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neonatal_vitaminK_administration_Scotland_analysis.R

+####################################################################################
+###                    ANALYSIS OF PHS VITAMIN K DATASET                         ###
+###                THOMAS WILLIAMS UNI EDINBURGH FEBRUARY 2023                  ###
+####################################################################################
+#load pdplyr
+library(dplyr)
+library(tidyr)
+
+#set working directory
+setwd("Clinical/vitK/analysis/")
+
+#import data for pre and post pandemic
+VitK_overall_dataset <- read.table("vitK_rates_pre_post_pandemic.txt",
+                                        header = T, sep = "\t")
+
+
+#Fisher's exact test to look at rates pre and post pandemic
+oral_none_pre_pandemic <- sum(VitK_overall_dataset$X2018[2:3]) + sum(VitK_overall_dataset$X2019[2:3])
+IM_pre_pandemic <- VitK_overall_dataset$X2018[1] + VitK_overall_dataset$X2019[1]
+oral_none_post_pandemic <- sum(VitK_overall_dataset$X2021[2:3])
+IM_post_pandemic <- VitK_overall_dataset$X2021[1]
+
+
+#Fisher's exact test to look at dataset
+fisher_test_pre_post <- fisher.test(rbind(c(IM_pre_pandemic,IM_post_pandemic),c(oral_none_pre_pandemic,oral_none_post_pandemic)),
+                                    alternative = "two.sided")
+
+#Fisher's exact test to compare 2018 to other years
+oral_none_2018 <- sum(VitK_overall_dataset$X2018[2:3])
+IM_2018 <- VitK_overall_dataset$X2018[1]
+oral_none_2019_2021 <-  sum(VitK_overall_dataset$X2019[2:3]) + sum(VitK_overall_dataset$X2020[2:3])+ sum(VitK_overall_dataset$X2021[2:3])
+IM_2019_2021        <-  VitK_overall_dataset$X2019[1]+VitK_overall_dataset$X2020[1]+VitK_overall_dataset$X2021[1]
+
+fisher_test_2018 <- fisher.test(rbind(c(oral_none_2018,oral_none_2019_2021),c( IM_2018,IM_2019_2021)),
+                                    alternative = "two.sided")
+
+#Fisher's exact test to compare 2019 to 2020/21
+oral_none_2019 <- sum(VitK_overall_dataset$X2019[2:3])
+IM_2019 <- VitK_overall_dataset$X2019[1]
+oral_none_2020_2021 <-  sum(VitK_overall_dataset$X2020[2:3])+ sum(VitK_overall_dataset$X2021[2:3])
+IM_2020_2021        <-VitK_overall_dataset$X2020[1]+VitK_overall_dataset$X2021[1]
+
+fisher_test_2019 <- fisher.test(rbind(c(oral_none_2019,oral_none_2020_2021),c(IM_2019,IM_2020_2021)),
+                                alternative = "two.sided")
+
+#ethnicity
+#import data
+ethnicity_data <- read.table("VitaminK_Analysis_HV_ethnicity_aggregate.txt", 
+                             header = T, sep = "\t")
+
+#run chi squared test on the dataset
+chisq.test(ethnicity_data$Oral_none,ethnicity_data$IM)
+
+#English as a first language
+English_first_language <- read.table("VitaminK_Analysis_english_first_language_for_testing.txt",
+                                     header = T, sep = "\t")
+#run Fisher's exact test
+fisher.test(rbind(c(English_first_language$oral_none[1],English_first_language$oral_none[2]),
+                  c(English_first_language$IM[1],English_first_language$IM[2])))
+
+
+#SIMD data
+#import data
+SIMD_data <- read.table("VitaminK_Analysis_SES_for_testing.txt", 
+                             header = T, sep = "\t")
+
+#run chi squared test on the dataset
+chisq.test(SIMD_data$oral_none,SIMD_data$IM)
+
+#maternal age data
+#import data
+maternal_age_data <- read.table("VitaminK_Analysis_maternal_age_for_testing.txt", 
+                        header = T, sep = "\t")
+
+#run chi squared test on the dataset
+chisq.test(maternal_age_data$oral_none,maternal_age_data$IM)
+
+