 Canadian 2year
## 28 4.85 Canadian Mature
## 29 4.85 Jersey 2year
## 30 4.83 Guernsey Mature
## 31 4.80 Jersey Mature
## 32 4.79 Guernsey 2year
## 33 4.77 Jersey 2year
## 34 4.76 Jersey 2year
## 35 4.72 Guernsey Mature
## 36 4.66 Canadian 2year
## 37 4.66 Guernsey 2year
## 38 4.64 Guernsey Mature
## 39 4.62 Canadian Mature
## 40 4.59 Guernsey Mature
## 41 4.55 Guernsey 2year
## 42 4.54 Guernsey Mature
## 43 4.50 Guernsey 2year
## 44 4.49 Jersey 2year
## 45 4.47 Canadian Mature
## 46 4.46 Canadian Mature
## 47 4.44 Ayrshire Mature
## 48 4.43 Canadian Mature
## 49 4.43 Holstein-Fresian Mature
## 50 4.41 Ayrshire Mature
## 51 4.40 Canadian Mature
## 52 4.38 Canadian Mature
## 53 4.37 Ayrshire 2year
## 54 4.37 Ayrshire Mature
## 55 4.33 Canadian 2year
## 56 4.29 Canadian Mature
## 57 4.29 Canadian 2year
## 58 4.28 Canadian 2year
## 59 4.27 Ayrshire Mature
## 60 4.25 Ayrshire 2year
## 61 4.25 Ayrshire Mature
## 62 4.22 Jersey 2year
## 63 4.11 Ayrshire Mature
## 64 4.11 Ayrshire 2year
## 65 4.10 Ayrshire Mature
## 66 4.10 Canadian 2year
## 67 4.08 Ayrshire Mature
## 68 4.07 Canadian Mature
## 69 4.06 Ayrshire 2year
## 70 4.01 Ayrshire 2year
## 71 4.00 Canadian 2year
## 72 3.98 Canadian 2year
## 73 3.95 Holstein-Fresian 2year
## 74 3.94 Ayrshire 2year
## 75 3.94 Holstein-Fresian 2year
## 76 3.93 Holstein-Fresian 2year
## 77 3.92 Canadian Mature
## 78 3.90 Ayrshire 2year
## 79 3.88 Guernsey 2year
## 80 3.83 Holstein-Fresian Mature
## 81 3.79 Holstein-Fresian Mature
## 82 3.78 Ayrshire 2year
## 83 3.77 Ayrshire Mature
## 84 3.74 Ayrshire Mature
## 85 3.71 Ayrshire 2year
## 86 3.71 Holstein-Fresian Mature
## 87 3.70 Holstein-Fresian 2year
## 88 3.66 Holstein-Fresian 2year
## 89 3.59 Holstein-Fresian Mature
## 90 3.58 Holstein-Fresian Mature
## 91 3.58 Holstein-Fresian Mature
## 92 3.55 Holstein-Fresian 2year
## 93 3.55 Holstein-Fresian 2year
## 94 3.55 Holstein-Fresian Mature
## 95 3.54 Holstein-Fresian 2year
## 96 3.53 Ayrshire 2year
## 97 3.43 Holstein-Fresian 2year
## 98 3.40 Holstein-Fresian Mature
## 99 3.38 Holstein-Fresian 2year
## 100 3.30 Holstein-Fresian Mature

bf_1 <- subset(bf, subset = Breed %in% c("Jersey", "Holstein-Fresian"))

bf1 <- bf %>%

group_by(Breed) %>%
summarise(P_Bf = mean(Butterfat))
bf1

## # A tibble: 5 x 2
## Breed P_Bf
## <fct> <dbl>
## 1 Ayrshire 4.06
## 2 Canadian 4.44
## 3 Guernsey 4.95
## 4 Holstein-Fresian 3.67
## 5 Jersey 5.29

g1 <- ggplot(bf, aes( x = Breed , y = Butterfat )) + geom_jitter(width

= 0.2) + geom_boxplot(alpha = 0.5) + geom_point(data= bf1 , aes(Breed,
P_Bf) , color = "red", size = 2)
g1

1. QuÃÃ © razas tiene el mÃÃ ¡s alto y el mÃÃ ¡s bajo contenido de grasa en su leche?
Muestra un grÃÃ ¡fico para el modelo resultante y los valores medios para ambas
razas.
Se pueden observar seguú n el graú fico para el modelo sobre porcentaje de grasa, que
las razas Jersey y Holstein-Fresian son las de mayor y menor valor. La raza Jersey
tiene una media en porcentaje de grasa de 5.925, mientras que la raza Holstein-
Fresian tiene una media de 3.6695
Lm_Bf <- lm(Butterfat ~ Breed, data = bf_1)
visreg(Lm_Bf)

2.
Cuanto mÃÃ ¡s contenido de grasa en porcentaje tiene la raza Jersey con respecto a la
raza Holstein-Fresian? Muestra el tamaÃÃ ±o del efecto.
Se puede ver en este caso que la raza Jersey tiene un porcentaje de grasa 1.6230
mayor que la raza Holstein-Fresian.
summary(Lm_Bf)

##
## Call:
## lm(formula = Butterfat ~ Breed, data = bf_1)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.0725 -0.1742 -0.0845 0.1855 1.2575
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 3.6695 0.1032 35.55 < 2e-16 ***
## BreedJersey 1.6230 0.1460 11.12 1.66e-13 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4616 on 38 degrees of freedom
## Multiple R-squared: 0.7649, Adjusted R-squared: 0.7587
## F-statistic: 123.6 on 1 and 38 DF, p-value: 1.656e-13
bf2 <- bf %>%
group_by(Age) %>%
summarise(Media = mean(Butterfat))

bf2

## # A tibble: 2 x 2
## Age Media
## <fct> <dbl>
## 1 2year 4.43
## 2 Mature 4.53

Cual es la diferencia del contenido de grasa en procentaje para vacas de 2 aÃÃ ±os y
mayores de 4 aÃÃ ±os? Muestra un grÃÃ ¡fico y el tamaÃÃ ±o del efecto.
g2 <- ggplot(bf_1, aes( x = Age , y = Butterfat)) + geom_jitter(width
= 0.2) + geom_point(data= bf2 , aes(Age, Media) , color = "red", size
= 2)
g2

lm1 <- lm(Butterfat ~ Age, data = bf)

visreg(lm1)
summary(lm1)

##
## Call:
## lm(formula = Butterfat ~ Age, data = bf)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.2344 -0.4923 -0.1044 0.5427 2.0202
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 4.4298 0.1014 43.672 <2e-16 ***
## AgeMature 0.1046 0.1434 0.729 0.468
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.7172 on 98 degrees of freedom
## Multiple R-squared: 0.005396, Adjusted R-squared: -0.004753
## F-statistic: 0.5317 on 1 and 98 DF, p-value: 0.4676

Se puede ver en este caso que las vacas mayores de 4 anñ os, tienen un porcentaje de
grasa del 0.1046 porciento mayor que vas de 2 anñ os de edad.