agricolae: Statistical Procedures for Agricultural Research

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Original idea was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, National Engineering University (UNI), Lima-Peru. Some experimental data for the examples come from the CIP and others research. Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, factorial, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.

Author
Felipe de Mendiburu
Date of publication
2016-06-12 23:33:27
Maintainer
Felipe de Mendiburu <f.mendiburu@cgiar.org>
License
GPL
Version
1.2-4
URLs

View on CRAN

Man pages

agricolae-package
Statistical Procedures for Agricultural Research
AMMI
AMMI Analysis
AMMI.contour
AMMI contour
audpc
Calculating the absolute or relative value of the AUDPC
audps
The Area Under the Disease Progress Stairs
bar.err
Plotting the standard error or standard deviance of a...
bar.group
Plotting the multiple comparison of means
BIB.test
Finding the Variance Analysis of the Balanced Incomplete...
carolina
North Carolina Designs I, II and III
Chz2006
Data amendment Carhuaz 2006
CIC
Data for late blight of potatoes
clay
Data of Ralstonia population in clay soil
ComasOxapampa
Data AUDPC Comas - Oxapampa
consensus
consensus of clusters
corn
Data of corn
correl
Correlation Coefficient
correlation
Correlation analysis. Methods of Pearson, Spearman, Kendall...
cotton
Data of cotton
cv.model
Coefficient of the experiment variation
cv.similarity
Coefficient of the similarity matrix variation
DAU.test
Finding the Variance Analysis of the Augmented block Design
DC
Data for the analysis of carolina genetic design
delete.na
Omitting the rows or columns with missing observations of a...
design.ab
Design of experiments for a factorial
design.alpha
Alpha design type (0,1)
design.bib
Randomized Balanced Incomplete Block Designs. BIB
design.crd
Completely Randomized Design
design.cyclic
Cyclic designs
design.dau
Augmented block design
design.graeco
Graeco - latin square design
design.lattice
Lattice designs
design.lsd
Latin Square Design
design.rcbd
Randomized Complete Block Design
design.split
Split Plot Design
design.strip
Strip Plot Design
diffograph
Plotting the multiple comparison of means
disease
Data evaluation of the disease overtime
duncan.test
Duncan's new multiple range test
durbin.test
Durbin test and multiple comparison of treatments
friedman
Friedman test and multiple comparison of treatments
frijol
Data of frijol
genxenv
Data of potato yield in a different environment
Glycoalkaloids
Data Glycoalkaloids
graph.freq
Histogram
grass
Data for Friedman test
greenhouse
Data in greenhouse
growth
Data growth of trees
haynes
Data of AUDPC for nonparametrical stability analysis
Hco2006
Data amendment Huanuco 2006
hcut
Cut tree of consensus
heterosis
Data of potato, Heterosis
hgroups
groups of hclust
HSD.test
Multiple comparisons: Tukey
huasahuasi
Data: Rainfall thresholds as support for timing fungicide...
indexAMMI
