This holds all of the data (except fastq files) and code for "Neural networks allow simulation-based inference of evolutionary parameters from adaptation dynamics". Each individual inference procedure also has an associated pdf that shows the observation for which inference was performed, the joint and marginal posterior distributions, and the posterior predictive check.
All code and a README is in the zipped archive cnv_sims_inference-master.zip
SData 1: *Assessing inference method performance on single experiments.*
This is a zip folder containing the results of inference on single observations. Each file in the folder is named with the following naming convention: Model_Method_FlowType_SimulationBudget_InferenceSet_all.pdf. Each file contains 20 pages, each page corresponding to one of the 20 simulated synthetic observations. For NPE, each file corresponds to one training set (each observation was evaluated on a single amortized posterior was used) each page contains 6 panels, from top left to bottom right: a description of parameters used to generate the synthetic observation, a plot of the synthetic observation, the marginal posterior distribution for CNV formation rate, a plot of the posterior predictive check, the joint posterior distribution, and the marginal posterior distribution for CNV selection coefficient. For ABC-SMC, each page contains 8 panels from top left to bottom right: a description of parameters used to generate the synthetic observation, a plot of the synthetic observation, the effective sample size for each iteration of inference, epsilon values for each iteration of inference, the marginal posterior distribution for CNV formation rate for each iteration of inference, a plot of the posterior predictive check, the final joint posterior distribution, and the marginal posterior distribution for CNV selection coefficient for each iteration of inference. When the starting particle size = 100, the simulation budget was 10,000; when starting particle size = 1000, the simulation budget was 100,000.
The specific data for the main figure and the associated supplemental figures is:
- Figure 1A and supp
- Data from Lauer et al. 2018/*
- Figure 3 and supp
- Results of inference/Inference on single synthetic observations/HDR.csv
- Results of inference/Inference on single synthetic observations/Inferred parameters/*est_real_params.csv
- Figure 4 and supp
- The same data as Figure 2
- Results of inference/Cross simulation/HDR_cross_sim.csv
- Results of inference/Cross simulation/Inferred parameters/*est_real_params.csv
- Figure 5 and supp
- Results of inference/Direct inference of DFE/Inferred parameters/*est_real_params.csv
- Results of inference/Each experiment inferred individually/Inferred parameters/*est_real_params.csv
- Figure 6 and supp
- Results of inference/Lauer et al 2018/Using all generations/Inferred parameters/*est_real_params.csv
- Results of inference/Lauer et al 2018/Using up to generation 116/Inferred parameters/*est_real_params.csv
- Figure 7 and supp
- Barcode data/*
- Fitness assays/*
- Results of inference/Lauer et al 2018/Using up to generation 116/Inferred parameters/*est_real_params.csv
Raw barcode sequencing data is available on the SRA: BioProject ID PRJNA767552.