LBWDataVisualization_TablesandPlots.Rmd

---
title: "LBW_TablesandPlots"
author: "MSR"
date: "June 23, 2019"
output: pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r}
#Creating Descriptive Tables for each year

#install.packages('tableone')
library(tableone)
var.table1 <- c("motherage","fatherage","father_eth","mother_eth","mother_cal","father_cal","mother_edu","father_edu","facility","sex","bweight","birth_term","medpay","mother_wic","tobacco_us","alcohol_us","smoking_pr")
tableOne <- CreateTableOne(vars = var.table1, data = dat.1)
csv1 <- print(tableOne, showAllLevels = TRUE)
# Use the showAllLevels argument to see all levels for all variables
#this creates the csv file
write.csv(as.data.frame(csv1), "DescriptiveStats2005.csv")
```

```{r}
var.table2 <- c("motherage","fatherage","father_eth","mother_eth","mother_cal","father_cal","mother_edu","father_edu","facility","sex","bweight","birth_term","medpay","mother_wic","tobacco_us","alcohol_us","smoking_pr")
tableOne.2 <- CreateTableOne(vars = var.table2, data = dat.2)
csv2 <- print(tableOne.2, showAllLevels = TRUE)

write.csv(as.data.frame(csv2), "DescriptiveStats2010.csv")
```

```{r}
var.table3 <- c("motherage","fatherage","father_eth","mother_eth","mother_cal","father_cal","mother_edu","father_edu","facility","sex","bweight","birth_term","medpay","mother_wic","tobacco_us","alcohol_us","smoking_pr")
tableOne.3 <- CreateTableOne(vars = var.table3, data = dat.3)
csv3 <- print(tableOne.3, showAllLevels = TRUE)

write.csv(as.data.frame(csv3), "DescriptiveStats2015.csv")
```

```{r}
#Visualizing the ROC Curves for each year 
library(ggplot2)
library(plotROC)
library(pROC)

round(auc(roccurve.BW2005),2)
round(auc(roccurve.BW2010),2)
round(auc(roccurve.BW2015),2)

#Creating ROC Curve and plotting AUC
png("ROCplot.png") 
plot(roccurve.BW2005, col = 2, lwd = 3, main = "Receiver Operator Characteristic (ROC) Curves")
plot(roccurve.BW2010, col = 4, lwd = 3, add = TRUE)
plot(roccurve.BW2015, col = 1, lwd = 3, add = TRUE)
plot(legend("bottomright", legend=c("2005: AUC = 0.75", "2010: AUC = 0.79", "2015: AUC = 0.87"), col=c(2, 4,1), lwd=3))
dev.off() 
```

```{r}
#Helpful packages
#install.packages('ggstance')
#install.packages('jtools')
#install.packages('huxtable')
#install.packages('officer')
#install.packages('flextable')
#install.packages('rcompanion')
#install.packages('sjPlot')

library(ggstance)
library(jtools)
library(ggstance)
library(jtools)
library(huxtable)
library(officer)
library(flextable)
library(tidyr)

#Export regression summaries to tables from final GLM models
export_summs(BW2005.glm, BW2010.glm, BW2015.glm, scale = TRUE, to.file = "docx", file.name = "modelsummary.docx")
```

```{r}
#Calculating Odds Ratios
BW2005.OR = exp(cbind(OR = coef(BW2005.glm), confint(BW2005.glm)))
BW2010.OR = exp(cbind(OR = coef(BW2010.glm), confint(BW2010.glm)))
BW2015.OR = exp(cbind(OR = coef(BW2015.glm), confint(BW2015.glm)))

BW2005.OR
BW2010.OR
BW2015.OR
```

```{r}
#Writing Odds Ratios as a csv file
write.csv(BW2005.OR, file = "BW2005_ORjuly.csv")
write.csv(BW2010.OR, file = "BW2010_ORjuly.csv")
write.csv(BW2015.OR, file = "BW2015_ORjuly.csv")
#data should be reported in scientific notation
```


```{r}
#citing R
citation()
```