This repository contains all primary simulation code and outputs used in the manuscript "Seeing the Forest for the trees: Assessing genetic offset predictions from Gradient Forest" Final data from six example runs are included as RData objects. Each object is identified with the type of simulation (Neutral=NL, Single locus=SL, Multilocus case 1 = Case1, Multilocus case 2=Case2, Multilocus case 3=Case3, Multilocus case 4=Case4) followed by the SLiM seed value. All Python and R scripts assumes an environment set up within a folder containing the following subdirectories src/ - a folder containing all simulation and analytical scripts src/Pyslim_code - a folder containing all Pyslim scripts (requires Python3) src/R_analysis_code - a folder containing all R scripts results/ a folder containing all output files from scripts in the ../src/ folder results/R_results/ - a folder containing all R script outputs results/SLiM_output/ - a folder containing all output files from SLiM and Pyslim results/SLiM_output/Sim_sum/ - a folder containing simulation summaries from the SLiM scripts results/SLiM_output/CG_files/ - a folder containing common garden fitness summaries from the SLiM scripts results/SLiM_output/Mig_mat/ - a folder containing migration matrices output by the SLiM scripts results/SLiM_output/TSR_files/ - a folder containing Tree Sequence Recording (TSR) files output by the SLiM scripts results/SLiM_output/VCF_files/ - a folder containing VCF files output by the Pyslim scripts File descriptions Files located in main folder (no subdirectory): seeds_Neutral.txt - seed values for each replicate of all neutral SLiM simulations seeds_SingleLocus.txt - seed values for each replicate of the single locus SLiM simulation seeds_source_R.txt - seed values for each replicate of the multilocus SLiM simulations Code located in src/SLiM_code/: NL_WF_Neutral.slim - SLiM code for the neutral model simulation SL_WF_SingleLocus.slim - SLiM code for the single locus model simulation ML_WF_Case1.slim - SLiM code for the multi locus Case 1 model simulation ML_WF_Case2.slim - SLiM code for the multi locus Case 2 model simulation ML_WF_Case3.slim - SLiM code for the multi locus Case 3 model simulation ML_WF_Case4.slim - SLiM code for the multi locus Case 4 model simulation Code located in src/Pyslim_code/: TSR_time_AJL.py - Pyslim code that reads in TSR files, recapitates and adds neutral mutations, and outputs filtered and unfiltered subset and non-subset VCF files Code located in src/R_analysis_code/: TTT_VCF_analysis_Neutral.R - R code to analize the neutral simulation output TTT_VCF_analysis_SingleLocus.R - R code to analize the single locus simulation output TTT_VCF_analysis_ML_cases.R - R code to analize the multilocus simulation output