From 369e775fd33cdedf619f1c02aa0b9615641486b0 Mon Sep 17 00:00:00 2001
From: mjgaughan <mgaughan@proton.me>
Date: Wed, 8 May 2024 18:58:43 -0500
Subject: [PATCH] messing with figuring out postVar

---
 R/readmeRDDAnalysis.R | 24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/R/readmeRDDAnalysis.R b/R/readmeRDDAnalysis.R
index e59496b..777d7e5 100644
--- a/R/readmeRDDAnalysis.R
+++ b/R/readmeRDDAnalysis.R
@@ -61,13 +61,22 @@ library(optimx)
 library(lattice)
 all_model <- lmer(log1p_count ~ D * I(week_offset)+ scaled_project_age + (D * I(week_offset)| upstream_vcs_link), data=all_actions_data, REML=FALSE, control = lmerControl(
   optimizer ='optimx', optCtrl=list(method='L-BFGS-B')))
-summary(all_model)
+summary_of_all <- summary(all_model)
 #identifying the quartiles of effect for D
-all_model_ranef <- ranef(all_model, condVar=TRUE)
-dotplot(all_model_ranef)
-df_ranefs <- as.data.frame(all_model_ranef)
+all_model_ranef_condvar <- ranef(all_model, condVar = TRUE)
+all_model_ranef <- ranef(all_model, condVar = FALSE)
+attr(all_model_ranef_condvar$upstream_vcs_link, "postVar")
+
+all_coefficients <- coef(all_model)
+all_standard_errors <- sqrt(diag(vcov(all_model)))[1]
+#all_conf_intervals <- cbind(all_coefficients - 1.96 * all_standard_errors, 
+#                        all_coefficients + 1.96 * all_standard_errors)
+
+df_ranefs <- as.data.frame(all_model_ranef_condvar)
+df_rn_no_cv <- as.data.frame(all_model_ranef)
 D_df_ranef <- df_ranefs[which(df_ranefs$term == "D"),]
 #below this groups the ranefs
+"""
 has_zero <- function(condval, condsd){
   bounds <- condsd * 1.96
   return(ifelse(((condval - bounds) < 0),ifelse(((condval + bounds) > 0), 1, 0), 2))
@@ -75,14 +84,17 @@ has_zero <- function(condval, condsd){
 df_ranefs <- df_ranefs |>
     mutate(ranef_grouping = has_zero(condval, condsd)) |>
     mutate(rank = rank(condval))
-D_df_ranef <- df_ranefs[which(df_ranefs$term == "D"),]
+D_df_ranef <- df_ranefs[which(df_ranefs$term == ),]
+D_df_ranef <- D_df_ranef |>
+  mutate(rank = rank(condval))
 hist(D_df_ranef$ranef_grouping)
 #plot the ranefs 
 library(ggplot2)
 D_df_ranef |>
   ggplot(aes(x=rank, y=condval, col = as.factor(ranef_grouping))) +
   geom_linerange(aes(ymin= condval - (1.96 * condsd), ymax= condval + (1.96 * condsd))) +
-  geom_bw()
+  theme_bw()
+"""
 #d_effect_ranef_all <- all_model_ranef$upstream_vcs_link
 #d_effect_ranef_all$quartile <- ntile(d_effect_ranef_all$condval, 4)
 #model residuals