Merge pull request #15 from bkotzen/main

inference results for 11.03.23
broadinstitute · Dec 2, 2023 · 8460e2f · 8460e2f
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diff --git a/README.md b/README.md
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 # BVAS: Bayesian Viral Allele Selection 
 
-Welcome to the GitHub repository for [*Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection*](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010540). The results from our main analysis are available
-in [paper](paper/). More recent inference results are also available: [08.10.22](paper/08.10.22/), [09.22.22](paper/09.22.22/), [05.18.23](paper/05.18.23/), [06.15.23](paper/06.15.23/), [06.30.23](paper/06.30.23/), [07.11.23](paper/07.11.23), [09.13.23](paper/09.13.23), and [09.20.23](paper/09.20.23).
+Welcome to the GitHub repository for [*Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection*](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010540). The results from our main analysis are available in [paper](paper/). More recent inference results are also available: [08.10.22](paper/08.10.22/),
+[09.22.22](paper/09.22.22/), [05.18.23](paper/05.18.23/), [06.15.23](paper/06.15.23/), [06.30.23](paper/06.30.23/), [09.13.23](paper/09.13.23), [09.20.23](paper/09.20.23), [11.03.2023](paper/11.03.23), [11.17.23](paper/11.17.23), and [11.29.2023](paper/11.29.23).
 Thanks to Benjamin Kotzen ([@bkotzen](https://www.github.com/bkotzen)) for help generating these more recent results!
 
 

diff --git a/paper/11.03.23/allele_summary.csv b/paper/11.03.23/allele_summary.csv
diff --git a/paper/11.03.23/growth_rates_summary.csv b/paper/11.03.23/growth_rates_summary.csv
diff --git a/paper/11.03.23/metadata.txt b/paper/11.03.23/metadata.txt
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+Number of regions: 187
+Number of viral sequences: 11988851
+Effective population size estimation strategy: "two-bucket" strategy
+Number of lineage clusters L: 5000
+Expected number of non-neutral alleles a priori S: 50.0
+Prior precision tau: 100.0
diff --git a/paper/11.03.23/pip_ranked_alleles.png b/paper/11.03.23/pip_ranked_alleles.png
diff --git a/paper/11.03.23/top_growth_rates.png b/paper/11.03.23/top_growth_rates.png
diff --git a/paper/11.17.23/allele_summary.csv b/paper/11.17.23/allele_summary.csv
diff --git a/paper/11.17.23/growth_rates_summary.csv b/paper/11.17.23/growth_rates_summary.csv
diff --git a/paper/11.17.23/metadata.txt b/paper/11.17.23/metadata.txt
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+Number of regions: 187
+Number of viral sequences: 12012821
+Effective population size estimation strategy: "two-bucket" strategy
+Number of lineage clusters L: 5000
+Expected number of non-neutral alleles a priori S: 50.0
+Prior precision tau: 100.0
diff --git a/paper/11.17.23/pip_ranked_alleles.png b/paper/11.17.23/pip_ranked_alleles.png
diff --git a/paper/11.17.23/top_growth_rates.png b/paper/11.17.23/top_growth_rates.png
diff --git a/paper/11.29.23/allele_summary.csv b/paper/11.29.23/allele_summary.csv
diff --git a/paper/11.29.23/growth_rates_summary.csv b/paper/11.29.23/growth_rates_summary.csv
diff --git a/paper/11.29.23/metadata.txt b/paper/11.29.23/metadata.txt
@@ -0,0 +1,6 @@
+Number of regions: 187
+Number of viral sequences: 12025864
+Effective population size estimation strategy: "two-bucket" strategy
+Number of lineage clusters L: 5000
+Expected number of non-neutral alleles a priori S: 50.0
+Prior precision tau: 100.0
diff --git a/paper/11.29.23/pip_ranked_alleles.png b/paper/11.29.23/pip_ranked_alleles.png
diff --git a/paper/11.29.23/top_growth_rates.png b/paper/11.29.23/top_growth_rates.png