Data from: Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record

 

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Title suppFigure_09-17-13
Downloaded 52 times
Description 120 supplemental figures, with the analysis, simulation scenario and data sources labeled. See the ReadMe for more detail.
Download suppFigure_09-17-13.pdf (179.2 Kb)
Download README.txt (1.634 Kb)
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Title rdata_workspaces_12-29-13
Downloaded 35 times
Description A zip file containing 15 .Rdata saved workspaces, each containing the analytical results from a respective simulation scenario, as indicated in the file names. Can be used with the figure-making scripts to remake the majority of the analytical figures in the main paper and all of the figures shown in the supplement.
Download rdata_workspaces_12-29-13.zip (21.17 Mb)
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Title methodTest_analysis
Downloaded 22 times
Description The main simulation "workhorse" script, for the computer language R. Called and run with the runMethodTest R script to perform the different simulation scenarios and saves the analytical results as a workspace to an .rdata file.
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Title runMethodTest_03-05-13
Downloaded 8 times
Description A script for the R programming language, which runs analyses in the 15 simulation scenarios described in the main paper, via calls to the methodTest script.
Download runMethodTest_03-05-13.R (4.855 Kb)
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Title making_mainfigures_12-06-13
Downloaded 7 times
Description R script which, if given the 15 workspaces contained in the zip file included in this archive, will generate figures 2-9 in the main paper. (Unfortunately, the final-final figures I submitted had to be converted to a different file format and resized in GIMP, so they may not be 100% identical).
Download making_mainfigures_12-06-13.R (15.84 Kb)
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Title make_supp_files_09-15-13
Downloaded 3 times
Description R script which, if given the 15 workspace files contained in the zip file included in this archive, will generate the 120 supplemental figures for this paper, and save them as a single PDF file, which should be identical to the PDF file containing the supplemental figures already included here on Dryad.
Download make_supp_files_09-15-13.R (6.235 Kb)
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Title ZLB_tests_01-23-13
Downloaded 7 times
Description An R script for running and recreating the figures related to zero-length branch simulations described in the Discussion section of the main paper, and was used to create Figure 10. If the attached 'ZLB' workspace file is used, it should be able to recreate Figure 10 exactly.
Download ZLB_tests_01-23-13.R (3.02 Kb)
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Title ZLB_test_01-23-13
Downloaded 4 times
Description The saved R workspace (as an .Rdata file) from the zero length branch simulations described in the Discussion of the paper, and produced using the ZLB_test R script. Can be used with the same script to recreate Figure 10 from the main paper.
Download ZLB_test_01-23-13.Rdata (11.66 Kb)
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When using this data, please cite the original publication:

Bapst DW (2014) Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record. Paleobiology 40(3): 331-351. http://dx.doi.org/10.1666/13033

Additionally, please cite the Dryad data package:

Bapst DW (2014) Data from: Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.187nt
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