## ---- echo=FALSE, message=FALSE------------------------------------------
library('ggplot2')
library('maps')
library('dplyr')
library('tidyr')
library('xtable')
library('ISDSWorkshop')
workshop(launch_index=FALSE)
# Read csv files and create additional columns
icd9df = read.csv("icd9.csv")
GI = read.csv("GI.csv") %>%
mutate(
date = as.Date(date),
weekC = cut(date, breaks="weeks"),
week = as.numeric(weekC),
weekD = as.Date(weekC),
facility = as.factor(facility),
icd9class = factor(cut(icd9,
breaks = icd9df$code_cutpoint,
labels = icd9df$classification[-nrow(icd9df)],
right = TRUE)),
ageC = cut(age,
breaks = c(-Inf, 5, 18, 45 ,60, Inf)),
zip3 = trunc(zipcode/100))
## ------------------------------------------------------------------------
# Summarize data by facility and age category
fa_l <- GI %>%
group_by(facility, ageC) %>%
summarize(count = n())
# Reshape data from long to wide format
fa_w <- fa_l %>%
spread(ageC, count)
# Create HTML table
tab = xtable(fa_w,
caption = "Total GI cases by Facility and Age Category",
label = "myHTMLanchor",
align = "ll|rrrrr") # rownames gets a column
# Save HTML to file
print(tab, file="table.html", type="html", include.rownames=FALSE)
# Copy-and-paste table into Word
## ------------------------------------------------------------------------
# Here is some code to get you started
states = map_data("state")
# Read in the data from http://www.google.org/flutrends/us/data.txt
# ** you will need to figure this part out **
# ** it is NOT trivial **
fluTrends = read.csv(file="http://www.google.org/flutrends/about/data/flu/us/data.txt",
skip = 11,
check.names=FALSE)
# Keep only the last row for the states
flu_w = fluTrends[nrow(fluTrends), c(1,3:53)]
# Reshape to long format
flu_l <- flu_w %>%
gather(region, index, -Date)
# Merge flutrends data with map_data
flu_l$region = tolower(flu_l$region)
states_merged = merge(states, flu_l, sort=FALSE, by='region')
# Find the date
states_merged$Date = as.Date(states_merged$Date)
mx_date = max(states_merged$Date)
# Construct plot
ggplot(states_merged, aes(x=long, y=lat, group=group, fill=index)) +
geom_polygon() +
labs(title=paste('Google Flu Trends on', mx_date), x='', y='') +
theme_minimal() +
theme(legend.title = element_blank()) +
coord_map("cylindrical")
## ---- eval=FALSE---------------------------------------------------------
# install.packages("surveillance")
# help(package=surveillance)
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