Package 'agrostab'

Stability Analysis for Agricultural Research

Description

The agrostab package provides functionalities to perform stability analysis in plant breeding. The package includes statistical procedures to identify stable genotypes under diverse environments.

Author(s)

Anna Cheshkova <[email protected]>

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Experimental data for stability analysis

Description

Data obtained from the agrotechnical experiments carried out in 2009-2011 to evaluate grain yield of seven Siberian common winter wheat cultivars.

Usage

data(exp_data)

Format

A data.frame 126 obs. of 4 variables.

Details

• env Environment

• gen Genotype

• rep Replicate

• yield Yield Response

References

Siberian Research Institute of Plant Growing and Breeding - Branch of the Institute of Cytology and Genetics, Krasnoobsk, Novosibirsk region, Russia

Examples

data(exp_data)

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Coefficient of variation

Description

This function calculates the Francis&Kannenberg's parameters of stability

Usage

stability.cv(dataf, res_var, gen_var, env_var, rep_var, plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

Returns a data frame:

CV

the genotype's coefficient of variation

Mean

the genotype's mean

References

Francis, T.R. and L.W. Kannenberg. 1978. Yield stability studies in short-season maize. I. A descriptive method for grouping genotypes. Can J Plant Sci 58: 1029?1034. doi: 10.4141/cjps78-157

Examples

data(exp_data)
stability.cv(exp_data,"yield","gen","env","rep")

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Environmental variance

Description

This function calculates the Roemer's environmental variance.

Usage

stability.env_var(dataf, res_var, gen_var, env_var, rep_var,
  plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

A numeric vector with environmental variances of genotypes.

References

Becker, H.C. and J. Leon. 1988. Stability analysis in plant breeding. Plant Breeding 101: 1-23.

Examples

data(exp_data)
stability.env_var(exp_data,"yield","gen","env","rep")

---

Regression on Environmental Index

Description

This function calculates the Erberhart&Rassel's stability parameters and the Dragavtsev's coefficient of multiplicativity.

Usage

stability.er(dataf, res_var, gen_var, env_var, rep_var, plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

Returns a list of three objects:

ANOVA

the analysis of variance table

scores

the data frame object of stability analysis results:

• bi regression of genotype means on environmental index

• t_value t-values for gypothesis that bi=1

• p_value p-values for gypothesis that bi=1

• s2di individual squared deviation from regression

• pf_value p-values for gypothesis that s2di=0

• ai Dragavtsev's coefficient of multiplicativity

Ij

enviromental indexes

References

Eberhart, S.A. and W.A. Russell. 1966. Stability parameters for comparing varieties. Crop Sci 6: 36-40. doi:10.2135/cropsci1966.0011183X000600010011x

Examples

data(exp_data)
stability.er(exp_data,"yield","gen","env","rep")

---

Coefficient of homeostaticity

Description

This function calculates the Khangildin's coefficient of homeostaticity

Usage

stability.hom(dataf, res_var, gen_var, env_var, rep_var, plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

Returns a data frame:

mean_all

the genotype's mean

mean_opt

the genotype's max yield value

mean_lim

the genotype's min yield value

sd

the genotype's standard deviation

hom

the genotype's coefficient of homeostaticity

References

Khangildin V.V., Shayakhmetov I.F., Mardamshin A.G. 1979. Homeostasis of crop components and prerequisites for creating a model of a spring wheat variety. In Genetic analysis of quantitative traits of plants, 5-39. Ufa. (In Russian)

Examples

data(exp_data)
stability.hom(exp_data,"yield","gen","env","rep")

---

Nonparametric stability analysis

Description

This function calculates the Nassar&Huehn's stability parameters.

Usage

stability.hue(dataf, res_var, gen_var, env_var, rep_var, alpha = 0.05,
  plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
alpha	the significance level; default is 0.5
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

Returns a list of two objects:

statistic

the data frame object of stability analysis results:

• S1-value of genotype

• Z1-value of genotype

• S2-value of genotype

• Z2-value of genotype

scores

the data frame object of summary results:

• Z1.sum sum of Z1

• Z2.sum sum of Z2

• chi.ind chi-squared for (choosen alpha level)/(number of genotypes) and one degree of freedom

• chi.sum chi-squared for choosen alpha level and number of genotypes degree of freedom

References

Nassar, R. and M. Huehn. 1987. Studies on estimation of phenotypic stability: Tests of significance for nonparametric measures of phenotypic stability. Biometrics 43: 45-53. doi: 10.2307/2531947

Examples

data(exp_data)
stability.hue(exp_data,"yield","gen","env","rep")

---

Variance of specific adaptive ability

Description

This function calculates several stability parameters suggested by Kilchevsky & Khotyleva.

