Package DiallelAnalysisR
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1 Type Package Title Diallel Analysis with R Version Package DiallelAnalysisR April 9, 2016 Maintainer Muhammad Yaseen <myaseen208@gmail.com> Description Performs Diallel Analysis with R using Griffing's and Hayman's approaches. Four different methods (1: Method-I (Parents + F1's + reciprocals; 2: Method-II (Parents and one set of F1's; 3: Method-III (One set of F1's and reciprocals; 4: Method- IV (One set of F1's only and two methods (1: Fixed Effects Model; 2: Random Effects Model can be applied using Griffing's approach. Depends R (>= 3.1 Imports ggplot2, stats License GPL-2 LazyData TRUE RoxygenNote NeedsCompilation no Author Muhammad Yaseen [aut, cre], Kent M. Eskridge [ctb] Repository CRAN Date/Publication :18:36 R topics documented: Griffing GriffingData GriffingData GriffingData GriffingData Hayman HaymanData Index 14 1
2 2 Griffing Griffing Diallel Analysis using Griffing Approach Description Usage Griffing is used for performing Diallel Analysis using Griffing s Approach. y, Rep, Cross1, Cross2, data, Method, Model Arguments y Rep Cross1 Cross2 data Details Value Numeric Response Vector Replicate as factor Cross 1 as factor Cross 2 as factor A data.frame Method Method for Diallel Analysis using Griffing s approach. It can take 1, 2, 3, or 4 as argument depending on the method being used. 1. Method-I (Parents + F 1 s + reciprocals; 2. Method-II (Parents and one set of F 1 s; 3. Method-III (One set of F 1 s and reciprocals; 4. Method-IV (One set of F 1 s only. Model Model for Diallel Analysis using Griffing s approach. It can take 1 or 2 as arguments depending on the model being used. 1. Fixed Effects Model; 2. Random Effects Model. Diallel Analysis using Griffing s approach. Means Means ANOVA Analysis of Variance (ANOVA table Genetic.Components Genetic Components Effects Effects of Crosses StdErr Standard Errors of Crosses Author(s Muhammad Yaseen (<myaseen208@gmail.com>
3 Griffing 3 References 1. Griffing, B. (1956 Concept of General and Specific Combining Ability in relation to Diallel Crossing Systems. Australian Journal of Biological Sciences, 9(4, Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. New Delhi: Kalyani. See Also Hayman, GriffingData1, GriffingData2, GriffingData3, GriffingData4 Examples # ## Diallel Analysis with Griffing s Aproach Method 1 & Model 1 # Griffing1Data1 <-, data = GriffingData1, Method = 1, Model = 1 names(griffing1data1 Griffing1Data1 Griffing1Data1Means <- Griffing1Data1$Means Griffing1Data1ANOVA <- Griffing1Data1$ANOVA Griffing1Data1Genetic.Components <- Griffing1Data1$Genetic.Components Griffing1Data1Effects <- Griffing1Data1$Effects Griffing1Data1StdErr <- as.matrix(griffing1data1$stderr ## Diallel Analysis with Griffing s Aproach Method 1 & Model 2 Griffing2Data1 <-, data = GriffingData1, Method = 1, Model = 2 names(griffing2data1 Griffing2Data1 Griffing2Data1Means <- Griffing2Data1$Means Griffing2Data1ANOVA <- Griffing2Data1$ANOVA
4 4 Griffing Griffing2Data1Genetic.Components <- Griffing2Data1$Genetic.Components ## Diallel Analysis with Griffing s Aproach Method 2 & Model 1 Griffing1Data2 <-, data = GriffingData2, Method = 2, Model = 1 names(griffing1data2 Griffing1Data2 Griffing1Data2Means <- Griffing1Data2$Means Griffing1Data2ANOVA <- Griffing1Data2$ANOVA Griffing1Data2Genetic.Components <- Griffing1Data2$Genetic.Components Griffing1Data2Effects <- Griffing1Data2$Effects Griffing1Data2StdErr <- as.matrix(griffing1data2$stderr ## Diallel Analysis with Griffing s Aproach Method 2 & Model 2 Griffing2Data2 <-, data = GriffingData2, Method = 2, Model = 2 names(griffing2data2 Griffing2Data2 Griffing2Data2Means <- Griffing2Data2$Means Griffing2Data2ANOVA <- Griffing2Data2$ANOVA Griffing2Data2Genetic.Components <- Griffing2Data2$Genetic.Components ## Diallel Analysis with Griffing s Aproach Method 3 & Model 1 Griffing1Data3 <-
5 Griffing 5, data = GriffingData3, Method = 3, Model = 1 names(griffing1data3 Griffing1Data3 Griffing1Data3Means <- Griffing1Data3$Means Griffing1Data3ANOVA <- Griffing1Data3$ANOVA Griffing1Data3Genetic.Components <- Griffing1Data3$Genetic.Components Griffing1Data3Effects <- Griffing1Data3$Effects Griffing1Data3StdErr <- as.matrix(griffing1data3$stderr ## Diallel Analysis with Griffing s Aproach Method 3 & Model 2 Griffing2Data3 <-, data = GriffingData3, Method = 3, Model = 2 names(griffing2data3 Griffing2Data3 Griffing2Data3Means <- Griffing2Data3$Means Griffing2Data3ANOVA <- Griffing2Data3$ANOVA Griffing2Data3Genetic.Components <- Griffing2Data3$Genetic.Components ## Diallel Analysis with Griffing s Aproach Method 4 & Model 1 Griffing1Data4 <-, data = GriffingData4, Method = 4, Model = 1 names(griffing1data4 Griffing1Data4 Griffing1Data4Means <- Griffing1Data4$Means Griffing1Data4ANOVA <- Griffing1Data4$ANOVA Griffing1Data4Genetic.Components <- Griffing1Data4$Genetic.Components Griffing1Data4Effects <- Griffing1Data4$Effects