AMMI index and yield stability
index.bio
Biodiversity Index
index.smith
Uniformity soil. Smith's Index of Soil Heterogeneity
intervals.freq
Class intervals
join.freq
Join class for histogram
kendall
Correlation of Kendall
kruskal
Kruskal Wallis test and multiple comparison of treatments.
kurtosis
Finding the Kurtosis coefficient
lastC
Setting the last character of a chain
lateblight
LATEBLIGHT - Simulator for potato late blight Version LB2004
lineXtester
Line x Tester Analysis
LSD.test
Multiple comparisons, "Least significant difference" and...
LxT
Data Line by tester
markers
Data of molecular markers
melon
Data of yield of melon in a Latin square experiment
montecarlo
Random generation by Montecarlo
natives
Data of native potato
nonadditivity
Nonadditivity model test
normal.freq
Normal curve on the histogram
ogive.freq
Plotting the ogive from a histogram
order.group
Ordering the treatments according to the multiple comparison
orderPvalue
Grouping the treatments averages in a comparison with a...
order.stat
Grouping the treatments averages in a comparison with a...
pamCIP
Data Potato Wild
paracsho
Data of Paracsho biodiversity
path.analysis
Path Analysis
PBIB.test
Analysis of the Partially Balanced Incomplete Block Design
plotAMMI
PLOT AMMI
plot.graph.freq
Histogram
plots
Data for an analysis in split-plot
plrv
Data clones from the PLRV population
polygon.freq
The polygon of frequency on the histogram
potato
Data of cutting
ralstonia
Data of assessment of the population in the soil...
reg.homog
Homologation of regressions
REGW.test
Ryan, Einot and Gabriel and Welsch multiple range test
resampling.cv
Resampling to find the optimal number of markers
resampling.model
Resampling for linear models
rice
Data of Grain yield of rice variety IR8
RioChillon
Data and analysis Mother and baby trials
scheffe.test
Multiple comparisons, scheffe
similarity
Matrix of similarity in binary data
simulation.model
Simulation of the linear model under normality
sinRepAmmi
Data for AMMI without repetition
skewness
Finding the skewness coefficient
SNK.test
Student-Newman-Keuls (SNK)
soil
Data of soil analysis for 13 localities
sp.plot
Splip-Plot analysis
ssp.plot
Split-split-Plot analysis
stability.nonpar
Nonparametric stability analysis
stability.par
Stability analysis. SHUKLA'S STABILITY VARIANCE AND KANG'S
stat.freq
Descriptive measures of grouped data
strip.plot
Strip-Plot analysis
sturges.freq
Class intervals for a histogram, the rule of Sturges
summary.graph.freq
frequency Table of a Histogram
sweetpotato
Data of sweetpotato yield
table.freq
frequency Table of a Histogram
tapply.stat
Statistics of data grouped by factors
VanderWarden
Multiple comparisons. The van der Waerden (Normal Scores)
vark
Variance K, ties, Kendall
waller
Computations of Bayesian t-values for multiple comparisons
waller.test
Multiple comparisons, Waller-Duncan
wilt
Data of Bacterial Wilt (AUDPC) and soil
yacon
Data Yacon
zigzag
order plot in serpentine

