USSeerBG: USSeerBG border group datasets to support use with U.S. 20 Seer areas/registries

Description

The micromapST function has the ability to generate linked micromaps for any geographical area. To specify the geographical area, the bordGrp call argument is used to specify the border group dataset for the geographical area. The USSeerBG border group dataset supports creating linked micromaps for the 20 Seer registries in the U. S. When the bordGrp call argument is set to USSeerBG, the appropriate name table (county names and abbreviations) and the 20 sub-areas (Seer registries) boundary data is loaded in micromapST. The user's data is then linked to the boundary data via the Seer registry's name, abbreviated, alias match or ID based on the table below.

The 20 U. S. Seer registries are the accepted registries as of January 2010 funded by NCI.

Arguments

Source

NCI

Details

The USSeerBG border group dataset contains the following data.frames:

The Seer Registries border group contains 20 Seer Registry sub-areas. Each registry has a row in the ]varareaNamesAbbrsIDs data.frame and a set of polygons in the areaVisBorders data.frame datasets.

Regions are defined in this border group as the 4 census regions in the U. S. The regions feature is enable. The four census regions are: NorthEast, South, MidWest, and West. The states and Seer registries in each region are:

state	Seer Registries
region	Alabama
	South
Alaska	Alaska Natives
West	Arizona
Arizona Natives	West
Arkansas
South	California
California-LA,	West
	California-Other,

California-SF,
	California-SJ
	Colorado
	West
Connecticut	Connecticut
NorthEast	Delaware
	South
District of Columbia
South	Florida
	South
Georgia	Georgia-Atlanta,
South
Georgia-Other,
	Georgia-Rural
	Hawaii
Hawaii	West
Idaho
West	Illinois
	MidWest
Indiana
MidWest	Iowa
Iowa	MidWest
Kansas
MidWest	Kentucky
Kentucky	South
Louisiana	Louisiana
South	Maine
	NorthEast
Maryland
South	Massachusetts
	NorthEast
Michigan	Michigan-Detroit
MidWest	Minnesota
	MidWest
Mississippi
South	Missouri
	MidWest
Montana
West	Nebraska
	MidWest
Nevada
West	New Hampshire
	NorthEast
New Jersey	New Jersey
NorthEast	New Mexico
New Mexico	West
New York
NorthEast	North Carolina
	South
North Dakota
MidWest	Ohio
	MidWest
Oklahoma	Oklahoma-Cherokee
South	Oregon
	West
Pennsylvania
NorthEast	Rhode Island
	NorthEast
South Carolina
South	South Dakota
	MidWest
Tennessee
South	Texas
	South
Utah	Utah
West	Vermont
	NorthEast
Virginia
South	Washington
Washington-Seattle	South
West Virginia
South	Wisconsin
	MidWest
Wyoming
West	state

The L3VisBorders dataset contains the outline of the United States.

The details on each of these data.frame structures can be found in the "bordGrp" section of this document. The areaNamesAbbrsIDs data.frame provides the linkages to the boundary data for each sub-area (registry) using the fullname, abbreviation, and numerical identifier for each country to the data based on the setting of the rowNames call argument.

A column or the data.frame row.names must match one of the types of names in the areaNamesAbbrsIDs data.frame name table. If the data row does not match a value in the name table, an warning is issued and the data is ignored. If no data is present for a sub-area (registry) in the name table, the sub-area (registry) is mapped but not colored.

The following are a list of the names, abbreviations, alias and IDs for each country in the USSeerBG border group.

