feat: calculate confidence interval of evolutionary rate

Author: ahmig

workflow/rules/distances.smk

@@ -71,6 +71,7 @@ rule time_signal_data:
     conda: "../envs/renv.yaml"
     params:
         outgroup_id = config["ALIGNMENT_REFERENCE"],
+        confidence_interval = 0.95,
     input:
         tree = report(REPORT_DIR_TABLES/"allele_freq_tree.nwk"),
         metadata = config["METADATA"],

workflow/scripts/report/time_signal_data.R

@@ -60,12 +60,15 @@ write_csv(time.signal, snakemake@output$table)
 log_debug("Building linear model")
 model <- lm(distance ~ date_interval, data = time.signal)
 p.value <- summary(model)$coefficients[2, 4]
+ci_models <- confint(model, level = snakemake@params$confidence_interval)
 
 # TREE STATS
 log_debug("Saving linear model")
 list(
   "sub_rate" = model$coefficients[[2]] * 365,
   "r2" = summary(model)$r.squared[[1]],
+  "ci_low" = ci_models[2, 1] * 365,
+  "ci_high" = ci_models[2, 2] * 365,
   "pvalue" = ifelse(p.value < 0.001, "< 0.001", p.value)
 ) %>%
   toJSON() %>%