6 6 GriffingData1 Griffing1Data4StdErr <- as.matrix(griffing1data4$stderr ## Diallel Analysis with Griffing s Aproach Method 4 & Model 2 Griffing2Data4 <-, data = GriffingData4, Method = 4, Model = 2 names(griffing2data4 Griffing2Data4 Griffing2Data4Means <- Griffing2Data4$Means Griffing2Data4ANOVA <- Griffing2Data4$ANOVA Griffing2Data4Genetic.Components <- Griffing2Data4$Genetic.Components GriffingData1 Data for Diallel Analysis using Griffing Approach Method 1 Description Griffing is used for performing Diallel Analysis using Griffing s Approach. Usage data(griffingdata1 Format A data.frame with 256 rows and 4 variables. Details Cross1 Cross 1 Cross2 Cross 2 Rep Replicate Yield Yield Response Author(s Muhammad Yaseen (<myaseen208@gmail.com>
7 GriffingData2 7 References See Also 1. Griffing, B. (1956 Concept of General and Specific Combining Ability in relation to Diallel Crossing Systems. Australian Journal of Biological Sciences, 9(4, Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. New Delhi: Kalyani. Griffing, GriffingData2, GriffingData3, GriffingData4 Examples data(griffingdata1 GriffingData2 Data for Diallel Analysis using Griffing Approach Method 2 Description Usage Format Details Griffing is used for performing Diallel Analysis using Griffing s Approach. data(griffingdata2 A data.frame with 144 rows and 4 variables. Author(s Cross1 Cross 1 Cross2 Cross 2 Rep Replicate Yield Yield Response Muhammad Yaseen (<myaseen208@gmail.com> References 1. Griffing, B. (1956 Concept of General and Specific Combining Ability in relation to Diallel Crossing Systems. Australian Journal of Biological Sciences, 9(4, Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. New Delhi: Kalyani.
8 8 GriffingData3 See Also Griffing, GriffingData1, GriffingData3, GriffingData4 Examples data(griffingdata2 GriffingData3 Data for Diallel Analysis using Griffing Approach Method 3 Description Usage Format Details Griffing is used for performing Diallel Analysis using Griffing s Approach. data(griffingdata3 A data.frame with 224 rows and 4 variables. Author(s Cross1 Cross 1 Cross2 Cross 2 Rep Replicate Yield Yield Response Muhammad Yaseen (<myaseen208@gmail.com> References See Also 1. Griffing, B. (1956 Concept of General and Specific Combining Ability in relation to Diallel Crossing Systems. Australian Journal of Biological Sciences, 9(4, Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. New Delhi: Kalyani. Griffing, GriffingData1, GriffingData2, GriffingData4 Examples data(griffingdata3
9 GriffingData4 9 GriffingData4 Data for Diallel Analysis using Griffing Approach Method 4 Description Griffing is used for performing Diallel Analysis using Griffing s Approach. Usage data(griffingdata4 Format A data.frame with 112 rows and 4 variables. Details Cross1 Cross 1 Cross2 Cross 2 Rep Replicate Yield Yield Response Author(s Muhammad Yaseen (<myaseen208@gmail.com> References 1. Griffing, B. (1956 Concept of General and Specific Combining Ability in relation to Diallel Crossing Systems. Australian Journal of Biological Sciences, 9(4, Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. New Delhi: Kalyani. See Also Griffing, GriffingData1, GriffingData2, GriffingData3 Examples data(griffingdata4
10 10 Hayman Hayman Diallel Analysis using Hayman Approach Description Hayman is used for performing Diallel Analysis using Hayman s Approach. Usage Hayman(y, Rep, Cross1, Cross2, data Arguments y Rep Cross1 Cross2 data Numeric Response Vector Replicate as factor Cross 1 as factor Cross 2 as factor A data.frame Details Diallel Analysis using Haymans s approach. Value Means Means ANOVA Analysis of Variance (ANOVA table Genetic.Components Genetic Components Effects Effects of Crosses StdErr Standard Errors of Crosses Author(s Muhammad Yaseen (<myaseen208@gmail.com> References 1. Hayman, B. I. (1954 a The Theory and Analysis of Diallel Crosses. Genetics, 39, Hayman, B. I. (1954 b The Analysis of Variance of Diallel Tables. Biometrics, 10, Hayman, B. I. (1957 Interaction, Heterosis and Diallel Crosses. Genetics, 42, Singh, R. K. and Chaudhary, B. D. (2004 Biometrical Methods in Quantitative Genetic Analysis. New Delhi: Kalyani.
