University of Minnesota,
Twin Cities
School of Statistics
Charlie Geyer's Home Page
Department of Ecology, Evolution, and Behavior
Ruth Shaw's Home Page
Chicago Botanic Garden
Institute for Plant Conservation Biology
Stuart Wagenius's Home Page
Echinacea Project Page
Last changed: Wed Dec 26 14:52:04 CST 2007
The software is now at CRAN. The package name is aster. Now at version 0.7-5.
To install the software in an installation of R which you own
(not the Administrator
or root
user), just do
install.packages("aster")
at an R command line. Otherwise, ask your friendly local system administrator to do this.
Since version 0.3 the package includes an example dataset and examples on all the help pages for functions we expect users to use. Since version 0.7-2 the package includes four more example datasets echin2 and chamae and chamae2 and aphid, which are used in a new technical report.
The library also contains a hopefully useful tutorial (package vignette in R terminology).
The paper
Ruth G. Shaw, Charles J. Geyer, Stuart Wagenius, Helen H. Hangelbroek, and Julie R. Etterson (2008).
Unifying Life History Analyses for Inference of Fitness and Population Growth.
American Naturalist, 172, E35–E47.
is now available, as are three technical reports that contain the full data analysis for the examples in the paper.
The paper
Charles J. Geyer, Stuart Wagenius, and Ruth G. Shaw (2007).
Aster Models for Life History Analysis.
Biometrika, 94, 415—426.
is now available, as is a technical report that contains the full data analysis for the example in the paper and many theoretical details left out of the paper, as is a tutorial (package vignette) that gives a more basic introduction to the software.
| PDF File | Description |
|---|---|
| tr671.pdf | New! Technical report titled Model Selection in Estimation of Fitness Landscapes, which is a detailed explication of what to do when many phenotypic traits are measured and, although one wants model fitness as a function of all of them, to get good statistical estimation one must use submodels with fewer parameters. File needed to recreate the TR, which include all R code for all calculations, are in this folder. |
| tr670.pdf | New! Technical report titled Commentary on Lande-Arnold Analysis, which is a detailed explication of the theory in Lande and Arnold (1983) and also has some supplementary plots for a talk to be given at Evolution 2008, University of Minnesota, June 20–24. File needed to recreate the TR, which include all R code for all calculations, are in this folder. |
| tr669.pdf | New! Technical report having all the calculations and plots for a talk to be given at Evolution 2008, University of Minnesota, June 20–24. File needed to recreate the TR, which include all R code for all calculations, are in this folder. |
| aster2.rgs.pdf | The second paper on aster analysis. This one contains a review of life history analysis and how aster analysis fits in and three examples, including analysis of fitness landscapes and estimation of population growth rate. This has been revised and resubmitted to American Naturalist. (Of historical interest only, the first submitted version) |
| tr666.pdf | Technical report that has yet another calculation for one example for the on-line supplement in the second (and final) resubmission of the paper by Shaw, Geyer, Wagenius, Hangelbroek, and Etterson described above. Files needed to recreate the TR, which include all R code for all calculations, are in this folder. |
| tr661.pdf | Technical report that has the the calculations for one example in the revised resubmission of the paper by Shaw, Geyer, Wagenius, Hangelbroek, and Etterson described above. (This TR was slightly revised, Nov 24, 2007, revised again, adding one more page and plot at the end, Nov 26, 2007, then revised yet again Dec 26, 2007 changing only some plot labels.) Files needed to recreate the TR, which include all R code for all calculations, are in this folder. |
| tr658.pdf | Technical report that has all of the calculations for the rest of the examples in the revised resubmission of the paper by Shaw, Geyer, Wagenius, Hangelbroek, and Etterson described above (plus calculations for the other example in the original submission, which are improved by the calculations in TR 661). Files needed to recreate the TR, which include all R code for all calculations, are in this folder. |
| aster-submit3.pdf | revised and resubmitted paper, double spaced. This paper has appeared in Biometrika. The printed version is available from Oxford University Press. (Of historical interest only, the first submitted version and the second submitted version) |
| tr644.pdf | Technical report that has the the calculations for one example in the revised resubmission of the paper by Geyer, Wagenius, and Shaw described above. |
| tutor.pdf | tutorial (package vignette) |
| white.pdf | expansion of last section of tutorial about parametric bootstrap |
| multi.pdf | technical report (653) allowing correlated child nodes. Of historical interest only, incorporated in the published version of the paper by Geyer, Wagenius, and Shaw described above. |
Ruth Shaw gave a talk at Evolution 2008. Here are the slides for this talk.
Stuart Wangenius gave a talk at Evolution 2008. Here are the slides for this talk.
Charlie Geyer gave a talk at Evolution 2008. Here are the slides for this talk.
Charlie Geyer gave a talk at WNAR. Here are the slides for this talk.
Ruth Shaw gave a talk at the Peter Yodzis Colloquium. Here are the slides for this talk.
Stuart Wagenius gave a talk at the annual Ecology/ESA meeting
August 2006, Memphis, TN titled Joint analysis of survival and reproduction
over 10 years in perennial Echinacea plants from seven populations
Here are the slides for this talk.
Charlie Geyer gave a talk in the School of Statistics seminar on March 30, 2006. Here are the slides for this talk.
Ruth Shaw gave a talk about this at the Society for the Study of Evolution meeting in Fairbanks, Alaska (June, 2005). Here are the original Microsoft PowerPoint form of the presentation and the Adobe PDF (Portable Document Format) form produced by OpenOffice.org.
Here is the full data analysis that provides the example for this talk. This has now been replaced by Appendix D of the aster modelling technical report.
The reason why I chose to call the package aster
is that the
organism for the data we are using for the initial analysis is the
purple coneflower (Echinacea angustifolia)
which is in the
aster family. The submitted draft of the paper says
We named our models after flowers because the name is short and much nicer than forest graph exponential family conditional or unconditional canonical statistic models or any other descriptive name we could think of.
Not a very good reason perhaps, but bootstrap
and jackknife
and simulated annealing
have even less
connection to the actual statistics.
You can call it what you like, LHA for life history analysis
or FEF for flat exponential family
or whatever. But it would
be too annoying at this point to change the name of the R package,
since the function names
aster summary.aster anova.aster predict.aster
should not change.
UROP (Undergraduate Research Opportunities Program) opportunities involving aster models are described on this web page.