Today we'll have a look at how to turn paper map resources into electronic maps. For this, we'll be using mouse digitization (digitizing tablets are also commonly used, especially for industrial-sized jobs). Michael Reiskind used this technique in his project, to create an electronic database of houses in a study of Dengue fever in Peru (as shown in this figure).
Before getting into this new technique, however, warm up with a review of prior labs, and ArcView: create a project in ArcView for the French Flu data we'll be studying in the surveillance unit. Once we've loaded in that project, we'll throw in a wrinkle and have you try out an "ArcView extension" which allows one to calculate simple spatial statistics on the data.
Lab Objectives: at the end of this lab you should have
UMich students: work in C:\temp. If you want to save anything to your personal space you can do it in the end. In the meantime this may make ArcView more stable, and reduce problems of storage.
In preparation for the surveillance module you need to begin to use the flu data. We will thus create a new project (e.g. flu.apr). You should have already downloaded the historical (through 2000) flu data (from the first module). Now we need to combine that with the geography of France, which is available from the French Flu data page of the GeoMed project.
Pick up the zipped shapefiles of France (w/o Corsica); uncompress this file, and add the france_wo_corsica.shp shapefile as a theme. Now you will want to add in the flu data, which you downloaded in the first lab (called flu.txt - here provided as a zipped file).
UMich students: go ahead and replace the flu.txt in your directory with the zipped file above: it is more current than the one you downloaded the in the first lab.
You must first add flu.txt as a table, then join it to the attribute table for the france_wo_corsica theme, as was done in the GIS and Spatial data handling lab.
Convert the resulting joined theme to a new shapefile: with the
france_wo_corsica.shp theme active, click
Theme -> Convert to
Shapefile
and save this theme as flu.shp. [This shapefile
takes up about a meg of space.] ArcView will ask if you want to add it to
your view: go ahead.
The value in creating the new shapefile is that everything is included in one set of files with the names flu (and extensions like .dbf, .shp, etc.). It's easy to load everything rapidly into ArcView this way, or to share this information with a friend. Taking someone through the join process, etc. can be rather unpleasant.
We're going to use an extension to ArcView to compute a spatial statistic (Moran's I) from within ArcView. Extensions are written, often by interested users, to augment the capabilities of ArcView. ArcView doesn't do any spatial statistics by default. The MapStat extension was created by Dr. Daniel Griffith, of Syracuse University, one of the consultants on the GeoMed project. We will download the zip file and extract MapStat.avx to the C:\temp directory (this directory is important! ArcView looks in this directory by default for any new extensions). Download and extract this file now.
Now let's practice using some spatial statistics with the flu.shp theme which you just created. By double clicking on its legend you will enter the legend editor: choose "Graduated Color" as your Legend Type. For Classification Field choose variable 199951 (the 51st week of 1999), and click the Apply button.
We now need to load the MapStat extension:
File menu -> Extensions -> MapStat
A new menu item ("Statistics") should appear on the menu bar of the View of
the French data.
Try two of the options:
UMich students: DO NOT run the Local Moran's I - it's been crashing computers on this data set....
The maps we are using in this lab were scanned in from books. Scanning is a skill worth acquiring, as you may wish to scan and digitize something of your own someday (perhaps even today!). Scanning text is also sometimes very useful (e.g. some of the glossaries on the GeoMed site were scanned in, and the text retrieved using OCR (Optical Character Recognition) software; and the next module includes a table of data read in this way).
UMich students: PHISA offers short courses in scanning. Check one out! The PHISA library multimedia center has scanners that you can use anytime their facilities are open.
If you're going to use the default images, download them (from the browser) by right-clicking on the links to the images above - you'll be offered the option of saving the links as....
This is the Draw Point icon; click on it, and you can now start digitizing. As you click on a black dot, a small dot will be drawn in; choose a good color for the new theme, so that it is clearly visible against the black dot. This way you will be able to easily see that you have digitized all the dots (haven't missed any).
If you've zoomed so far that you can't see the whole image, then as you digitize, you may want to switch back and forth between the Draw Point button and the Pan button (the little hand icon), which allows you to move the image to new areas to digitize.
When you're done, run statistics on the field, to make sure that you have a max, a mean, and a min of 1:
I created this GRASS-based data because I was frustrated when I digitized the smallpox data as you just did and couldn't figure out how to look at the coordinates of the points I created. They're stored in ESRI's proprietary shapefile format, and I couldn't figure out how to get ArcView to show the coordinates in the attribute table (I've since discovered that there is an ArcView Script to add coordinates to the attribute table). So I converted the shapefile to an Arc export file, then imported that into GRASS (which is a free, public domain GIS).
Follow the instructions for adding an image theme, only this time add snow.jpg. Once you have it loaded you will again create a new theme (let's call it snow.shp), only this time it will be a polygon theme.
Click (and hold!) the rectangle button. You have your choice of what sort of polygons you want to add, and we'll only be adding two types. The first one to choose is the odd polygonal shape following the circle:
Beware spurious rapid double clicks! That signals "all done". I try to consciously pause a bit between clicks as I move.
This cryptic symbol means that you're going to add an adjoining region. To do so, let's work on the 37/103 region next to the ND region. The strategy is to click inside the ND region, then click on a point where our new region will join the ND region (the northeast corner is good). Then click on the northwest corner, and descend the winding region edge, clicking as you go. If all goes well, you'll click all the way back to the first region. Go a little bit into the first region, double click, and the second region should magically appear.
Keep this up until your hand hurts, until time runs out, or until you run screaming from the lab shouting "I never want to see another mouse again as long as I live!": then quit.
UMich students: as of this lab - approximately Wed Jan 26 14:58:53 - the Federal site which provides the data is down, so the geocoder will not work.
When you get down to the tract level, you could consult the Census TIGER files to find the lat/longs of the centroids of the tracts (these too are available from the CIESIN site) - but this would be a lot of work. I'm sure that soon (if not already) some good soul will put a really good full address -> lat/long geocoder on the web. Right now this one is the best we've got!
snow.jpg has the same geographical structure as the map and data set that was used for the BW join statistics example that you saw in your reading and lecture. If you finish this map, then you could create the BW map by adding a rate variable (derived from Population and Deaths), and coding by above and below the median. Here's one way to do it:
Page by Andy Long. Comments appreciated.
aelon@sph.umich.edu