Update README.md

Author: Wang-RJ

README.md

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-# Generation times
+# Human generation times across the past 250,000 years
+
+The generation times of our recent ancestors can tell us about both the biology and social organization of prehistoric humans, placing human evolution on an absolute timescale. We implement a method for predicting historical male and female generation times based on changes in the mutation spectrum.
+
+Our method combines data from two different types of studies:
+- **Mutations from pedigree studies** <br>
+We apply a Dirichlet-multinomial regression to mutation count data to capture the relationship between the underlying mutation spectrum and parental ages. 
+- **Variants from population genetic studies** <br>
+We use human variants from the 1000 Genomes Project with allele ages estimated from the Genealogical Estimation of Variant Age (GEVA) approach.
+
+## Summary of analysis workflow:
+1. Preprocess 1000 Genomes variant data with ages from GEVA
+2. Count binned variants, including for each continental population
+3. Load mutation data and build Dirichlet-multinomial model
+4. Estimate best-fit parental ages for variant spectrum in each bin
+
+## Brief descriptions for folders and files in top-level of repository:
+### folders
+- bootstraps/<br>
+Recalculate estimates for each 100x100 double-bootstrap of model and variants
+- neanderthal_masked/<br> 
+Reanalysis masking genomic tracts with potential Neanderthal introgression
+- resample_alleleage/<br>
+Reanalysis after drawing new allele ages based on 95% CI from GEVA
+- var_count/<br>
+Preprocess variant data, bin variants, and count each mutation class
+### files
+* age_modeling.R<br>
+Loads mutation data and builds the probabilistic model for estimating parental ages
+* analyze_main.R<br>
+Analysis script for main plots, depends on age_modeling.R and plot_helper.R
+* analyze_populations.R<br>
+Analysis script for separate continental human populations
+* calculate_SSE.R<br>
+Calculate the sum of squared error (SSE) for generation time estimates
+* cross_validation.R<br>
+Short script for calculating sample variance SSE
+* plot_helper.R<br>
+Auxillary scripts for shaping output and plotting
+* recombination_analysis.R<br>
+Investigation of connection between recombination rate and mutation spectrum
+* sim_famvariance.R<br>
+Simulate variance in parental ages and calculate SSE