update README and add Author_affiliations

Author_affiliations.md

@@ -0,0 +1,172 @@
+*Author affiliations*:
+
+Nicholas J. Gotelli
+Department of Biology
+University of Vermont
+Burlington, Vermont 05405 USA
+ORCid ID: 0000-0002-5409-7456
+[Nicholas.Gotelli@uvm.edu](mailto:Nicholas.Gotelli@uvm.edu)
+
+Douglas B. Booher
+Yale Center for Biodiversity and Global Change
+Yale University
+195 Prospect Street
+New Haven, Connecticut 06511 USA
+
+and 
+
+Georgia Museum of Natural History
+101 Cedar Street
+Athens, GA 30602 USA
+ORCid ID: 0000-0002-4257-7401
+[dbooher@antmuseum.com](mailto:dbooher@antmuseum.com)
+
+Mark C. Urban
+Department of Ecology and Evolutionary Biology
+Center of Biological Risk
+University of Connecticut
+75 N. Eagleville Road, Unit 3043
+Storrs, Connecticut USA 06269-3043
+ORCid ID: 0000-0003-3962-4091
+[mark.urban@uconn.edu](mailto:mark.urban@uconn.edu)
+
+Werner Ulrich
+Department of Ecology and Biogeography
+Faculty of Biological and Veterinary Sciences
+Nicolaus Copernicus University
+Lwowska 1
+87-100 Torun, POLAND
+ORCid ID: 0000-0002-8715-6619
+[ulrichw@umk.pl](mailto:ulrichw@umk.pl) 
+
+Andrew V. Suarez
+Department of Evolution, Ecology and Behavior
+Department of Entomology
+University of Illinois
+515 Morrill Hall
+505 S. Goodwin Ave
+Urbana, Illinois 61801 USA
+ORCid ID: 0000-0002-2257-3366
+[suarez2@illinois.edu](mailto:suarez2@illinois.edu)
+
+David K. Skelly
+Yale Peabody Museum of Natural History
+School of Forestry & Environmental Studies
+Yale University
+195 Prospect Street
+New Haven, Connecticut 06511 USA
+ORCid ID: 0000-0002-5067-4535
+[david.skelly@yale.edu](mailto:david.skelly@yale.edu)
+
+David J. Russell
+Senckenberg Museum of Natural History
+Am Museum 1
+02826 Görlitz, GERMANY
+ORCid ID: 0000-0002-0129-0375
+[david.russell@senckenberg.de](mailto:david.russell@senckenberg.de)
+
+Rebecca J. Rowe
+Department of Natural Resources and the Environment
+University of New Hampshire
+Durham, New Hampshire 03824 USA
+ORCid ID: 0000-0002-0492-568X
+[rebecca.rowe@unh.edu](mailto:rebecca.rowe@unh.edu)
+
+Matthew Rothendler
+Department of Biology
+Boston University
+Boston, Massachusetts 02215 USA
+ORCid ID: 0000-0001-9705-2568
+[mrothendler@gmail.com](mailto:mrothendler@gmail.com)
+
+Nelson Rios 
+Yale Peabody Museum of Natural History 
+School of Forestry & Environmental Studies 
+Yale University 
+195 Prospect Street 
+New Haven, Connecticut 06511 USA 
+ORCid ID: 0000-0003-4831-655X
+[nelson.rios@yale.edu](mailto:nelson.rios@yale.edu)
+
+Sandra M. Rehan
+Department of Biology
+York University
+Toronto, Ontario, CANADA
+ORCid ID: 0000-0002-6441-5155
+[sandra.rehan@gmail.com](mailto:sandra.rehan@gmail.com)
+
+George Ni
+Department of Biology
+University of Vermont
+Burlington, Vermont 05405 USA
+ORCid ID: 0000-0001-5558-7564
+[George.Ni@uvm.edu](mailto:George.Ni@uvm.edu)
+
+Corrie S. Moreau
+Cornell University
+Department of Entomology
+Department of Ecology and Evolutionary Biology
+129 Garden Ave
+3136 Comstock Hall
+Ithaca, NY, 14853, USA
+ORCid ID: 0000-0003-1139-5792
+[corrie.moreau@cornell.edu](mailto:corrie.moreau@cornell.edu)
+
+Anne E. Magurran
+Centre for Biological Diversity and Scottish Oceans Institute
+School of Biology
+University of St Andrews
+St Andrews, Fife KY16 9TH, UK
+ORCid ID: 0000-0002-0036-2795
+[aem1@st-andrews.ac.uk](mailto:aem1@st-andrews.ac.uk)
+
+Faith A.M. Jones
+Department of Forest and Conservation
+Faculty of Forestry
+University of British Columbia
+Vancouver, British Columbia, CANADA
+ORCid ID: 0000-0001-6571-714X
+[Faith.jones@ubc.ca](mailto:Faith.jones@ubc.ca) 
+
+and
+
+Centre for Biological Diversity and Scottish Oceans Institute
+School of Biology
+University of St Andrews
+St Andrews, Fife KY16 9TH, UK
+
+Gary R. Graves
+Department of Vertebrate Zoology
+National Museum of Natural History
+Smithsonian Institution
+Washington, DC 20013, USA
+ORCid ID: 0000-0003-1406-5246 
+[gravesg@si.edu](mailto:gravesg@si.edu)
+
+and 
+
+Center for Macroecology, Evolution and Climate
+Globe Institute
+University of Copenhagen
+2100 Copenhagen Ø, DENMARK
+
+Cristina Fiera
+Institute of Biology Bucharest
+Romanian Academy
+296 Splaiul Independenţei, P.O. Box 56-53, 060031
+Bucharest, ROMANIA
+ORCid ID: 0000-0002-0125-5879
+[cristina.ivanescu@ibiol.ro](mailto:cristina.ivanescu@ibiol.ro)
+
+Ulrich Burkhardt
+Struvestr. 9, D-02826
+Gorlitz, GERMANY
+ORCid ID: 0000-0002-1943-9393
+[ulrich_burk@gmx.de](mailto:ulrich_burk@gmx.de)
+
+Richard B. Primack
+Department of Biology
+Boston University
+Boston, Massachusetts 02215 USA
+ORCid ID: 0000-0002-3748-9853
+[primack@bu.edu](