Files in this package

agricolae
agricolae/inst
agricolae/inst/doc
agricolae/inst/doc/tutorial.Rnw
agricolae/inst/doc/tutorial.pdf
agricolae/inst/doc/tutorial.R
agricolae/inst/external
agricolae/inst/external/severity.csv
agricolae/inst/external/weather.csv
agricolae/NAMESPACE
agricolae/NEWS
agricolae/data
agricolae/data/DC.rda
agricolae/data/paracsho.rda
agricolae/data/genxenv.rda
agricolae/data/yacon.rda
agricolae/data/frijol.rda
agricolae/data/rice.rda
agricolae/data/wilt.rda
agricolae/data/pamCIP.rda
agricolae/data/RioChillon.rda
agricolae/data/markers.rda
agricolae/data/grass.rda
agricolae/data/Chz2006.rda
agricolae/data/growth.rda
agricolae/data/disease.rda
agricolae/data/corn.rda
agricolae/data/potato.rda
agricolae/data/plrv.rda
agricolae/data/LxT.rda
agricolae/data/melon.rda
agricolae/data/clay.rda
agricolae/data/ralstonia.rda
agricolae/data/Hco2006.rda
agricolae/data/cotton.rda
agricolae/data/plots.rda
agricolae/data/soil.rda
agricolae/data/ComasOxapampa.rda
agricolae/data/natives.rda
agricolae/data/CIC.rda
agricolae/data/Glycoalkaloids.rda
agricolae/data/greenhouse.rda
agricolae/data/sinRepAmmi.rda
agricolae/data/sweetpotato.rda
agricolae/data/haynes.rda
agricolae/data/heterosis.rda
agricolae/data/huasahuasi.rda
agricolae/R
agricolae/R/summary.graph.freq.R
agricolae/R/audpc.R
agricolae/R/polygon.freq.R
agricolae/R/intervals.freq.R
agricolae/R/delete.na.R
agricolae/R/order.group.R
agricolae/R/cv.similarity.R
agricolae/R/design.strip.R
agricolae/R/reg.homog.R
agricolae/R/design.lattice.R
agricolae/R/index.smith.R
agricolae/R/stability.nonpar.R
agricolae/R/waller.test.R
agricolae/R/nonadditivity.R
agricolae/R/path.analysis.R
agricolae/R/design.youden.R
agricolae/R/LSD.test.R
agricolae/R/resampling.model.R
agricolae/R/waerden.test.R
agricolae/R/design.split.R
agricolae/R/design.rcbd.R
agricolae/R/diffograph.R
agricolae/R/normal.freq.R
agricolae/R/lineXtester.R
agricolae/R/scheffe.test.R
agricolae/R/design.graeco.R
agricolae/R/BIB.test.R
agricolae/R/stat.freq.R
agricolae/R/audps.R
agricolae/R/friedman.R
agricolae/R/design.crd.R
agricolae/R/duncan.test.R
agricolae/R/design.ab.R
agricolae/R/design.cyclic.R
agricolae/R/lateblight.R
agricolae/R/design.dau.R
agricolae/R/order.stat.R
agricolae/R/PBIB.test.R
agricolae/R/strip.plot.R
agricolae/R/bar.group.R
agricolae/R/resampling.cv.R
agricolae/R/sp.plot.R
agricolae/R/correl.R
agricolae/R/stability.par.R
agricolae/R/design.lsd.R
agricolae/R/kendall.R
agricolae/R/table.freq.R
agricolae/R/montecarlo.R
agricolae/R/ssp.plot.R
agricolae/R/ogive.freq.R
agricolae/R/design.alpha.R
agricolae/R/weatherSeverity.R
agricolae/R/cv.model.R
agricolae/R/zigzag.R
agricolae/R/join.freq.R
agricolae/R/kruskal.R
agricolae/R/waller.R
agricolae/R/skewness.R
agricolae/R/index.bio.R
agricolae/R/hcut.R
agricolae/R/HSD.test.R
agricolae/R/Median.test.R
agricolae/R/design.bib.R
agricolae/R/REGW.test.R
agricolae/R/SNK.test.R
agricolae/R/carolina.R
agricolae/R/tapply.stat.R
agricolae/R/lastC.R
agricolae/R/simulation.model.R
agricolae/R/index.AMMI.R
agricolae/R/similarity.R
agricolae/R/hgroups.R
agricolae/R/bar.err.R
agricolae/R/kurtosis.R
agricolae/R/orderPvalue.R
agricolae/R/AMMI.R
agricolae/R/graph.freq.R
agricolae/R/vark.R
agricolae/R/AMMI.contour.R
agricolae/R/sturges.freq.R
agricolae/R/DAU.test.R
agricolae/R/plot.AMMI.R
agricolae/R/plot.graph.freq.R
agricolae/R/durbin.test.R
agricolae/R/correlation.R
agricolae/R/consensus.R
agricolae/vignettes
