library('ggplot2') 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")
install.packages("surveillance") help(package=surveillance)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.