DOI: 10.5061/dryad.h38p3b6/1
title: De_Solan_et_al_Ecography_2019

description: ReadMe for data associated with De Solan et al., Ecography, 2019 (DOI: 10.1111/ecog.04122)  

## Author:  

Thomas De Solan
Jean-Yves Barnagaud

## Contact:  

email to jean-yves.barnagaud@cefe.cnrs.fr

## Version:  

last modified 31/10/2018

## Contents:  

This DRYAD repository contains all materials to replicate the analyses found in De Solan et al., Ecography, 2019:
- pre-processed data files
- R scripts to perform the analyses

## Note:  

- We do not include scripts to replicate the figures as they are completely standard and directly originate from the 
data summaries provided in the R scripts. 

- We do not provide the initial raw material (data tables) as it cannot be shared to third-parties according to the terms of 
property agreements with the multiple data providers. Hence, only processed data reduced to the minimum columns necessary to 
run the analyses performed in De Solan et al, 2019 are provided. Raw data can be applied for to Jean-Yves Barnagaud 
(jean-yves.barnagaud@cefe.cnrs.fr) at the Centre d'Ecologie Fonctionnelle et Evolutive, 1919 route de Mende, 34090 Montpellier, Fr. 

## Files description:  

# Folder scripts:  

script_regional_scale.R: prepares data and runs the ppm at the regional scale
script_local_scale.R: prepares data and runs the ppm at the local scale
Script_traits_analysis.R: performs the analysis of traits against ppm coefficients
Script_phylogenetic_analysis.R: checks for a phylogenetic signal in ppm coefficients and traits

# Folder phylogenetic_tree:  

contains the phylogenetic tree of the considered species. 

-&gt; tree_timing_3.NWK
Description: phylogenetic tree in the Newick format.
Note: The tree was computed by Pierre-André Crochet and a full description is provided in the supplementary materials of De Solan et al, Ecography 2019. For any further questions 
please contact Pierre-André Crochet (pierre-andre.crochet@cefe.cnrs.fr)

# Folder local_covariates:  

contains all the land use, topographic and sampling variables used in the Point Process Models at the local scale. All variables are in the TIFF format. 

-&gt; Local_point_pattern.txt
Description: coordinates (WGS84) of the opportunistic records within the local window, with species names.
Column 1: name of the observed species
Column 2: longitudinal coordinate of the record
Column 3: latitudinal coodinate of the record

-&gt; Agriculture.tiff
Description: land-use variable used in the Point Process Models at the local scale. Defined with a 250x250m resolution. 

-&gt; Distance_to_water.tiff
Description: land-use variable used in the Point Process Models at the local scale. Defined with a 100x100m resolution.

-&gt; Forest.tiff
Description:land-use variable used in the Point Process Models at the local scale. Defined with a 250x250m resolution.

-&gt; Open_habitats.tiff
Description: land-use variable used in the Point Process Models at the local scale. Defined with a 250x250m resolution.

-&gt; Urbanization.tiff
Description: land-use variable used in the Point Process Models at the local scale. Defined with a 250x250m resolution.

-&gt; Altitude.tiff
Description: topographic variable used in the Point Process Models at the local scale. Defined with a 25x25m resolution.

-&gt; Consultant_effect.tiff
Description: sampling variable used in the Point Process Models at the local scale. Defined with a 250x250m resolution.

-&gt; Accessibilty_effect.tiff
Description: sampling variable used in the Point Process Models at the local scale. Defined with a 250x250m resolution.

-&gt; Location_effect.tiff
Description: sampling variable used in the Point Process Models at the local scale. Defined with a 250x250m resolution.

-&gt; Local_scale_window.shp
Description: defines the spatial extent of the analysis

# Folder regional_covariates:  
contain all the land use, topographic and sampling variables used in the Point Process Models at the regional scale. All variables are in the TIFF format. 


-&gt; Regional_point_pattern.txt
Description: coordinates (WGS84) of the opportunistic records within the regional window, with species names.
Column 1: name of the observed species
Column 2: longitudinal coordinate of the record
Column 3: latitudinal coodinate of the record

-&gt; Agriculture.tiff
Description: land-use variable used in the Point Process Models at the regional scale. Defined with a 1000x1000m resolution. 

-&gt; Distance_to_water.tiff
Description: land-use variable used in the Point Process Models at the regional scale. Defined with a 100x100m resolution.

