Code for linear and linear mixed-effects models, as well as cline analyses can be found in 
Erebia_models_clines_and_plots.R
input file = phenotypics_FINAL.txt for models and clines
input file = Revision_FINAL.eigenvec, Revision_FINAL.eigenval, classifiers.txt for PCA based on genomic data
input file = Admixture_2.Q, Indvdata.txt for processing the results of the k=2 ADMIXTURE analysis.

Code for P matrix analysis (input file = phenotypics_FINAL.txt):
R script calculating theta and implementing a bootstrap approach (from Lucek et al. 2014 JEB) + bootstrap and calculation of the Mahalanobis distance between subsets:
Functions_for_Pmatrices_and_Mahalanobis_distances.R

R script for all P analyses for the allopatric comparisons:
P_matrices_and_Mahalanobis_distances_allopatric.R

R script for all P analyses along the zone of secondary contact:
P_matrices_and_Mahalanobis_distances_contact_zone.R

Output files from the P matrix analyses and Mahalanobis distance calculations:

Output files/wing_allo_pmax.txt					=> Output for P matrix of wing shape of allopatric populations
Output files/mahal_wings.txt 					=> Output of Mahalanobis distances between allopatric populations for wing shape
Output files/wing_pmax.txt						=> Output for wing shape along the secondary contact zone
Output files/wings_pmax_eigenvalues.txt			=> Eigenvalues of individual p matrices for wing shape along the secondary contact zone
Output files/wing_mahal.txt 					=> Output of Mahalanobis distances for wing shape

Output files/orange_allo_pmax.txt					=> Output for P matrix of orange spot of allopatric populations
Output files/mahal_orange.txt 					=> Output of Mahalanobis distances between allopatric populations for orange spot
Output files/orange_pmax.txt						=> Output for orange spot along the secondary contact zone
Output files/orange_pmax_eigenvalues.txt			=> Eigenvalues of individual p matrices for orange spot along the secondary contact zone
Output files/orange_mahal.txt 					=> Output of Mahalanobis distances for orange spot

Output files/genit_allo_pmax.txt					=> Output for P matrix of genital shape of allopatric populations
Output files/mahal_genit.txt 					=> Output of Mahalanobis distances between allopatric populations for genital shape
Output files/genit_pmax.txt					=> Output for genital shape along the secondary contact zone
Output files/genit_pmax_eigenvalues.txt			=> Eigenvalues of individual p matrices for genital shape along the secondary contact zone
Output files/genit_mahal.txt 					=> Output of Mahalanobis distances across the contact zone for genital shape



Code for ecological variable selection and PCA = Erebia_vars_sel_sub.R, input files = phenotypics_FINAL.txt, output files = z_pca_all.txt, dat_niche_sel.txt
Code for niche overlap calculations = Erebia_niche_overlap_sub.R, input files = dat_niche_sel.txt