This README_Bugmann&Seidl_v2.txt file was generated on 2022-08-23 by Harald Bugmann


GENERAL INFORMATION
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This repository contains all data and scripts required to reproduce the analysis published by Bugmann & Seidl (2022), J Ecol.

Corresponding author: Harald Bugmann, Forest Ecology, ETH Zurich, CH-8092 Zurich, e-mail harald.bugmann@env.ethz.ch

Time of data collection: September 2021 to January 2022


DATA & FILE OVERVIEW
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These data were collected by Harald Bugmann from a review of 28 models of long-term forest dynamics by consulting published model documentations (papers), technical reports, and sometimes e-mail conversations with the PIs of the corresponding model. The data were used for a meta-analysis of the evolution (since 1972), complexity and diversity of this class of models. Fifty-two attributes ("genes") were defined to characterise each model, and between two and six expressions ("alleles") of each attribute were defined and assigned to each model. 

File 1: "Attribute_Definition_for_R_(export).xlsx". This is an MS Exel v16.0 file.
Description: This file contains fhe definition of the attributes and their alleles.

File 2: "Summary_Definition of genes and alleles.zip". This is a Zip archive that expands into an MS Exel v16.0 file.
The data for the meta-analysis were compiled for each of the 28 models in this file.

File 3: "Genealogy.R". This is a file for the statistical software package R, version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing. It was used on the platform x86_64-apple-darwin17.0 (64-bit), i.e. a MacBook Pro 2019.
This file contains all software code used to import, post-process, and analyse the data contained in File 2.

File 4: "Genealogy_Paper_SM1_(atttributes).docx". This is an MS Word v16.0 document.
This is the contents of Supplementary Material 1, as described in the paper.

File 5: "Genealogy_Paper_SM2_3_(tables___figures).docx". This is an MS Word v16.0 document.
This is the contents of Supplementary Materials 2 & 3, as described in the paper.


DATA-SPECIFIC INFORMATION
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Note that all analyses were conducted using the collection of scripts (and snippets) in the file "Genealogy.R". This file cannot be run from top to bottom, but the individual parts need to be executed individually. In the current state of the file, all output will go to disk, not the graphics window (see corresponding boolean variables).

Data-specific information for "Attribute_Definition_for_R_(export).xlsx":
1. Number of variables (attributes, rows): 52; 8 "Basic assumptions", 21 "Growth", 13 "Establishment", 7 "Mortality" and 3 "Soil moisture" attributes. Each attribute is a row, with empty rows containing sub-headings in the first column
2. Number of expressions ("alleles", columns): two to six, depending on the attribute. "NA" denotes "not defined", as in the R convention.

Data-specific information for "Summary_Definition of genes and alleles.xlsx":
1. Number of variables (attributes, rows): exactly the same as in file "Attribute_Definition_for_R_(export).xlsx", with three additions at the bottom (rows 60-62): Scale of the model, Genome length, and date of first publication of the model.
2. Number of cases (models, columns): 28 entries that were used in the meta-analysis in columns B through AC; the data on FORHCCN in column AD was not completed because this model turned out to be unsuitable for the analysis. This column is ignored in the corresponding code in "Genealogy.R".