Sclerotinia Sclerotiorum com outliers
library(readxl)
library(agricolae)
library(dplyr)
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library(PerformanceAnalytics)
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library(plotly)
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library(tidyverse)
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library(reshape2)
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library(rgl)
library(car)
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library(sf)
## Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 6.3.1
library(tmap)
library(rgdal)
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library(esquisse)
library(ggplot2)
library(gridExtra)
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dt <- read_excel("C:/Users/User/Desktop/Sclerotinia_Sclerotiorum.xlsx",
sheet = "re3")
attach(dt)
names(dt)
## [1] "genot" "trat" "bloco" "folf" "talf" "folsec" "talsec" "rasec"
a <- as.factor(genot)
b <- as.factor(trat)
inter<-as.factor(a:b)
############ 1.1 anova folha fresca ###########################
summary(aov(folf ~ a+b+inter, data = dt))
## Df Sum Sq Mean Sq F value Pr(>F)
## a 4 32.1 8.0 1.709 0.174
## b 1 761.0 761.0 162.084 1.25e-13 ***
## inter 4 9.5 2.4 0.508 0.730
## Residuals 30 140.9 4.7
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
LSD.test(aov(folf ~ a + b + inter, data = dt),
"a", alpha = 0.05)["groups"]
## $groups
## folf groups
## MT 7.89000 a
## VF.1 6.16750 ab
## VG 5.68750 ab
## VA 5.53875 b
## VF 5.52000 b
LSD.test(aov(folf ~ a + b + inter, data = dt),
"b", alpha = 0.05)["groups"]
## $groups
## folf groups
## noinoc 10.5225 a
## ino 1.7990 b
LSD.test(aov(folf ~ a + b + inter, data = dt),
"inter", alpha = 0.05)["groups"]
## $groups
## folf groups
## MT:noinoc 13.0575 a
## VF.1:noinoc 10.6800 ab
## VG:noinoc 9.9775 ab
## VA:noinoc 9.7075 b
## VF:noinoc 9.1900 b
## MT:ino 2.7225 c
## VF:ino 1.8500 c
## VF.1:ino 1.6550 c
## VG:ino 1.3975 c
## VA:ino 1.3700 c
shapiro.test(unlist(aov(folf ~ a + b + inter,
data = dt)["residuals"]))
##
## Shapiro-Wilk normality test
##
## data: unlist(aov(folf ~ a + b + inter, data = dt)["residuals"])
## W = 0.91788, p-value = 0.006611
res <-sort(unlist(aov( folf ~ a + b + inter,
data = dt)["residuals"]),decreasing = TRUE)
ks.test(res, "pnorm" ,mean(res),sd(res))
##
## One-sample Kolmogorov-Smirnov test
##
## data: res
## D = 0.15311, p-value = 0.2763
## alternative hypothesis: two-sided
kruskal(folf, inter)["groups"]
## $groups
## folf groups
## MT:noinoc 34.000 a
## VF.1:noinoc 31.250 a
## VG:noinoc 30.500 a
## VA:noinoc 29.000 a
## VF:noinoc 27.750 a
## MT:ino 15.125 b
## VF:ino 12.250 b
## VF.1:ino 9.875 b
## VG:ino 8.250 b
## VA:ino 7.000 b
##### 1.2 anova talo fresco#########################################
summary(aov(talf ~ a+b+inter, data = dt))
## Df Sum Sq Mean Sq F value Pr(>F)
## a 4 67.6 16.9 13.149 2.66e-06 ***
## b 1 325.0 325.0 253.004 3.65e-16 ***
## inter 4 13.9 3.5 2.704 0.0491 *
## Residuals 30 38.5 1.3
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
LSD.test(aov(talf ~ a + b + inter, data = dt),
"a", alpha = 0.05)["groups"]
## $groups
## talf groups
## MT 7.12250 a
## VF 5.62125 b
## VF.1 5.54000 b
## VA 4.12250 c
## VG 3.38250 c
LSD.test(aov(talf~ a + b + inter, data = dt),
