Update p-value calculation

Author: ahmig

workflow/scripts/report/NV_description.R

@@ -488,12 +488,9 @@ model <- lm(n ~ CollectionDate, data = figur_SNP_table)
 
 # Calculate correlation, if possible
 if (nrow(figur_SNP_table) > 2) {
-  p.cor <- cor.test(
-    figur_SNP_table$n,
-    as.numeric(figur_SNP_table$CollectionDate)
-  )$p.value
+  p.value <- summary(model)$coefficients[2,4]
 } else {
-  p.cor <- NA
+  p.value <- NA
 }
 
 list(
@@ -502,7 +499,7 @@ list(
   "window" = snakemake@params[["window"]],
   "step" = snakemake@params[["step"]],
   "r2" = summary(model)$r.squared[[1]],
-  "value" = ifelse(p.cor < 0.001, "< 0.001", p.cor)
+  "value" = ifelse(p.value < 0.001, "< 0.001", p.value)
 ) %>%
   toJSON() %>%
   write(snakemake@output[["json"]])

workflow/scripts/report/phylo_plots.R

@@ -277,6 +277,7 @@ tempest %>%
 
 # TEMPEST STATS
 model <- lm(distance ~ date_interval, data = tempest)
+p.value <- summary(model)$coefficients[2,4]
 
 # TREE STATS
 study.node <- tree_ml$node.label[study.mrca - length(tip.color)]
@@ -285,11 +286,7 @@ monophyletic <- ifelse(is.monophyletic(tree_ml, study_names), "are", "are not")
 list(
   "sub_rate" = model$coefficients[[2]] * 365,
   "r2" = summary(model)$r.squared[[1]],
-  "pvalue" = ifelse(
-    cor.test(tempest$distance, tempest$date_interval)$p.value < 0.001,
-    "< 0.001",
-    cor.test(tempest$distance, tempest$date_interval)$p.value
-  ),
+  "pvalue" = ifelse(p.value < 0.001, "< 0.001", p.value),
   "boot" = strsplit(study.node, "/")[[1]][2] %>% as.numeric(),
   "alrt" = strsplit(study.node, "/")[[1]][1] %>% as.numeric(),
   "monophyly" = monophyletic,