Data from: three models of ecological community assembly: terrestrial species inventories
Data files
Jul 10, 2023 version files 1.86 MB
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Ecological_Register_data.txt.gz
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Ecological_Register_references.txt.gz
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Ecological_Register_samples.txt.gz
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README.md
Nov 19, 2023 version files 1.86 MB
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Ecological_Register_data.txt.gz
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Ecological_Register_references.txt.gz
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Ecological_Register_samples.txt.gz
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README.md
Mar 20, 2024 version files 1.86 MB
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Ecological_Register_data.txt.gz
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Ecological_Register_references.txt.gz
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Ecological_Register_samples.txt.gz
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README.md
Abstract
Species abundance distributions, meaning counts of individuals apportioned among species, are fundamental patterns in ecology. Numerous distribution models have been proposed, and most suffer from poor fit to data, complex formulation, excessive parameterisation, or unrealistic modelling of processes. I discuss three that meet all the basic criteria, are easily distinguished, and stem from simple and distinct population dynamics. The log series can be produced by assuming taxonomically and temporally fixed turnover rates. A model derived from scaled odds ratios assumes highly variable dynamics, and one derived from exponential variates assumes taxonomically variable but temporally fixed rates. Mathematical derivations are elementary. Maximum likelihood fits to published empirical data suggest that the two new distributions are more common in nature. Saturated models are rarely better. Ecological communities may be assembled by processes that are easily discerned, instead of being as mysterious as many have thought.
README: Ecological Register Dataset
This file includes all species inventories downloaded from the Ecological Register on 23 October 2022.
Description of the data and file structure
Ecological_Register_data.txt.gz is a single self-contained, tab delimited data matrix including a header that describes the data columns. The file is a list of species occurrences within species inventories. The reference.no field points to a list of references to publications in the Ecological_Register_references.txt.gz file. The sample no field points to a table with additional species inventory metadata to be found in the Ecological_Register_samples.txt.gz file. The blank cells in the files represent cases where no data were entered into the relevant fields, and will be interpreted as NAs when uploaded by an R script. There are no hidden values.
Sharing/Access information
The Ecological Register website is at http://ecoregister.org.
Code/Software
The underlying code used to run the analyses is in the richness.tar.gz file that includes the R library called richness. The code used to prepare the figures, tables, and individual statistics reported in the text is included in the script called three_models.R.
Methods
The gzipped Ecological Register data file (Ecological_Register_data.txt.gz) is a full set of published species inventories of trees and terrestrial animals downloaded from the Ecological Register website on 23 October 2022. The additional files include metadata pertaining to the references used to document the inventories (Ecological_Register_references.txt.gz) and to the species inventories themselves (Ecological_Register_samples.txt.gz) .The gzipped and tarred richness R library (richness.tar.gz) was used to prepare the data and analyses in the associated paper. The blank cells in the files represent cases where no data were entered into the relevant fields, and will be interpreted as NAs when uploaded by an R script. There are no hidden values.
Usage notes
The R programming environment is required to open the richness library and the scripts.