Package stability. R topics documented: August 23, Type Package
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1 Type Package Package stability August 23, 2018 Title Stability Analysis of Genotype by Environment Interaction (GEI Version Author Muhammad Yaseen [aut, cre], Kent M. Eskridge [aut, ctb] Maintainer Muhammad Yaseen Functionalities to perform Stability Analysis of Genotype by Environment Interaction (GEI to identify superior and stable genotypes under diverse environments. It performs Eberhart & Russel's ANOVA (1966 (<doi: /cropsci x x>, Finlay and Wilkinson (1963 Joint Linear Regression (<doi: /ar >, Wricke (1962, 1964 Ecovalence, Shukla's stability variance parameter (1972 (<doi: /hdy > and Kang's (1991 (<doi: /agronj x> simultaneous selection for high yielding and stable parameter. Depends R (>= 3.1 Imports dplyr, ggplot2, ggfortify, lme4, magrittr, matrixstats, reshape2, rlang, scales, stats, tibble, tidyr License GPL-2 Encoding UTF-8 LazyData true RoxygenNote Note Department of Mathematics and Statistics, University of Agriculture Faisalabad, Faisalabad-Pakistan. NeedsCompilation no Repository CRAN Date/Publication :00:03 UTC R topics documented: add_anova ammi
2 2 add_anova ammi_biplot er_anova ge_data ge_effects ge_means gge_biplot stability stab_asv stab_dist stab_fox stab_kang stab_masv stab_measures stab_par stab_reg Index 21 add_anova Additive ANOVA for Genotypes by Environment Interaction (GEI model Additive ANOVA for Genotypes by Environment Interaction (GEI model add_anova(,.y,,, add_anova(,.y,,, Additive ANOVA
3 ammi 3 Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. YieldANOVA <- add_anova( = ge_data, = Rep, = Gen, = Env YieldANOVA ammi Additive Main Effects and Multiplicative Interaction (AMMI Performs Additive Main Effects and Multiplicative Interaction (AMMI Analysis for Genotypes by Environment Interaction (GEI ammi(,.y,,, ammi(,.y,,,
4 4 ammi_biplot Stability Measures Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. Yield.ammi <- ammi( = ge_data, = Rep, = Gen, = Env Yield.ammi ammi_biplot Additive Main Effects and Multiplicative Interaction (AMMI Biplot Plots Additive Main Effects and Multiplicative Interaction (AMMI for Genotypes by Environment Interaction (GEI ammi_biplot(,.y,,, ammi_biplot(,.y,,,
5 er_anova 5 Stability Measures Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. ammi_biplot( = ge_data, = Rep, = Gen, = Env er_anova Eberhart & Russel s Model ANOVA ANOVA of Eberhart & Russel s Model
6 6 er_anova er_anova(,.y,,, er_anova(,.y,,, Additive ANOVA Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. Yield.er_anova <- er_anova( = ge_data, = Rep, = Gen, = Env Yield.er_anova
7 ge_data 7 ge_data Data for Genotypes by Environment Interaction (GEI ge_data is used for performing Genotypes by Environment Interaction (GEI Analysis. Format A 1320 obs. of 6 variables. Details Gen Genotype Institute Institute Rep Replicate Block Block Env Environment Yield Yield Response Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis.
8 8 ge_effects ge_effects Genotype by Environment Interaction Effects Calcuates Genotype by Environment Interaction Effects ge_effects(,.y,, ge_effects(,.y,, Effects Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. Yield.Effects <- ge_effects( = ge_data, = Gen, = Env names(yield.effects
9 ge_means 9 Yield.Effects$ge_means Yield.Effects$ge_effects Yield.Effects$gge_effects ge_means Genotype by Environment Interaction Means and Ranks Calcuates Genotype by Environment Interaction Means along with their Ranks ge_means(,.y,, ge_means(,.y,, Means and Ranks Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis.