"b", alpha = 0.05)["groups"]
## $groups
## talf groups
## noinoc 8.0080 a
## ino 2.3075 b
LSD.test(aov(talf ~ a + b + inter, data = dt),
"inter", alpha = 0.05)["groups"]
## $groups
## talf groups
## MT:noinoc 10.8150 a
## VF.1:noinoc 8.6050 b
## VF:noinoc 8.3550 b
## VA:noinoc 7.0150 b
## VG:noinoc 5.2500 c
## MT:ino 3.4300 d
## VF:ino 2.8875 de
## VF.1:ino 2.4750 def
## VG:ino 1.5150 ef
## VA:ino 1.2300 f
shapiro.test(unlist(aov(talf ~ a + b + inter,
data = dt)["residuals"]))
##
## Shapiro-Wilk normality test
##
## data: unlist(aov(talf ~ a + b + inter, data = dt)["residuals"])
## W = 0.9805, p-value = 0.7082
res <-sort(unlist(aov( talf ~ a + b + inter,
data = dt)["residuals"]),decreasing = TRUE)
ks.test(res, "pnorm" ,mean(res),sd(res))
##
## One-sample Kolmogorov-Smirnov test
##
## data: res
## D = 0.094294, p-value = 0.8364
## alternative hypothesis: two-sided
kruskal(talf, inter)["groups"]
## $groups
## talf groups
## MT:noinoc 37.50 a
## VF.1:noinoc 32.75 ab
## VF:noinoc 32.25 ab
## VA:noinoc 27.50 bc
## VG:noinoc 21.50 cd
## MT:ino 16.25 de
## VF:ino 14.00 e
## VF.1:ino 11.00 ef
## VG:ino 7.50 fg
## VA:ino 4.75 g
#######1.3 anova folhas secas #################################
summary(aov(folsec ~ a+b+inter, data = dt))
## Df Sum Sq Mean Sq F value Pr(>F)
## a 4 0.3634 0.0909 1.264 0.3057
## b 1 0.4906 0.4906 6.828 0.0139 *
## inter 4 0.0590 0.0148 0.205 0.9334
## Residuals 30 2.1556 0.0719
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
LSD.test(aov(folsec ~ a + b + inter, data = dt),
"a", alpha = 0.05)["groups"]
## $groups
## folsec groups
## MT 0.68125 a
## VF 0.61875 a
## VF.1 0.51750 a
## VA 0.46000 a
## VG 0.42875 a
LSD.test(aov(folsec ~ a + b + inter, data = dt),
"b", alpha = 0.05)["groups"]
## $groups
## folsec groups
## ino 0.6520 a
## noinoc 0.4305 b
LSD.test(aov(folsec ~ a + b + inter, data = dt),
"inter", alpha = 0.05)["groups"]
## $groups
## folsec groups
## MT:ino 0.8450 a
## VF:ino 0.7675 ab
## VF.1:ino 0.5825 abc
## VA:ino 0.5500 abc
## MT:noinoc 0.5175 abc
## VG:ino 0.5150 abc
## VF:noinoc 0.4700 abc
## VF.1:noinoc 0.4525 bc
## VA:noinoc 0.3700 c
## VG:noinoc 0.3425 c
shapiro.test(unlist(aov(folsec ~ a + b + inter,
data = dt)["residuals"]))
##
## Shapiro-Wilk normality test
##
## data: unlist(aov(folsec ~ a + b + inter, data = dt)["residuals"])
## W = 0.95772, p-value = 0.1399
res <-sort(unlist(aov( folsec ~ a + b + inter,
data = dt)["residuals"]),decreasing = TRUE)
ks.test(res, "pnorm" ,mean(res),sd(res))
##
## One-sample Kolmogorov-Smirnov test
##
## data: res
## D = 0.095758, p-value = 0.8229
## alternative hypothesis: two-sided
kruskal(folsec, inter)["groups"]
## $groups
## folsec groups
## MT:ino 31.375 a
## VF:ino 28.250 a
## VA:ino 22.250 ab
## MT:noinoc 22.125 ab
## VF.1:ino 21.500 ab
## VG:ino 21.250 ab
## VF:noinoc 18.500 ab
## VF.1:noinoc 17.250 ab
## VA:noinoc 11.875 b
## VG:noinoc 10.625 b
#######1.4 anova talo seco #################################
summary(aov(talsec ~ a+b+inter, data = dt))
## Df Sum Sq Mean Sq F value Pr(>F)
## a 4 0.0060 0.001500 0.238 0.915
## b 1 0.0162 0.016201 2.566 0.120
## inter 4 0.0097 0.002424 0.384 0.818
## Residuals 30 0.1894 0.006315
LSD.test(aov(talsec ~ a + b + inter, data = dt),
