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## Load all the libraries needed and the data
library(readr)
library(mosaic)
library(FSA)
library("ggplot2")
library(readxl)
library(knitr)
library(doBy)
library(agricolae)
options(scipen=999, digits = 0)
mydata <- read_excel("./data/2016-Solanum-01-11_Isolates(Germplasms).xlsx")
## getwd()
####Eggs PER PLANT ####
##Create a subset of the desire variable
Sub.Eggs <- subset(mydata,
                   select=c(Nger, 
                            Isolate, 
                            EggsP) ) 
####Isolate: MIAd####
Sub.Eggs.MIAd <- subset(Sub.Eggs, Isolate == "MIAd", select=c(Nger, EggsP)) 
Sub.Eggs.MIAd$Nger = factor (Sub.Eggs.MIAd$Nger, labels=c("EC", "TB", "TE", "TS", "TT")) 
###Descriptive statistics calculation###
Sub.Eggs.MIAd.EC <- subset(Sub.Eggs.MIAd, Nger == "EC", select=c(Nger,EggsP))
Me.EP.MIAd.EC <- mean(Sub.Eggs.MIAd.EC$EggsP, na.mr=FALSE)
Me.EP.MIAd.EC <- round(Me.EP.MIAd.EC, digits=2)
Se.EP.MIAd.EC <- se(Sub.Eggs.MIAd.EC$EggsP)
Se.EP.MIAd.EC <- round(Se.EP.MIAd.EC, digits=2)
Sub.Eggs.MIAd.SB <- subset(Sub.Eggs.MIAd, Nger == "TB", select=c(Nger,EggsP))
Me.EP.MIAd.TB <- mean(Sub.Eggs.MIAd.SB$EggsP, na.mr=FALSE)
Me.EP.MIAd.TB <- round(Me.EP.MIAd.TB, digits=2)
Se.EP.MIAd.TB <- se(Sub.Eggs.MIAd.SB$EggsP)
Se.EP.MIAd.TB <- round(Se.EP.MIAd.TB, digits=2)
Sub.Eggs.MIAd.SB <- subset(Sub.Eggs.MIAd, Nger == "TE", select=c(Nger,EggsP))
Me.EP.MIAd.TE <- mean(Sub.Eggs.MIAd.SB$EggsP, na.mr=FALSE)
Me.EP.MIAd.TE <- round(Me.EP.MIAd.TE, digits=2)
Se.EP.MIAd.TE <- se(Sub.Eggs.MIAd.SB$EggsP)
Se.EP.MIAd.TE <- round(Se.EP.MIAd.TE, digits=2)
Sub.Eggs.MIAd.SB <- subset(Sub.Eggs.MIAd, Nger == "TS", select=c(Nger,EggsP))
Me.EP.MIAd.TS <- mean(Sub.Eggs.MIAd.SB$EggsP, na.mr=FALSE)
Me.EP.MIAd.TS <- round(Me.EP.MIAd.TS, digits=2)
Se.EP.MIAd.TS <- se(Sub.Eggs.MIAd.SB$EggsP)
Se.EP.MIAd.TS <- round(Se.EP.MIAd.TS, digits=2)
Sub.Eggs.MIAd.SB <- subset(Sub.Eggs.MIAd, Nger == "TT", select=c(Nger,EggsP))
Me.EP.MIAd.TT <- mean(Sub.Eggs.MIAd.SB$EggsP, na.mr=FALSE)
Me.EP.MIAd.TT <- round(Me.EP.MIAd.TT, digits=2)
Se.EP.MIAd.TT <- se(Sub.Eggs.MIAd.SB$EggsP)
Se.EP.MIAd.TT <- round(Se.EP.MIAd.TT, digits=2)
####Kruskall-Wallis test calculation####
KTMIAd = kruskal.test(Sub.Eggs.MIAd$EggsP ~ Sub.Eggs.MIAd$Nger)
####Dunn test calculation####
DTMIAd = dunnTest(Sub.Eggs.MIAd$EggsP ~ Sub.Eggs.MIAd$Nger, method="bonferroni")
DTMIAd.Comparison <- DTMIAd$res$Comparison
DTMIAd.Padj <- round (DTMIAd$res$P.adj, digits=5)
KrusData = data.frame(DTMIAd.Comparison, DTMIAd.Padj)
RND = nrow(DTMIAd$res)
krustable=kable(KrusData[1:RND,])
if (KTMIAd$p.value>0.05) {
dif="There is no significative differences (P<0.05) between treatments (P<0.05)"
krustable="0"
} else {
dif="There is significative differences between treatments (P<0.05)."
krustable=kable(KrusData[1:RND,])
boxplot(Sub.Eggs.MIAd$EggsP ~ Sub.Eggs.MIAd$Nger, main = "MIAd", xlab = "Germplasm", ylab = "Eggs per plant")
DTMIAd$dtres

}

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\documentclass[11pt,twoside,a4paper,openright]{report}


%%%%% packages %%%%%

\usepackage{adjustbox}
\usepackage{amsmath}
\usepackage{array}

\usepackage[backend=biber, style=chicago-authordate, natbib=true, maxcitenames=2, maxbibnames=6, minbibnames=6,sorting=nyt, firstinits=true]{biblatex}
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\usepackage{fancyhdr}
\usepackage{float}
\usepackage{gensymb}
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\usepackage{graphicx}
\usepackage[utf8]{inputenc}
\usepackage{makecell}
\usepackage{multicol}
\usepackage{pgfplots, pgfplotstable}
\usepackage{rotating}
\usepackage{subcaption}
\usepackage{tikz}
\usepackage{wrapfig}
\usepackage{wallpaper}

%\usepackage[scaled=0.92]{helvet}

%%%%% Config %%%%%

\graphicspath{ {images/} }

\pagestyle{fancy}
%\fancyhead[LE,RO]{\scriptsize \slshape PhD dissertation}
%\fancyhead[LO,RE]{\tiny \slshape \leftmark}
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\fancyhead[C]{\small \slshape Chapter \thechapter: \leftmark}
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\usetikzlibrary{calc}
\usetikzlibrary{arrows}
\usetikzlibrary{shapes,snakes}

\pgfplotsset{compat=1.10}

\addbibresource{MyCollection.bib}

\DeclareFieldFormat
[article,inbook,incollection,inproceedings,patent,thesis,unpublished,online,misc]
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\title{Durability of resistance to \textit{Meloidogyne} mediated by R-genes in Solanaceae and Cucurbitaceae crops}
\author{Helio A. Garc\'ia Mend\'ivil}
\date{Day Month Year}


%%%%% Data tables %%%%%

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	1.618048097	4.415021645	a
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\AtBeginBibliography{\footnotesize}

%%%% Document %%%%%

\begin{document}


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