resolve conflict

Author: helenewegener

.DS_Store

@@ -0,0 +1,50 @@
+diab <- read_xlsx('../data/diabetes_clinical_toy_messy.xlsx')
+diabMeta <- read_csv('../data/diabetes_meta_toy_messy.csv')
+glu <- read_xlsx('../data/df_glucose.xlsx')
+
+
+diab_clean <- diab %>% 
+  filter(!if_any(everything(), is.na) & Age != 0 & BloodPressure !=0 & BMI!=0) %>%
+  mutate(Diabetes = as.integer(Diabetes), Age = as.integer(Age), Sex = ifelse(Sex == "male", "Male", 
+                      ifelse(Sex == "FEMALE", "Female", as.character(Sex)))) 
+
+
+diab_clean_meta <- left_join(diab_clean, diabMeta)
+
+diab_glu <- left_join(diab_clean_meta, glu)
+
+diabnum <- diab_glu %>% 
+  select(-ID) %>% 
+  select_if(is.numeric)
+  
+
+
+pca_res <- prcomp(diabnum, scale. = TRUE)
+autoplot(pca_res, data = diab_clean_meta, colour='Diabetes')
+
+
+pclist <- list()
+
+for (i in 1:length(pca_res$sdev)) {
+  varpc <- pca_res$sdev[i]^2/sum(pca_res$sdev^2)*100
+  npc <- paste0('PC', i)
+  
+  pclist[[i]] <- tibble(PC= npc, Variance = varpc)
+  
+}
+
+PCdf <- map_df(pclist, tibble::as_tibble)
+
+
+
+
+
+# Test for outliers and normality:
+
+# Cooks distance
+model1 <- lm(Diabetes ~ ., data = diab_glu)
+plot(model1, 4)
+
+# Zscore
+z_scores <- scale(diab_glu$PhysicalActivity)
+which(abs(z_scores) > 3.29)