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R_code_of_the_statistical_analysis.r

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+
+sessionInfo()
+
+options(repos = c(CRAN = "https://mran.revolutionanalytics.com/snapshot/2018-07-06"))
+
+getOption("repos")
+
+#install.packages("dplyr")
+library(dplyr)
+packageVersion("dplyr")
+
+#install.packages("prettyR")
+library(prettyR)
+packageVersion("prettyR")
+
+#install.packages("knitr")
+library(knitr)
+packageVersion("knitr")
+
+#install.packages("devtools")
+library(devtools)
+packageVersion("devtools")
+
+#install.packages("BiocInstaller", repos = "http://www.bioconductor.org/packages/3.5/bioc")
+library(BiocInstaller)
+packageVersion("BiocInstaller")
+
+if (file.exists(Sys.getenv("TAR")) == FALSE)  {
+    Sys.setenv(TAR = "/bin/tar")
+}
+
+install_github("hms-dbmi/Rcupcake", force = TRUE)
+library(Rcupcake)
+packageVersion("Rcupcake")
+
+sessionEx <- start.session( 
+              url         = "https://nhanes.hms.harvard.edu/", 
+              apiKey      = "bc5ulnvruft3036l47t3ld1tiu"
+              )
+sessionEx
+
+nhanesDemographics <- get.children( 
+   url         = "https://nhanes.hms.harvard.edu/", 
+   fieldname   = "/nhanes/Demo/demographics/demographics/"
+  )
+
+
+nhanesFood_recall <- get.children( 
+   url         = "https://nhanes.hms.harvard.edu/", 
+   fieldname   = "/nhanes/Demo/questionnaire/questionnaire/food component recall/"
+  )
+
+nhanesBody_measurements <- get.children( 
+   url         = "https://nhanes.hms.harvard.edu/", 
+   fieldname   = "/nhanes/Demo/examination/examination/body measures/"
+  )
+
+nhanesVector <- c( nhanesDemographics, nhanesFood_recall, nhanesBody_measurements)
+head(nhanesVector)
+
+query_example <- my.query( myfields  = "AGE|SEX|Body Mass Index (kg per m**2)|Waist Circumference (cm)|Sugarfree Diet", 
+                          myvector  = nhanesVector, 
+                          url       = "https://nhanes.hms.harvard.edu/"
+              )
+query_example
+
+nhanes_query <- my.data( 
+    query          = query_example,
+    url            = "https://nhanes.hms.harvard.edu/", 
+    responseFormat = "CSV", 
+    outputPath     = "./NHANES.txt")
+
+head(nhanes_query)
+
+glimpse(nhanes_query)
+
+names(nhanes_query)
+
+variables <- c('patient_id', 'sex', 'sugarfree_diet', 'age', 'waist_circumference', 'body_mass_index')
+
+names(nhanes_query) <- variables
+
+head(nhanes_query)
+
+nhanes_query$sugarfree_diet <- factor(nhanes_query$sugarfree_diet, levels=c('0','1'), labels=c('No','Yes'))
+
+head(nhanes_query)
+
+describe(nhanes_query[, -1], num.desc = c("mean", "sd", "median", "min", "max", "valid.n"))
+
+gender_distribution <- table(nhanes_query$sex)
+
+gender_distribution
+
+gender_proportion<- round(100*gender_distribution/sum(gender_distribution), 1)
+
+gender_proportion
+
+gender_percent <- paste(gender_proportion,"%",sep="")
+
+pie(gender_distribution, labels = gender_percent, main = "Gender distribution", col = c("pink", "blue"))
+legend("topright", c("female", "male"), fill = c("pink", "blue"))
+
+nhanes_query %>% group_by(sex)%>% summarise(first_quantile_age = quantile(age, probs = 0.25, na.rm = TRUE), median_age = median(age, na.rm = TRUE), third_quantile_age = quantile(age, probs = 0.75, na.rm = TRUE))
+
+boxplot(age~sex, data = nhanes_query, main = "Boxplot of age distribution by gender", xlab = "Gender", ylab = "Age in years", col = c("pink", "blue"))
+
+nhanes_query %>% group_by(sex)%>% summarise(first_quantile_bmi = quantile(body_mass_index, probs = 0.25, na.rm = TRUE), median_bmi = median(body_mass_index, na.rm = TRUE), third_quantile_bmi = quantile(body_mass_index, probs = 0.75, na.rm = TRUE))
+
+boxplot(body_mass_index~sex, data = nhanes_query, main = "Boxplot of BMI distibution by gender", xlab = "Gender", ylab = "BMI in kg/m^2", col = c("pink", "blue"))
+
+nhanes_over_two <- nhanes_query %>% filter(age >=2)
+
+#quick check of the number of observations and variables
+dim(nhanes_over_two)
+
+describe(nhanes_over_two[, -1], num.desc = c("mean", "sd", "median", "min", "max", "valid.n"))
+
+nhanes_over_two %>% group_by(sugarfree_diet)%>% summarise(count = n(), mean = mean(waist_circumference, na.rm = TRUE))
+
+nhanes_over_two %>% filter(is.na(nhanes_over_two$waist_circumference))%>% nrow()
+
+wilcox.test(waist_circumference~sugarfree_diet, conf.int=TRUE, data = nhanes_over_two)