10 10 gge_biplot Yield.ge_means <- ge_means( = ge_data, = Gen, = Env Yield.ge_means$ge_means Yield.ge_means$ge_ranks Yield.ge_means$g_means Yield.ge_means$e_means gge_biplot Genotype plus Genotypes by Environment (GGE Interaction Biplot Plots Genotype plus Genotypes by Environment (GGE Interaction Biplot for Genotypes by Environment Interaction (GEI gge_biplot(,.y,,, gge_biplot(,.y,,, Stability Measures
11 stability 11 Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. gge_biplot( = ge_data, = Rep, = Gen, = Env stability Stability Analysis of Genotype by Environment Interaction (GEI The stability package provides functionalities to perform Stability Analysis of Genotype by Environment Interaction (GEI to identify superior and stable genotypes under diverse environments. It performs Eberhart & Russel s ANOVA (1966, Finlay and Wilkinson (1963 Joint Linear Regression, Wricke (1962, 1964 Ecovalence, Shukla s stability variance parameter (1972 and Kang s (1991 simultaneous selection for high yielding and stable parameter.
12 12 stab_asv stab_asv Additive Main Effects and Multiplicative Interacion Stability Additive ANOVA for Genotypes by Environment Interaction (GEI model stab_asv(,.y,,, stab_asv(,.y,,, Additive ANOVA Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. YieldASV <- stab_asv( = ge_data, = Rep, = Gen, = Env
13 stab_dist 13 YieldASV stab_dist Stability Distance in AMMI Stability Distance of Genotypes in Additive ANOVA for Genotypes by Environment Interaction (GEI model stab_dist(,.y,,,,.m = 2 stab_dist(,.y,,,,.m = 2.m No of PCs retained Stability Distance YieldDist <- stab_dist( = ge_data, = Rep, = Gen, = Env,.m = 2
14 14 stab_fox YieldDist stab_fox Stability Fox Function Performs a stability analysis based on the criteria of Fox et al. (1990, using the statistical "TOP third" only. In Fox function, a stratified ranking of the genotypes at each environment separately is done. The proportion of locations at which the genotype occurred in the top third are expressed in TOP output. stab_fox(,.y,,, stab_fox(,.y,,, 1. Fox, P.N. and Skovmand, B. and Thompson, B.K. and Braun, H.J. and Cormier, R. (1990. Yield and adaptation of hexaploid spring triticale. Euphytica, 47,
15 stab_kang 15 YieldFox <- stab_fox( = ge_data, = Rep, = Gen, = Env YieldFox stab_kang Stability Kang Function Performs a stability analysis based on the Kang (1988 criteria. Kang nonparametric stability (ranksum uses both "trait single value" and stability variance (Shukla, 1972, and the genotype with the lowest ranksum is commonly the most favorable one. stab_kang(,.y,,, stab_kang(,.y,,, 1. Kang, M.S. (1988. A rank-sum method for selecting high-yielding, stable corn genotypes. Cereal Research Communications, 16, Shukla, G.K. (1972. Some aspects of partitioning genotype environmental components of variability. Heredity, 29,
16 16 stab_masv YieldKang <- stab_kang( = ge_data, = Rep, = Gen, = Env YieldKang stab_masv Modified Additive Main Effects and Multiplicative Interacion Stability Additive ANOVA for Genotypes by Environment Interaction (GEI model stab_masv(,.y,,,,.m = 2 stab_masv(,.y,,,,.m = 2.m No of PCs retained Additive ANOVA
17 stab_measures 17 Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. YieldMASV <- stab_masv( = ge_data, = Rep, = Gen, = Env,.m = 2 YieldMASV stab_measures Stability Measures for Genotypes by Environment Interaction (GEI Stability Measures for Genotypes by Environment Interaction (GEI stab_measures(,.y,, stab_measures(,.y,, Stability Measures
18 18 stab_par Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. Yield.StabMeasures <- stab_measures( = ge_data, = Gen, = Env Yield.StabMeasures stab_par Stability Parameters for Genotypes by Environment Interaction (GEI Stability Parameters for Genotypes by Environment Interaction (GEI stab_par(,.y,,,, alpha = 0.1, Cov = NULL stab_par(,.y,,,, alpha = 0.1, Cov = NULL alpha Level of Significance, default is 0.1 Cov Stability Parameters Environmental Covariate, default is NULL
19 stab_reg 19 Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. Yield.StabPar <- stab_par( = ge_data, = Rep, = Gen, = Env, alpha = 0.1, Cov = NULL Yield.StabPar stab_reg Individual Regression for each Genotype Individual Regression for each Genotype in Genotypes by Environment Interaction (GEI stab_reg(,.y,,, stab_reg(,.y,,,
20 20 stab_reg Additive ANOVA Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. Yield.StabReg <- stab_reg( = ge_data, = Rep, = Gen, = Env Yield.StabReg
21 Index Topic datasets ge_data, 7 add_anova, 2 ammi, 3 ammi_biplot, 4 er_anova, 5 ge_data, 7 ge_effects, 8 ge_means, 9 gge_biplot, 10 stab_asv, 12 stab_dist, 13 stab_fox, 14 stab_kang, 15 stab_masv, 16 stab_measures, 17 stab_par, 18 stab_reg, 19 stability, 11 stability-package (stability, 11 21
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Type Package Package baystability March 13, 2018 Title Bayesian Stability Analysis of Genotype by Environment Interaction (GEI Version 0.1.0 Maintainer Muhammad Yaseen Performs general
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Type Package Package clr December 3, 2018 Title Curve Linear Regression via Dimension Reduction Version 0.1.0 Author Amandine Pierrot with contributions and/or help from Qiwei Yao, Haeran Cho, Yannig Goude
GENOTYPE-ENVIRONMENT INTERACTION FOR FORAGE YIELD OF VETCH (VICIA SATIVA L.) IN MEDITERRANEAN ENVIRONMENTS. G. Pacucci and C.
