add rmd example

notebooks/rmd_mimic_los/mimic_los.Rmd

@@ -0,0 +1,56 @@
+---
+title: "Average length of ICU stay in MIMIC-III"
+author: "tom pollard"
+description: "Average length of ICU stay in MIMIC-III"
+output: pdf_document
+date: "10/10/2017"
+---
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+
+library(ggplot2)
+library(RPostgreSQL)
+```
+
+
+```{r dbconnect, include=FALSE}
+# Load configuration settings
+dbdriver <- 'PostgreSQL'
+host  <- '127.0.0.1'
+port  <- '5432'
+user  <- 'postgres'
+password <- 'postgres'
+dbname <- 'mimic'
+schema <- 'mimiciii'
+
+# Connect to the database using the configuration settings
+con <- dbConnect(dbDriver(dbdriver), dbname = dbname, host = host, port = port, 
+                 user = user, password = password)
+
+# Set the default schema
+dbExecute(con, paste("SET search_path TO ", schema, sep=" "))
+```
+
+
+```{r load_data, include=FALSE}
+sql_query <- "SELECT i.subject_id, i.hadm_id, i.los
+              FROM icustays i;"
+
+data <- dbGetQuery(con, sql_query)
+```
+
+This is an RMarkdown document that demonstrates a reproducible analysis using MIMIC-III (version 1.4). Let's calculate the mean length of stay in the ICU and then include this value in our document.
+
+```{r calculate_mean_los, include=FALSE}
+avg_los <- mean(data$los, na.rm=TRUE)
+rounded_avg_los <-round(avg_los, digits = 2)
+```
+
+So the mean length of stay in the ICU is `r avg_los` days. Rounded to two days, this is `r rounded_avg_los` days. We can plot the distribution of length of stay using the qplot function:   
+
+
+```{r plot_los, echo=FALSE, include=TRUE,  warning = FALSE}
+qplot(data$los, geom="histogram",xlim=c(0,25), binwidth = 1,
+      xlab = "Length of stay, days.",fill=I("#FF9999"), col=I("white"))
+```