agricolae/vignettes/tutorial.Rnw
agricolae/MD5
agricolae/build
agricolae/build/vignette.rds
agricolae/DESCRIPTION
agricolae/man
agricolae/man/ComasOxapampa.Rd
agricolae/man/lateblight.Rd
agricolae/man/Glycoalkaloids.Rd
agricolae/man/audpc.Rd
agricolae/man/sweetpotato.Rd
agricolae/man/duncan.test.Rd
agricolae/man/delete.na.Rd
agricolae/man/simulation.model.Rd
agricolae/man/paracsho.Rd
agricolae/man/scheffe.test.Rd
agricolae/man/agricolae-package.Rd
agricolae/man/potato.Rd
agricolae/man/kruskal.Rd
agricolae/man/graph.freq.Rd
agricolae/man/markers.Rd
agricolae/man/cotton.Rd
agricolae/man/summary.graph.freq.Rd
agricolae/man/ogive.freq.Rd
agricolae/man/strip.plot.Rd
agricolae/man/design.bib.Rd
agricolae/man/kendall.Rd
agricolae/man/nonadditivity.Rd
agricolae/man/genxenv.Rd
agricolae/man/carolina.Rd
agricolae/man/diffograph.Rd
agricolae/man/join.freq.Rd
agricolae/man/table.freq.Rd
agricolae/man/Hco2006.Rd
agricolae/man/design.split.Rd
agricolae/man/VanderWarden.Rd
agricolae/man/reg.homog.Rd
agricolae/man/RioChillon.Rd
agricolae/man/BIB.test.Rd
agricolae/man/plotAMMI.Rd
agricolae/man/skewness.Rd
agricolae/man/resampling.cv.Rd
agricolae/man/pamCIP.Rd
agricolae/man/similarity.Rd
agricolae/man/design.ab.Rd
agricolae/man/correlation.Rd
agricolae/man/index.smith.Rd
agricolae/man/ssp.plot.Rd
agricolae/man/normal.freq.Rd
agricolae/man/yacon.Rd
agricolae/man/index.bio.Rd
agricolae/man/waller.Rd
agricolae/man/AMMI.Rd
agricolae/man/hcut.Rd
agricolae/man/corn.Rd
agricolae/man/grass.Rd
agricolae/man/weatherSeverity.rd
agricolae/man/durbin.test.Rd
agricolae/man/greenhouse.Rd
agricolae/man/waller.test.Rd
agricolae/man/bar.err.Rd
agricolae/man/hgroups.Rd
agricolae/man/path.analysis.Rd
agricolae/man/SNK.test.Rd
agricolae/man/vark.Rd
agricolae/man/tapply.stat.Rd
agricolae/man/sp.plot.Rd
agricolae/man/rice.Rd
agricolae/man/plrv.Rd
agricolae/man/design.youden.rd
agricolae/man/design.lsd.Rd
agricolae/man/LSD.test.Rd
agricolae/man/consensus.Rd
agricolae/man/lastC.Rd
agricolae/man/kurtosis.Rd
agricolae/man/heterosis.Rd
agricolae/man/cv.model.Rd
agricolae/man/orderPvalue.Rd
agricolae/man/DAU.test.Rd
agricolae/man/HSD.test.Rd
agricolae/man/huasahuasi.Rd
agricolae/man/growth.Rd
agricolae/man/correl.Rd
agricolae/man/montecarlo.Rd
agricolae/man/AMMI.contour.Rd
agricolae/man/design.cyclic.Rd
agricolae/man/design.lattice.Rd
agricolae/man/audps.Rd
agricolae/man/plots.Rd
agricolae/man/design.graeco.Rd
agricolae/man/CIC.Rd
agricolae/man/natives.Rd
agricolae/man/stat.freq.Rd
agricolae/man/median.rd
agricolae/man/clay.Rd
agricolae/man/soil.Rd
agricolae/man/LxT.Rd
agricolae/man/melon.Rd
agricolae/man/polygon.freq.Rd
agricolae/man/disease.Rd
agricolae/man/plot.graph.freq.Rd
agricolae/man/sturges.freq.Rd
agricolae/man/design.rcbd.Rd
agricolae/man/resampling.model.Rd
agricolae/man/friedman.Rd
agricolae/man/design.strip.Rd
agricolae/man/sinRepAmmi.Rd
agricolae/man/cv.similarity.Rd
agricolae/man/zigzag.Rd
agricolae/man/indexAMMI.Rd
agricolae/man/REGW.test.Rd
agricolae/man/PBIB.test.Rd
agricolae/man/order.stat.Rd
agricolae/man/DC.Rd
agricolae/man/design.crd.Rd
agricolae/man/ralstonia.Rd
agricolae/man/Chz2006.Rd
agricolae/man/stability.par.Rd
agricolae/man/design.dau.Rd
agricolae/man/bar.group.Rd
agricolae/man/intervals.freq.Rd
agricolae/man/frijol.Rd
agricolae/man/haynes.Rd
agricolae/man/design.alpha.Rd
agricolae/man/wilt.Rd
agricolae/man/lineXtester.Rd
agricolae/man/stability.nonpar.Rd
agricolae/man/order.group.Rd