Name	ab	alias string	id	counties
region	Alaska Natives	AK-NAT	ALASKA NATIVES	18
all	West	Arizona Natives	AZ-NAT	ARIZONA NATIVES
20	all	West	California-LA	CA-LA
LOS ANGELES	4	Los Angeles	West	California-SF
CA-SF	SAN FRANCISCO	2	Alameda,	West
				Contra Costa,

Marin,
	San Francisco,
		San Mateo		California-SJ
CA-SJ	SAN JOSE	3	Montersey	West
				San Benito,

Santa Clara,
	Santa Cruz		California-Other	CA-OTH
CALIFORNIA EXCLUDING	5	all other counties	West	Connecticut
CT	CONNECTICUT	1	all	NorthEast
Georgia-Atlanta	GA-ATL	ATLANTA	6	Clayton, Cobb, DeKalb,
South
Fulton, Gwinnett		Georgia-Rural	GA-RUR	RURAL GEORGIA
8	Glascock, Greene, Hancock,	South
		Jasper, Jefferson, Morgan,
			Putnam, Taliaferro, Warren,
				Washington
	Georgia-Other	GA-OTH	GREATER GEORGIA	7
all other counties	South	Hawaii	HI	HAWAII
9	all	West	Iowa	IA
IOWA	10	all	MidWest	Kentucky
KY	KENTUCKY	14	all	South
Michigan-Detroit	MI-DET	DETROIT	15	Macomb,
MidWest
Oakland,
	Wayne		New Jersey	NJ
NEW JERSEY	11	all	NorthEast	New Mexico
NM	NEW MEXICO	12	all	West
Oklahoma-Cherokee	OK-CHE	OKLAHOMA	19	Adair,
South
Cherokee,
	Craig,
		Delaware,
			Mayes,
				McIntosh,

Muskogee,
	Nowata,
		Ottawa,
			Rogers,
				Seqouyah,

Tulsa,
	Wagnorer,
		Washington		Utah
UT	UTAH	16	all	West
Washington-Seattle	WA-SEA	SEATTLE	17	Clallam,
South
Grays Harbor,
	Island,
		Jefferson,
			King,
				Kitsap,

Mason,
	Pierce,
		San Juan,
			Skagit,
				Snohomish,

Thurston,
	Whatcom		Name	ab

The rowNames = alias and the regions = TRUE features are enabled in the USSeerBG border group.

The alias option is designed to allow the package to match the registry labels created by the Seer Stat website when exporting Seer data for analysis. The alias match is a "contains" match, so the registry field in the user data must "contain" the "alias" values listed in the above table. To help generalize the match, the user's registry value is stripped of any punctuation, control characters and multiple spaces (blanks, tabs, cr, lf) are reduced to a single blank and the string is converted to all upper case. Then the wild card match is performed.

The dataRegionOnly call parameter (when set to TRUE) instructs the package to only map the regions with Seer registers with data. The regions used are the four census regions: NorthEast, South, MidWest and West. The RegVisBorders data.frame contains the outline of each of these regions. For example: if Seer registry data is provided for the only the New Mexico, Utah and California Registries in the West region, then only the states and regional boundary for the West region are drawn.

The USSeerBG border group does not contain or support an alternate set of abbreviations. If rowNames is set to alt_ab, an warning is generated and the standard Seer registry abbreviations are used.

The following steps should be used to export data for micromapST's use from the SEER*Stat Website:

Log on to the SEER^Stat website.
Create the matrix of results you want in SEER*Stat.
Click on Matrix, Export, Results as Text File (if you created multiple matrices of results, make sure that the one you want to export is highlighted)
In the Matrix Export Options window, click on:
1. Output variables as Labels without quotes
2. Remove all thousands separators
3. Output variable names before data
4. Preserve matrix columns & rename fields
5. Leave defaults clicked for Line delimiter, Missing Character, and Field delimiter

Change names and locations of text and dictionary files from defaults to the appropriate name and directory location.

To read the resulting text file into R use the read.delim function with header = TRUE. Follow the read.delim call with a str function to verify the data was read correctly.

     dataT <- read.delim("c:\datadir\seerstat.txt",header=FALSE)
     str(dataT)

References

United States National Cancer Institute Seer Website at www.seer.cancer.gov; Seer Software at seer.cancer.gov/seerstat.; United States Census Bureau, Geography Division. "Census Regions and Divisions of the United States" (PDF). Retrieved 2013-01-10.