Usage

stability.kilch(dataf, res_var, gen_var, env_var, rep_var, plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

Returns a list of two objects:

ANOVA

the analysis of variance table

scores

the data frame object of stability analysis results:

• mean mean value

• OAC common adaptive ability

• sigma_ge variance of GE interaction

• sigma_CAC variance of specific adaptive ability

• S_g relative stability

References

Kilchevsky A.V., Khotyleva L.V. 1989. Genotype and environment in plant breeding. - Minsk: Science and technology. (In Russian).

Examples

data(exp_data)
stability.kilch(exp_data,"yield","gen","env","rep")

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Superiority measure

Description

This function calculates the Lin&Binn's superiority measure.

Usage

stability.linbin(dataf, res_var, gen_var, env_var, rep_var,
  plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

A numeric vector with superiority measure Pi of genotypes.

References

Lin, C.S. and M.R. Binns. 1988. A superiority measure of cultivar performance for cultivar x location data. Can J Plant Sci 68: 193?198. doi: 10.4141/cjps88-018

Examples

data(exp_data)
stability.linbin(exp_data,"yield","gen","env","rep")

---

Weighted homeostaticity index

Description

This function calculates the Martynov's weighted homeostaticity index.

Usage

stability.mart(dataf, res_var, gen_var, env_var, rep_var, alpha = 0.05,
  plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
alpha	alpha level of LSD; default is 0.05.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

A numeric vector with weighted homeostaticity index of genotypes.

References

Martynov S.P. 1990. A Method for the Estimation of Crop Varieties Stability. Biom. J. 7: 887-893.

Examples

data(exp_data)
stability.mart(exp_data,"yield","gen","env","rep")

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Stability variance

Description

This function calculates the Shukla's stability variance.

Usage

stability.shu(dataf, res_var, gen_var, env_var, rep_var, plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

Returns a list of two objects:

ANOVA

the analysis of variance table

scores

the data frame object of stability analysis results:

• bi regression of genotype means on environmental means

• t_value t-values for gypothesis that bi=0

• p_value p-values for gypothesis that bi=0

• sigma Shukla's stability variance value

• pf_value p-values for gypothesis that sigmai=0

References

Shukla, G.K. 1972. Some statistical aspects of partitioning genotype-environmental components of variability. Heredity 29: 237-245. doi: 10.1038/hdy.1972.87

Examples

data(exp_data)
stability.shu(exp_data,"yield","gen","env","rep")

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Tai's stability analysis

Description

This function calculates the Tai's stability parameters.

Usage

stability.tai(dataf, res_var, gen_var, env_var, rep_var, plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

Returns a list of two objects:

ANOVA

the analysis of variance table

scores

the data frame object of stability analysis results:

• alpha regression of genotype means on environmental means

• t_value t-values for gypothesis that alpha=0

• p_value p-values for gypothesis that alpha=0

• lambda deviation from linear responses

• pf_value p-values for gypothesis that lambda=0

References

Tai, G.C.C. 1971. Genotypic stability analysis and application to potato regional trials. Crop Sci. 11: 184-190. doi:10.2135/cropsci1971.0011183X001100020006x

Examples

data(exp_data)
stability.tai(exp_data,"yield","gen","env","rep")

---

Steadiness of stability index

Description

This function calculates the Udachin's parameters of stability

Usage

stability.udach(dataf, res_var, gen_var, env_var, rep_var, plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

Returns a data frame:

Ust

the genotype's Steadiness of stability index

intensity

the genotype's intensity value

max_val

the genotype's yield max value

min_val

the genotype's yield min value

S_opt

the genotype's standard deviation at optimal environment

S_lim

the genotype's standard deviation at limited environment

I_opt

the genotype's stability index at optimal environment

I_lim

the genotype's stability index at limited environment

References

Udachin R.A. 1990. Methods of assessing the ecological plasticity of wheat varieties. Selection and seed production. 5: 2-6. (In Russian)

Examples

data(exp_data)
stability.udach(exp_data,"yield","gen","env","rep")

---

Ecovalence

Description

This function calculates the Wricke's ecovalence.

Usage

stability.wricke(dataf, res_var, gen_var, env_var, rep_var,
  plotIt = TRUE)

Arguments

dataf	the name of the data frame containing the data to analyze.
res_var	the response variable.
gen_var	the genotypes variable.
env_var	the environments variable.
rep_var	the replications variable.
plotIt	a logical value specifying if plot should be drawn; default is TRUE

Value

A numeric vector with genotype's ecovalence.

References

Wricke, G., 1962. Tjber eine Methode zur Erfassung der okologischen Streubreite in Feldversuchen. Z. Pflanzenzuchtg. 47: 92-96.

Examples

data(exp_data)
stability.wricke(exp_data,"yield","gen","env","rep")

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