Data from: General models of ecological diversification. II. Simulations and empirical applications

Novack-Gottshall PM

Date Published: March 29, 2016

DOI: http://dx.doi.org/10.5061/dryad.621h4

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Life-habit/functional-trait codings for the Kope and Waynesville Formation species pool
Downloaded 7 times
Description KWTraits.csv is a comma-separated value (.csv) format file listing the aggregate species pool for the Kope and Waynesville Formation used in empirical analyses. (The file is also included as a data file within the 'ecospace' R package.) The first three columns list taxonomic information. The remaining columns list ecospace character states (functional traits). See supplementary appendix A and Novack-Gottshall (2007) for information on characters and states. See text for explanation of how multistate characters were rescaled.
Download K&WTraits.csv (28.06 Kb)
Details View File Details
Title Two-model model-selection support data files for Kope and Waynesville Formation samples, stratigraphic section, member, and formation aggregates
Downloaded 5 times
Description File is in comma-separated value (.csv) format. The first five columns describe the Paleobiology Database collection identification number, scale (hand sample, stratigraphic section, etc.) of the sample, and stratigraphic/section names. Columns 6–14 list sample size (S, species richness) and values for eight disparity statistics (with NA designating when a statistic could not be calculated, because there were fewer than four unique life habits in the sample); see text for descriptions and abbreviations of statistics. The last column identifies which model has the best support among those candidates considered. The remaining columns list the classification-tree support each sample has for each candidate model considered. emp2-modelfits.csv lists model support using the classification tree trained on the 50% and 100%-strength training data sets. emp3-modelfits.csv lists model support for the tree trained on 50%, 90%, and 100% training data.
Download emp2-modelfits.csv (48.01 Kb)
Details View File Details
Title Three-model model-selection support data files for Kope and Waynesville Formation samples, stratigraphic section, member, and formation aggregates
Downloaded 5 times
Description File is in comma-separated value (.csv) format. The first five columns describe the Paleobiology Database collection identification number, scale (hand sample, stratigraphic section, etc.) of the sample, and stratigraphic/section names. Columns 6–14 list sample size (S, species richness) and values for eight disparity statistics (with NA designating when a statistic could not be calculated, because there were fewer than four unique life habits in the sample); see text for descriptions and abbreviations of statistics. The last column identifies which model has the best support among those candidates considered. The remaining columns list the classification-tree support each sample has for each candidate model considered. emp3-modelfits.csv lists model support for the tree trained on 50%, 90%, and 100% training data.
Download emp3-modelfits.csv (51.57 Kb)
Details View File Details
Title Five-model model-selection support data files for Kope and Waynesville Formation samples, stratigraphic section, member, and formation aggregates
Downloaded 4 times
Description File is in comma-separated value (.csv) format. The first five columns describe the Paleobiology Database collection identification number, scale (hand sample, stratigraphic section, etc.) of the sample, and stratigraphic/section names. Columns 6–14 list sample size (S, species richness) and values for eight disparity statistics (with NA designating when a statistic could not be calculated, because there were fewer than four unique life habits in the sample); see text for descriptions and abbreviations of statistics. The last column identifies which model has the best support among those candidates considered. The remaining columns list the classification-tree support each sample has for each candidate model considered. emp5-modelfits.csv lists model support for the tree trained on 50%, 75%, 90%, 95%, and 100% training data.
Download emp5-modelfits.csv (58.33 Kb)
Details View File Details
Title Supplementary Appendices 1-4 for manuscript
Downloaded 4 times
Description Appendix 1 gives an example of how life-habit character states were inferred and coded. Appendix 2 describes technical details on classification tree methods and confusion matrices. Appendix 3-4 give further details for the other Supplementary data files on Data Dryad.
Download EcomodelsII_Appendices.docx (34.59 Kb)
Details View File Details
Title Supplementary Figure 6
Downloaded 2 times
Description Comparing statistical dynamics for different ecospace framework structures: varying number of characters, (A) 5 characters, (B) 15 characters, and (C) 25 characters. Each framework had mixed character types, in identical proportions (40% binary, 20% three-state factor, 20% five-state factor, and, 20% five-state ordered numeric character types). 5 "seed" species were chosen at random to begin each simulation. Other simulation details and graphical interpretation are the same as is Figure 2. Trends in total variance were excluded because the inclusion of factors prevented their calculation. The dynamics are generally similar, although larger frameworks allow modestly more powerful model selection using classification-tree methods (83%, 85%, and 86% of training models, respectively, classified correctly using classification-tree methods). See Supplementary Appendix 2 for additional details.
Download Novack-GottshallBSuppFigure6_2col.tif (509.0 Kb)
Details View File Details
Title Supplementary Figure 7
Downloaded 2 times
Description Comparing statistical dynamics for different ecospace framework structures: varying character types, (A) factor, (B) ordered factor, (C) ordered numeric, and (D) binary. Each framework had 15 characters, four states per character (except for binary, which had two binary states per character), and five seed species. Trends in total variance were excluded in parts A and B because the inclusion of factors prevented their calculation. Other simulation details and graphical interpretation are the same as in Supplementary Figure 6. Dynamics are generally similar, but frameworks built with ordered factors performed substantially better (94% of trained models classified correctly) than the others (78% for unordered factors, 79% for ordered numerics, and 81% for binaries). See Supplementary Appendix 2 for additional details.
Download Novack-GottshallBSuppFigure7_2col.tif (521.6 Kb)
Details View File Details
Title Supplementary Figure 8
Downloaded 1 time
Description Comparing statistical dynamics for different ecospace framework structures: varying number of "seed" species chosen at random at start of simulation, (A) 3 species, (B) 5 species, and (C) 10 species. Each framework had 15 mixed character types, such that part B is identical to Supplementary Figure 6B. Trends are only plotted starting at 5 species for comparative purposes, which explains idiosyncratic behaviors at low sample sizes (i.e., missing trend lines in part A and overlapping models in part C). Other simulation details and graphical interpretation are the same as is Supplementary Figure 6. Note that the functional-diversity statistics could not be calculated for the redundancy model in part A because their calculation requires a minimum of four unique life habits; however, all statistics (except V) were included as potential predictor variables in the classification tree algorithm. Dynamics are generally similar across models, but simulations with fewer seed species provide the most powerful model selection using classification-tree methods (85% of models classified correctly for both 3-seed and 5-seed simulations). Starting with larger numbers of seed species impedes enacting distinct model rules, and results in 75% of models classified correctly. See Supplementary Appendix 2 for additional details.
Download Novack-GottshallBSuppFigure8_2col.tif (492.0 Kb)
Details View File Details
Title Supplementary Figure 9
Downloaded 3 times
Description Performance of classification tree used on validation samples as a function of sample size. Please see README for additional details.
Download Novack-GottshallBSuppFigure9_2col.tif (2.049 Mb)
Download README.txt (6.275 Kb)
Details View File Details

When using this data, please cite the original publication:

Novack-Gottshall PM (2016) General models of ecological diversification. II. Simulations and empirical applications. Paleobiology 42(2): 209-239. http://dx.doi.org/10.1017/pab.2016.4

Additionally, please cite the Dryad data package:

Novack-Gottshall PM (2016) Data from: General models of ecological diversification. II. Simulations and empirical applications. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.621h4
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: