USSeerBG: USSeerBG border group datasets to support use with U.S. 20...

In micromapST: Linked Micromap Plots for U. S. and Other Geographic Areas

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.

Details

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

areaParms

- contains specific parameters for the border group

areaNamesAbbrsIDs

- containing the names, abbreviations, numerical identifier and alias matching string for each of the 20 Seer registries.

areaVisBorders

- the boundary point lists for each area.

L2VisBorders

- the boundaries for an intermediate level. For Seer registry border group, L2VisBorders contains the boundaries for the 51 states and DC in the U. S to help provide a geographical reference of the registries to the states.

RegVisBorders

- the boundaries for the 4 U. S. Census regions in the U. S in support of the region feature.

L3VisBorders

- the boundary of the U. S.

The Seer Registries border group contains 20 Seer Registry sub-areas. Each registry has a row in the areaNamesAbbrsIDs 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	<none>	South
Alaska	Alaska Natives	West
Arizona	Arizona Natives	West
Arkansas	<none>	South
California	California-LA,	West
	California-Other,
	California-SF,
	California-SJ
Colorado	<none>	West
Connecticut	Connecticut	NorthEast
Delaware	<none>	South
District of Columbia	<none>	South
Florida	<none>	South
Georgia	Georgia-Atlanta,	South
	Georgia-Other,
	Georgia-Rural
Hawaii	Hawaii	West
Idaho	<none>	West
Illinois	<none>	MidWest
Indiana	<none>	MidWest
Iowa	Iowa	MidWest
Kansas	<none>	MidWest
Kentucky	Kentucky	South
Louisiana	Louisiana	South
Maine	<none>	NorthEast
Maryland	<none>	South
Massachusetts	<none>	NorthEast
Michigan	Michigan-Detroit	MidWest
Minnesota	<none>	MidWest
Mississippi	<none>	South
Missouri	<none>	MidWest
Montana	<none>	West
Nebraska	<none>	MidWest
Nevada	<none>	West
New Hampshire	<none>	NorthEast
New Jersey	New Jersey	NorthEast
New Mexico	New Mexico	West
New York	<none>	NorthEast
North Carolina	<none>	South
North Dakota	<none>	MidWest
Ohio	<none>	MidWest
Oklahoma	Oklahoma-Cherokee	South
Oregon	<none>	West
Pennsylvania	<none>	NorthEast
Rhode Island	<none>	NorthEast
South Carolina	<none>	South
South Dakota	<none>	MidWest
Tennessee	<none>	South
Texas	<none>	South
Utah	Utah	West
Vermont	<none>	NorthEast
Virginia	<none>	South
Washington	Washington-Seattle	South
West Virginia	<none>	South
Wisconsin	<none>	MidWest
Wyoming	<none>	West

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 <statsDFrame> 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

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:

1. Log on to the SEER^Stat website.

2. Create the matrix of results you want in SEER*Stat.

3. 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)

4. 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

5. 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)
  

Source

NCI

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.

micromapST documentation built on Nov. 12, 2023, 5:06 p.m.