11 Hayman 11 See Also Griffing, HaymanData Examples # ## Diallel Analysis with Haymans s Aproach # Hayman1Data <- Hayman(, data = HaymanData Hayman1Data names(hayman1data Hayman1DataMeans <- Hayman1Data$Means Hayman1DataANOVA <- Hayman1Data$ANOVA Hayman1DataWr.Vr.Table <- Hayman1Data$Wr.Vr.Table Hayman1DataComponents.of.Variation <- Hayman1Data$Components.of.Variation Hayman1DataOther.Parameters <- Hayman1Data$Other.Parameters Hayman1DataFr <- Hayman1Data$Fr # # Wr-Vr Graph # VOLO <- Hayman1Data$VOLO In.Value <- Hayman1Data$In.Value a <- Hayman1Data$a b <- Hayman1Data$b Wr.Vr <- Hayman1Data$Wr.Vr.Table library(ggplot2 ggplot(data=data.frame(x=c(0, max(in.value, Wr.Vr$Vr, Wr.Vr$Wr, Wr.Vr$Wrei, aes(x + stat_function(fun=function(x {sqrt(x*volo}, color="blue" + geom_hline(yintercept = 0 + geom_vline(xintercept = 0 + geom_abline(intercept = a, slope = b + geom_abline(intercept = mean(wr.vr$wr-mean(wr.vr$vr, slope = 1 + geom_segment(aes( x = mean(wr.vr$vr, y = min(0, mean(wr.vr$wr, xend = mean(wr.vr$vr, yend = max(0, mean(wr.vr$wr
12 12 HaymanData, color = "green" + geom_segment(aes( x = min(0, mean(wr.vr$vr, y = mean(wr.vr$wr, xend = max(0, mean(wr.vr$vr, yend = mean(wr.vr$wr, color = "green" + lims(x=c(min(0, Wr.Vr$Vr, Wr.Vr$Wrei, max(wr.vr$vr, Wr.Vr$Wrei, y=c(min(0, Wr.Vr$Wr, Wr.Vr$Wrei, max(wr.vr$wr, Wr.Vr$Wri + labs( x = expression(v[r], y = expression(w[r], title = expression(paste(w[r]-v[r], " Graph" + theme_bw( HaymanData Data for Diallel Analysis using Hayman s Approach Description Griffing is used for performing Diallel Analysis using Hayman s Approach. Usage data(haymandata Format A data.frame with 256 rows and 4 variables. Details Cross1 Cross 1 Cross2 Cross 2 Rep Replicate Yield Yield Response Author(s Muhammad Yaseen (<myaseen208@gmail.com>
![Vr$Wri + labs( x = expression(v[r], y = expression(w[r], title = expression(paste(w[r]-v[r], " Graph" + theme_bw( HaymanData Data for Diallel Analysis using Hayman s Approach](/docs-images/47/20718448/images/page_12.jpg "Description Griffing is used for performing Diallel Analysis using Hayman s Approach. Usage data(haymandata Format A data.frame with 256 rows and 4 variables.")
13 HaymanData 13 References Examples 1. Griffing, B. (1956 Concept of General and Specific Combining Ability in relation to Diallel Crossing Systems. Australian Journal of Biological Sciences, 9(4, Test data(haymandata
14 Index Topic datasets GriffingData1, 6 GriffingData2, 7 GriffingData3, 8 GriffingData4, 9 HaymanData, 12 Griffing, 2, 7 9, 11 GriffingData1, 3, 6, 8, 9 GriffingData2, 3, 7, 7, 8, 9 GriffingData3, 3, 7, 8, 8, 9 GriffingData4, 3, 7, 8, 9 Hayman, 3, 10 HaymanData, 11, 12 14
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R Language Fundamentals
R Language Fundamentals Data Types and Basic Maniuplation Steven Buechler Department of Mathematics 276B Hurley Hall; 1-6233 Fall, 2007 Outline Where did R come from? Overview Atomic Vectors Subsetting
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Calculating P-Values. Parkland College. Isela Guerra Parkland College. Recommended Citation
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