README.md

@@ -1 +1,36 @@
-# FAMA
+# FAMA
+
+README.md updated: 08 July 2021
+
+Nicholas J. Gotelli
+
+This repository contains data files and R scripts for reproducing the numerical and graphical output from:
+
+> Gotelli N.J., D.B. Booher, M.C. Urban, W. Ulrich, A.V. Suarez, D.K. Skelly, D.J. Russell, R.J. Rowe, M. Rothendler, N. Rios, S.M. Rehan, G. Ni, C.S. Moreau, A.E. Magurran, F.A.M. Jones, G.R. Graves, C. Fiera, U. Burkhardt, R.B. Primack. in press. Estimating Species Relative Abundances From Museum Records. Methods in Ecology and Evolution.
+
+The repository is called FAMA (Field Abundance - Museum Abundance) and is organized as an R project with directories containing *Scripts* and *RawData*, and directories that will hold the *Output* and *DataObjects*.
+
+When you clone this repository, the *Output* and *DataObjects* directories are empty (except for a hidden `.keep` file so that github respects the empty directory). To populate these directories with all of the output, simply run the `BatchProcessFiles.R` script in the `Scripts` directory.
+
+## Directory Contents
+
+### *Scripts* Directory
+
+This directory contains all of the individual scripts for reading each of the separate data files and creating the graphs. If you are interesting in using some of the code for calculating the Dirichlet distribution and other statistics, you should find the functions you need in the `BetaDirFunctions.R` script.
+
+### *FormattedData* Directory
+
+This directory contains `.csv` files from each of the co-authors for the different data sets.  In these files, each row is a species, and there are columns for the number of museum records and the number of field records. For the four Walden Pond data sets, there are no field records, but qualitative estimates of abundance of each species.
+
+Although these files are all in the same format, the underlying data are extremely different for each data set. Carefully consult the main text and the supplement for the details of how these data sets were constructed and curated. Some of them may not be appropriate for your purposes. Keep in mind that some of these data sets represent years of field work and many hours spent working with musuem collections. Be respectful of this work by citing the original papers wherever possible, and not just the summary MEE citation. The repository contains contact information for each author so you can contact them if you need clarification or more details.
+
+### *DataObjects* Directory
+
+This directory contains data frames for each object stored in the RDS file format. These objects are then batch processed to extract standard statistics and graphics for each data set.
+
+### *Output* Directory
+
+This directory contains graphic components rendered as `.jpeg`, `.pdf` and `.tiff` files. There is also a single RDS object, `summary_stats`, that contains all of the summary statistics in Table 1 of the MEE paper.
+
+
+