GENOTYPE-ENVIRONMENT INTERACTION FOR FORAGE YIELD OF VETCH (VICIA SATIVA L.) IN MEDITERRANEAN ENVIRONMENTS ID # 12-16 G. Pacucci and C. Troccoli Department of Scienze delle Produzioni Vegetali, Università
Package icmm. October 12, 2017
Type Package Package icmm October 12, 2017 Title Empirical Bayes Variable Selection via ICM/M Algorithm Version 1.1 Author Vitara Pungpapong [aut, cre], Min Zhang [aut], Dabao Zhang [aut] Maintainer Vitara
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Package face January 19, 2018 Title Fast Covariance Estimation for Sparse Functional Data Version 0.1-4 Author Luo Xiao [aut,cre], Cai Li [aut], William Checkley [aut], Ciprian Crainiceanu [aut] Maintainer
Package riv. R topics documented: May 24, Title Robust Instrumental Variables Estimator. Version Date
Title Robust Instrumental Variables Estimator Version 2.0-5 Date 2018-05-023 Package riv May 24, 2018 Author Gabriela Cohen-Freue and Davor Cubranic, with contributions from B. Kaufmann and R.H. Zamar
Package beam. May 3, 2018
Type Package Package beam May 3, 2018 Title Fast Bayesian Inference in Large Gaussian Graphical Models Version 1.0.2 Date 2018-05-03 Author Gwenael G.R. Leday [cre, aut], Ilaria Speranza [aut], Harry Gray
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Type Package Package bhrcr November 12, 2018 Title Bayesian Hierarchical Regression on Clearance Rates in the Presence of Lag and Tail Phases Version 1.0.2 Date 2018-11-12 Author Colin B. Fogarty [cre]
Package MicroMacroMultilevel
Type Package Package MicroMacroMultilevel July 1, 2017 Description Most multilevel methodologies can only model macro-micro multilevel situations in an unbiased way, wherein group-level predictors (e.g.,
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Title Multiscalar Territorial Analysis Version 0.1.2 Package MTA May 14, 2018 Build multiscalar territorial analysis based on various contexts. License GPL-3 URL https://github.com/riatelab/mta/ BugReports
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Package tspi August 7, 2017 Title Improved Prediction Intervals for ARIMA Processes and Structural Time Series Version 1.0.2 Date 2017-08-07 Author Jouni Helske Maintainer Jouni Helske
Package cellwise. June 26, 2018
Type Package Version 2.0.10 Date 2018-06-25 Title Analyzing Data with Cellwise Outliers Depends R (>= 3.2.0) Package cellwise June 26, 2018 Suggests knitr, robusthd, robustbase, rrcov, MASS, svd, ellipse
Package SpatialVS. R topics documented: November 10, Title Spatial Variable Selection Version 1.1
Title Spatial Variable Selection Version 1.1 Package SpatialVS November 10, 2018 Author Yili Hong, Li Xu, Yimeng Xie, and Zhongnan Jin Maintainer Yili Hong Perform variable selection