This readme.txt file was generated on 20160328 by Georgia Huang ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Supporting Data Analysis for "An Application of Envelope Methodology and Aster Models" 2. Principal Investigator Contact Information A. Name: Eck, Daniel J B. Institution: University of Minnesota C. Email: eckxx049@umn.edu 3. Associate or Co-investigator Contact Information A. Name: Geyer, Charles J B. Institution: University of Minnesota C. Email: geyer@umn.edu 4. Associate or Co-investigator Contact Information A. Name: Cook, R. Dennis B. Institution: University of Minnesota C. Email: rdcook@umn.edu 5. Date files were created: 20160323 6. Are there multiple versions of the dataset? no -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution-NonCommercial-ShareAlike 3.0 United States 2. Links to publications that cite or use the data: Eck, D.J., Geyer, C.J., and Cook, R.D. (2016). An Application of Envelope Methodology and Aster Models. In prep. 3. Links to other publicly accessible locations of the data: The base data used for bootstrap simulations in Example 1 and Example 2 are stored in the R package 'envlpaster'. To access the data, install and load the package in R or RStudio. Then call on data(simdata30nodes) and data(Mguttatus). 4. Was data derived from another source? Aster_across_sites_DIV1.csv contains original data from Lowry, D.B. and Willis, J.H. (2010). Citation: Lowry, D.B. and Willis, J.H. (2010). Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation. PLoS Biol, 8(9): e1000500. 5. Recommended citation for the data: Eck, Daniel J; Geyer, Charles J; Cook, R. Dennis. (2016). Supporting Data Analysis for "An Application of Envelope Methodology and Aster Models" [dataset]. Retrieved from the Data Repository for the University of Minnesota, http://dx.doi.org/10.13020/D66K51. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List: A. Filename: envlpaster-fit-boot-Efron-techreport.pdf Short description: Technical Report B. Filename: envlpaster-fit-boot-Efron-techreport.Rnw Short description: Source File for Technical Report C. Filename: envlpaster-fit-boot-Efron-techreport.txt Short description: Archival Version of Source File D. Filename: envlpaster-fit-boot-Efron-techreport.tex Short description: Archival Version of Compiled Source File E. Filename: ex1-Efronboot.RData Short description: Supporting Calculations (Example1-Top Level of Bootstrapping) F. Filename: ex1-secondboot.RData Short description: Supporting Calculations (Example1-Second Level of Bootstrapping) G. Filename: ex1-AIC.RData Short description: Supporting Calculations (Example1-Efficiency Gain Based on AIC) H. Filename: techreport_eigenboot_fitboot.RData Description: Supporting Calculations (Example1-Bootstrapped Estimator of Variability) I. Filename: main-all-terms-DavidLowrydata.RData Description: Supporting Calculations (Example 2) J. Filename: Aster_across_sites_DIV1.csv Description: Raw Data File (Example 2) 2. Relationship Between Files: The first four files are the same technical report saved in the pdf, Rnw, txt, and tex formats. The pdf file is compiled from the source file (Rnw). The txt file is the archival version of the source file (Rnw). The tex file is the intermediary output when the source file (Rnw) is run in R and serves as an archival version for the compiled source file. The data analysis described in the technical report were performed in R. The calculations in the R workspace are stored in RData files. The RData files are loaded into the technical report (pdf) as it was being compiled from the source file. The csv file contains data from the Lowry and Willis (2010) research. It has observed characteristics on 2313 Mimulus guttatus flowers. These data were used to illustrate the second example in the technical report. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: The text and R code in the Rnw file are written with the Sweave function in R or RStudio. The file contains supporting data analysis for the related paper. The Rnw file can be executed using the R package "knitr", which produces the tex file and pdf file. The results from the R computations and graphics are embedded in the pdf file. The txt file was generated by saving the content of the Rnw file in the txt format. RData files were generated by saving R workspace images after running bootstraps and model selection procedures in R. Since these calculations take substantial time to run, they are not included in the Rnw file. Rather, the results of these calculations are elicited from the RData files as the Rnw file is being run by "knitr". The csv file contains the tabulated data from the study conducted by Lowry and Willis (2010). 2. Instrument-specific information needed to interpret/process the data: Open source environment R or RStudio is required to view and access the RData files and run the "knitr" script in the Rnw file. Two R packages "envlpaster" and "aster2" are needed to carry out the R calculations in the Rnw file. Both packages require R (version ≥ 2.10.0). See more information about R package "envlpaster" at See more information about R package "aster2" at ----------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR [Aster_across_sites_DIV1.csv] ----------------------------------------------------------- 1.Number of variables: 6 2.Number of cases/rows: 2313 3.Missing data codes: n/a 4.Variable List A. Name: site Description: the field site of the plant Boon = Boonville, CA N 38º59.221, W 123º21.059 Fraser = Manchester, CA N 39º00.498, W 123º41.637 B. Name: gen_bac Description: the genetic background of the plant Coast = Coastal Genetic Background Inland = Inland Genetic Background C. Name: type Description: the ecotype of the flower IL1 = Perennial Arrangement: Annual Genetic Background L = Inland Parent LN = Annual Arrangement: Annual Genetic Background S = Costal Parent SI1 = Annual Arrangement: Perennial Genetic Background SN1 = Perennial Arrangement: Perennial Genetic Background D. Name: inversion Description: the inversion orientation of the plant A = Annual Chromosomal Inversion P = Perennial Chromosomal Inversion E. Name: sur_flw Description: a binary variable indicating whether or not the plant lived 1 = the plant lived 0 = the plant died F. Name: flws Description: an integer valued variable indicating how many flowers a surviving plant had. 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