"a", alpha = 0.05)["groups"]
## $groups
## talsec groups
## MT 0.1712500 a
## VF 0.1574125 a
## VG 0.1485125 a
## VF.1 0.1390500 a
## VA 0.1387500 a
LSD.test(aov(talsec ~ a + b + inter, data = dt),
"b", alpha = 0.05)["groups"]
## $groups
## talsec groups
## ino 0.17112 a
## noinoc 0.13087 a
LSD.test(aov(talsec ~ a + b + inter, data = dt),
"inter", alpha = 0.05)["groups"]
## $groups
## talsec groups
## MT:ino 0.200000 a
## VF:ino 0.190475 a
## VA:ino 0.175000 a
## VG:ino 0.149525 a
## VG:noinoc 0.147500 a
## MT:noinoc 0.142500 a
## VF.1:ino 0.140600 a
## VF.1:noinoc 0.137500 a
## VF:noinoc 0.124350 a
## VA:noinoc 0.102500 a
shapiro.test(unlist(aov(talsec ~ a + b + inter,
data = dt)["residuals"]))
##
## Shapiro-Wilk normality test
##
## data: unlist(aov(talsec ~ a + b + inter, data = dt)["residuals"])
## W = 0.97402, p-value = 0.4777
res <-sort(unlist(aov( talsec ~ a + b + inter,
data = dt)["residuals"]),decreasing = TRUE)
ks.test(res, "pnorm" ,mean(res),sd(res))
##
## One-sample Kolmogorov-Smirnov test
##
## data: res
## D = 0.06826, p-value = 0.9859
## alternative hypothesis: two-sided
kruskal(talsec, inter)["groups"]
## $groups
## talsec groups
## MT:ino 28.500 a
## VF:ino 28.000 a
## VA:ino 24.625 a
## VG:ino 21.000 a
## VF.1:ino 20.500 a
## VG:noinoc 20.125 a
## MT:noinoc 19.000 a
## VF:noinoc 16.125 a
## VF.1:noinoc 14.750 a
## VA:noinoc 12.375 a
#######1.5 anova raiz seca #################################
summary(aov(rasec ~ a+b+inter, data = dt))
## Df Sum Sq Mean Sq F value Pr(>F)
## a 4 0.231 0.0577 0.464 0.7617
## b 1 0.643 0.6426 5.169 0.0303 *
## inter 4 0.042 0.0104 0.084 0.9868
## Residuals 30 3.729 0.1243
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
LSD.test(aov(rasec ~ a + b + inter, data = dt),
"a", alpha = 0.05)["groups"]
## $groups
## rasec groups
## MT 0.83500 a
## VF 0.73750 a
## VF.1 0.73125 a
## VG 0.63750 a
## VA 0.62750 a
LSD.test(aov(rasec ~ a + b + inter, data = dt),
"b", alpha = 0.05)["groups"]
## $groups
## rasec groups
## ino 0.8405 a
## noinoc 0.5870 b
LSD.test(aov(rasec ~ a + b + inter, data = dt),
"inter", alpha = 0.05)["groups"]
## $groups
## rasec groups
## MT:ino 0.9025 a
## VF.1:ino 0.8775 a
## VF:ino 0.8625 a
## VG:ino 0.8000 a
## MT:noinoc 0.7675 a
## VA:ino 0.7600 a
## VF:noinoc 0.6125 a
## VF.1:noinoc 0.5850 a
## VA:noinoc 0.4950 a
## VG:noinoc 0.4750 a
shapiro.test(unlist(aov(rasec ~ a + b + inter,
data = dt)["residuals"]))
##
## Shapiro-Wilk normality test
##
## data: unlist(aov(rasec ~ a + b + inter, data = dt)["residuals"])
## W = 0.98013, p-value = 0.6943
res <-sort(unlist(aov( rasec ~ a + b + inter,
data = dt)["residuals"]),decreasing = TRUE)
ks.test(res, "pnorm" ,mean(res),sd(res))
## Warning in ks.test(res, "pnorm", mean(res), sd(res)): ties should not be present
## for the Kolmogorov-Smirnov test
##
## One-sample Kolmogorov-Smirnov test
##
## data: res
## D = 0.080428, p-value = 0.9581
## alternative hypothesis: two-sided
kruskal(rasec, inter)["groups"]
## $groups
## rasec groups
## MT:ino 27.250 a
## VF.1:ino 24.625 a
## VF:ino 24.500 a
## MT:noinoc 23.000 a
## VA:ino 22.625 a
## VG:ino 22.625 a
## VF:noinoc 18.375 a
## VF.1:noinoc 16.000 a
## VG:noinoc 13.125 a
## VA:noinoc 12.875 a