![]() ![]() # for some reason, R Markdown won't compile when I use this approach. # the way I actually do this is to use apply(), which will convert to matrix - need to change back to ame # note that gsub() works on vectors, so need to cycle through the cols of the data frame # remove commas and convert from text to numeric Stitable <- htmltab(doc = url, which = "//th/ancestor::table", colNames=cnames, rm_nodata_rows=FALSE, rm_nodata_cols=FALSE) "Syphilis_Late_Latent_Cases", "Syphilis_Late_Latent_Rate", "Syphilis_Congenital_Cases", "Syphilis_Congenital_Rate", "Chlamydia_Cases","Chlamydia_Rate", "Gonorrhea_Cases", "Gonorrhea_Rate", "Chancroid_Cases", "Chancroid_Rate") The key is basically to find the anchor point for the html table that allows htmltab to parse the cells of the tableĬnames <- c("Year", "Syphilis_All_Cases","Syphilis_All_Rate", "Syphilis_Primary_Secondary_Cases", "Syphilis_Primary_Secondary_Rate", "Syphilis_Early_Latent_Cases", "Syphilis_Early_Latent_Rate", There is a useful vignette that delves more into the details of htmltab XML does not work with https either (and all Wikipedia pages have moved to https since 2015) Its been adapted by David Reitter, based on GNU Emacs by Richard Stallman and. Yet, it comes with all the ergonomics and extensibility youve come to expect from GNU Emacs. Aquamacs integrates with the Mac and offers the same comforts that any application on the Mac provides. Package htmltab parses multi-column spans (which is common on html tables) Aquamacs is a user-friendly build of the powerful Emacs text editor. Inc <- diff(yemen$Cases)/as.numeric(diff(dates)) Yemen <- read.csv("", skip=2, header=TRUE) To calculate the average number of cases per day in a reporting interval, simply divide the difference by number of days between reports Everything is great except when I make large black windows on the screen, the entire screen dims. To calculate incidence from the cumulative number of cases, use the R function diff() The ProMED Mail tables include average daily cases, but we can calculate that ourselves as well The reporting is somewhat irregular – there are often gaps of a week or two The International Society for Infectious Disease Research ProMed Mail system compiles the data from the occasional WHO reports and these data can be quite easily used WHO reports outbreak data in a pretty haphazard way
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