Type: | Package |
Title: | Stability Analysis for Agricultural Research |
Version: | 0.1.0 |
Date: | 2019-10-01 |
Author: | Anna Cheshkova [aut, cre] |
Maintainer: | Anna Cheshkova <cheshanf@gmail.com> |
Description: | Statistical procedures to perform stability analysis in plant breeding and to identify stable genotypes under diverse environments. It is possible to calculate coefficient of homeostaticity by Khangildin et al. (1979), variance of specific adaptive ability by Kilchevsky&Khotyleva (1989), weighted homeostaticity index by Martynov (1990), steadiness of stability index by Udachin (1990), superiority measure by Lin&Binn (1988) <doi:10.4141/cjps88-018>, regression on environmental index by Erberhart&Rassel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>, Tai's (1971) stability parameters <doi:10.2135/cropsci1971.0011183X001100020006x>, stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>, ecovalence by Wricke (1962), nonparametric stability parameters by Nassar&Huehn (1987) <doi:10.2307/2531947>, Francis&Kannenberg's parameters of stability (1978) <doi:10.4141/cjps78-157>. |
Depends: | R (≥ 3.1) |
Imports: | ggplot2, dplyr, graphics, stats, rlang |
License: | GPL-2 |
Encoding: | UTF-8 |
LazyData: | true |
RoxygenNote: | 6.1.1 |
NeedsCompilation: | no |
Packaged: | 2019-10-15 01:17:51 UTC; anna |
Repository: | CRAN |
Date/Publication: | 2019-10-16 11:50:06 UTC |
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 <cheshanf@gmail.com>
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)
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")
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 indext_value
t-values for gypothesis that bi=1p_value
p-values for gypothesis that bi=1s2di
individual squared deviation from regressionpf_value
p-values for gypothesis that s2di=0ai
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 genotypeZ1
-value of genotypeS2
-value of genotypeZ2
-value of genotype
- scores
the data frame object of summary results:
Z1.sum
sum of Z1Z2.sum
sum of Z2chi.ind
chi-squared for (choosen alpha level)/(number of genotypes) and one degree of freedomchi.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 valueOAC
common adaptive abilitysigma_ge
variance of GE interactionsigma_CAC
variance of specific adaptive abilityS_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")
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")
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 meanst_value
t-values for gypothesis that bi=0p_value
p-values for gypothesis that bi=0sigma
Shukla's stability variance valuepf_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")
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 meanst_value
t-values for gypothesis that alpha=0p_value
p-values for gypothesis that alpha=0lambda
deviation from linear responsespf_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")