-&gt; Forest.tiff
Description: land-use variable used in the Point Process Models at the regional scale. Defined with a 1000x1000m resolution.

-&gt; Open_habitats.tiff
Description: land-use variable used in the Point Process Models at the regional scale. Defined with a 1000x1000m resolution.

-&gt; Urbanization.tiff
Description: land-use variable used in the Point Process Models at the regional scale. Defined with a 1000x1000m resolution.

-&gt; Altitude.tiff
Description: topographic variable used in the Point Process Models at the regional scale. Defined with a 25x25m resolution.

-&gt; Consultant_effect.tiff
Description: sampling variable used in the Point Process Models at the regional scale. Defined with a 250x250m resolution.

-&gt; Accessibilty_effect.tiff
Description: sampling variable used in the Point Process Models at the regional scale. Defined with a 250x250m resolution.

-&gt; Location_effect.tiff
Description: sampling variable used in the Point Process Models at the regional scale. Defined with a 250x250m resolution.

-&gt; Regional_scale_window.shp
Description: defines the spatial extent of the analysis

# Folder phylogenetics_and_traits_analysis:  

contain what is need to perform phylogenetic and traits analyses

-&gt; Traits.xls  
Description: ecological traits used in the PCOA analysis.
Column 1: name of the species
Column 2: percentage of diurnal activity
Column 3: percentage of nocturnal activity (2+3 = 100%)
Column 4: reproduction mode
Column 5: percentage of use of aquatic habitat 
Column 6: percentage of use of rupicolous habitat
Column 7: percentage of use of terrestrial habitat
Column 8: percentage of use of arboreal habitat
Column 9: percentage of use of burrowing habitat (5+6+7+8+9= 100%)
Column 10: body size in mmm
Column 11: age at sexual maturity
Column 12: species’ mobility (categorical, explicit in the data)
Column 13: activity period (nb days)
Column 14: number of eggs by years
Column 15: percentage of use of fish prey
Column 16: percentage of use of amphibians prey
Column 17: percentage of use of reptiles prey
Column 18: percentage of use of mammals prey
Column 19: percentage of use of birds prey
Column 20: percentage of use of arthropods prey
Column 21: percentage of use of mollusk/worms prey
Column 22: percentage of use of plant (15 to 22 = 100%)

-&gt; estimates_ppm_regional_scale.csv  
Description: estimates in absolute scale obtained from Point Process Models at regional scale.
Column 1: species acronyms.
Column 2: names of the land-use or topographic variables (agricole: agriculture; eau: water; foret: forest; milieu_ouvert: open habitats; altitude: altitude; 
urbain: urbanization; lineaire: accessibility effect).
Column 3: estimates obtained from Point Process Models.
Column 4: standard errors of the estimates.

-&gt; estimates_ppm_local_scale.csv  
Description: estimates in absolute scale obtained from Point Process Models at the local scale.
Column 1: species acronyms.
Column 2: names of the land-use or topographic variables (agricole: agriculture; eau: water; foret: forest; milieu_ouvert: open habitats; altitude: altitude; 
urbain: urbanization; lineaire: accessibility effect).
Column 3: estimates obtained from Point Process Models.
Column 4: standard errors of the estimates.

-&gt; pcoa.csv  
Description: species scores obtained from the PCoA made on ecological traits.
Column 1: species acronyms.
Column 2-14: species scores for the axes 1 to 13.

# Species names and acronyms:  

ANGFRA : Anguis fragilis (Linnaeus, 1758)
CHASTR : Chalcides striatus (Cuvier, 1829)
LACBIL : Lacerta bilineata (Daudin, 1802)
MALMON : Malpolon monspessulanus (Hermann, 1804)
NATMAU : Natrix maura (Linnaeus, 1758)
NATNAT : Natrix natrix (Linnaeus, 1758)
PODLIO : Podarcis liolepis (Boulenger, 1905
PODMUR : Podarcis muralis (Laurenti, 1768)
PSAALG : Psammodromus algirus (Linnaeus, 1758)
PSAEDW : Psammodromus edwardsianus (Dugès, 1829)
RHISCA : Rhinechis scalaris (Schinz, 1822)
TARMAU : Tarentola mauritanica (Linnaeus, 1758)
TIMLEP : Timon lepidus (Daudin, 1802)
ZAMLON : Zamenis longissimus (Laurenti, 1768)


##### End of readme #####