The Not So Short Introduction to agricolae

Felipe de Mendiburu1, Muhammad Yaseen2

2020-05-02

Source: vignettes/Introduction.Rmd

  1. Professor of the Academic Department of Statistics and Informatics of the Faculty of Economics and Planning.National University Agraria La Molina-PERU.

  1. Department of Mathematics and Statistics, University of Agriculture Faisalabad, Pakistan.

Introduction

The package agricolae offers a broad functionality in the design of experiments, especially for experiments in agriculture and improvements of plants, which can also be used for other purposes. It contains the following designs: lattice, alpha, cyclic, balanced incomplete block designs, complete randomized blocks, Latin, Graeco-Latin, augmented block designs, split plot and strip plot. It also has several procedures of experimental data analysis, such as the comparisons of treatments of Waller-Duncan, Bonferroni, Duncan, Student-Newman-Keuls, Scheffe, Ryan, Einot and Gabriel and Welsch multiple range test or the classic LSD and Tukey; and non-parametric comparisons, such as Kruskal-Wallis, Friedman, Durbin, Median and Waerden, stability analysis, and other procedures applied in genetics, as well as procedures in biodiversity and descriptive statistics, Mendiburu (2009)

Installation

The main program of R should be already installed in the platform of your computer (Windows, Linux or MAC). If it is not installed yet, you can download it from the R project https://www.r-project.org/ of a repository CRAN.

install.packages("agricolae")

Once the agricolae package is installed, it needs to be made accessible to the current R session by the command:

library(agricolae)

For online help facilities or the details of a particular command (such as the function waller.test) you can type:

help(package="agricolae")
help(waller.test)

For a complete functionality, agricolae requires other packages
MASS: for the generalized inverse used in the function PBIB.test
nlme: for the methods REML and LM in PBIB.test
klaR: for the function triplot used in the function AMMI
cluster: for the use of the function consensus
AlgDesign: for the balanced incomplete block design design.bib

Use in R

Since agricolae is a package of functions, these are operational when they are called directly from the console of R and are integrated to all the base functions of R. The following orders are frequent:

detach(package:agricolae) # detach package agricole
library(agricolae) # Load the package to the memory
designs<-apropos("design")
print(designs[substr(designs,1,6)=="design"], row.names=FALSE)
 [1] "design.ab"      "design.alpha"   "design.bib"     "design.crd"    
 [5] "design.cyclic"  "design.dau"     "design.graeco"  "design.lattice"
 [9] "design.lsd"     "design.rcbd"    "design.split"   "design.strip"  
[13] "design.youden" 
For the use of symbols that do not appear in the keyboard in Spanish, such as:

~, [, ], &, ^, |. <, >, {, }, \% or others, use the table ASCII code.
library(agricolae) # Load the package to the memory:

In order to continue with the command line, do not forget to close the open windows with any R order. For help:

help(graph.freq)
? (graph.freq)
str(normal.freq)
example(join.freq)

Data set in agricolae 

A<-as.data.frame(data(package="agricolae")$results[,3:4])
A[,2]<-paste(substr(A[,2],1,35),"..",sep=".")
head(A)
            Item                                  Title
1            CIC    Data for late blight of potatoes...
2        Chz2006         Data amendment Carhuaz 2006...
3  ComasOxapampa         Data AUDPC Comas - Oxapampa...
4             DC Data for the analysis of carolina g...
5 Glycoalkaloids                 Data Glycoalkaloids...
6        Hco2006         Data amendment Huanuco 2006...

References

Mendiburu, F. de (2009). Una herramienta de análisis estadístico para la investigación agrícola.