satscanMapper: Function to map Results data produced by a SaTScan (TM)...
In satscanMapper: 'SaTScan' (TM) Results Mapper
satscanMapper R Documentation
Function to map Results data produced by a SaTScan (TM) cluster analysis
Description
The satscanMapper creates maps based on the information and statistics
data provide by in the SaTScan (TM) Results Files.
The package can map the 50 U.S. states, District of Columbia and the Puerto Rico Territory at
the state, county and census tract levels.
The locations are identified using the U. S. FIPS codes for the State (and DC/Territories),
Counties with in a state, and Census Tracts with a state.
The boundary data used by this package is based on the 2000 and 2010 U. S.
Census and were pulled from the Census Bureau web site. The SeerMapper
package is used for the mapping and the source of all boundary data.
Usage
satscanMapper( resDir = NULL, # no default, must be provided
prmFile = NULL, # no default, must be provided
outDir = NULL, # default = NULL, uses value in resDir
censusYear = NULL, # default = census year 2000.
categ = NULL, # default = 5
title = NULL, # no default, optional
pValue = NULL, # default = 0.05
report = NULL, # default = TRUE
runId = NULL, # default = ""
bndyCol = NULL, # default = grey(0.9)
label = NULL, # default = TRUE
outline = NULL, # default = TRUE
locO_EMap = NULL, # default = TRUE
clusO_EMap = NULL # default = TRUE
)
Arguments
resDir
is the name of the directory containing the SaTScan (TM) saved session parameter
file (.PRM). This directory will be used to hold the output graphics (PDF) and
text output report (.txt) files.
prmFile
is the file name of the SaTScan (TM) saved session parameter file (.PRM).
The saved session parameter file contains all of the information about
the SaTScan analysis to be mapped, including the location of the
results cluster, location and RR files.
The base of the .PRM filename (without extension) is used to create the
filenames for the graphic and text output files. If the output filename already exists,
a new name based on the original name is created and used. or you can specify
the runId to prepend a few characters to the filenames to make them
unique for each satscanMapper run.
outDir
is the name of the directory to write the PDF graphic map file and
the TXT summary report file. Normally, the output files are written to the
directory specified in the resDir parameter to keep the input and output information
in the same location. However, if the output files need to be written to a different
directory, the outDir parameter can be used to specify the different
directory. If the outDir parameter is missing or NULL, the value of
the resDir parameter is used as the output directory.
If parameter is set to "", the current working directory will be used when the
output files are written. If the parameter is set to a
character string, it must be a valid/existing directory and will be used as the destination when
the output files are written. The default value is NULL.
censusYear
This is a character value of the census year of the location IDs
in the population and case data records or the SatScan (TM) results data files.
The acceptable values for the censusYear parameter are "2000" and "2010".
The default value is "2000" for the 2000 census year.
categ
This is an integer value specifying the number of categories to be
used when coloring the locations in the cluster maps. A preset of Observed/Expected
value break points is used based on the number of categories specified
in the categ argument. categ can range from 3 to var10.
The default categ value is 5.
The breakpoints for each categ value from 3 to 10 are
hard coded into the package as follows:
categ breakpoint list
3 -Inf, 0.9, 1.1, Inf
4 -Inf, 0.9, 1.1, 3.0, Inf
5 -Inf, 0.5, 0.9, 1.1, 3.0, Inf
6 -Inf, 0.5, 0.9, 1.1, 2.0, 3.0, Inf
7 -Inf, 0.33, 0.5, 0.9, 1.1, 2.0, 3.0, Inf
8 -Inf, 0.33, 0.5, 0.9, 1.1, 1.5, 2.0, 3.0, Inf
9 -Inf, 0.33, 0.5, 0.67, 0.9, 1.1, 1.5, 2.0, 3.0, Inf
10 -Inf, 0.33, 0.4, 0.5, 0.67, 0.9, 1.1, 1.5, 2.0, 3.0, Inf
Future plans include allowing the caller to specify their own set of break points.
title
A character string(vector) used as the main title for the cluster
maps. A title may be one or two lines. If two lines, code
title=c("line 1", "line 2").
for the title call parameter. If no title is provided (NULL or ""),
the prmFile argument is used for
the main title. The default is NULL, the package uses the prmFile argument
as the title.
pValue
The package uses a default P Value of 0.05. Only cluster with a
P Value < 0.05 are colored on the resulting map by default.
If the P Value needs to be a different value, then the user
can specify the override P Value using the PValue argument.
The PValue argument must be between var0.001 and var0.5 to be valid.
report
This is logical value. If TRUE a text report of the statistics from each
cluster and location in a tier format by State, County, Place, and Location (Census Tract)
will be created. If varFALSE, a summary report is generated. The default is TRUE
for a full report.
runId
If a user is creating multiple mappings of the same SaTScan (TM)
Results Data Files, but with different arguments and options, they will want
to save the PDF and report text files for each run. Normally the PDF and report text
files would be overlaid. The runId argument provides a way to modify the
output PDF and text filenames to make a unique filename for the output.
The runId string is inserted near the end of the output filename. This allows
multiple mapping runs against the same data and a collection of resulting maps.
If runId is not specified, the package will append to the '.prm' filename the
string of "-Rnn", where 'nn' is a number from 01 to 99. If an output set already exists,
'nn' is increased by 1 until an unused output file name is discovered.
label
This is a logical argument that indicates whether or not the outlines of
each cluster on a map is labeled with the cluster number from the SaTScan (TM) data.
If a cluster spans multiple years, the number of years is added to the label.
For example: "1-2", this is cluster number 1 and the cluster existing over a two
year period including the current year being mapped.
The default value for label is varTRUE.
outline
This is a logical value specifying whether or not draw the outline of the
cluster on the cluster map. If TRUE, an outline is draw. If FALSE, no outlines
are drawn.
The default value is TRUE.
bndyCol
is a character string that defines the color to use for the
area boundaries. The default color value is grey50.
The value provided is verified against the values returned from
the colors() function.
locO_EMap
a logical variable. This parameter enables the use of the location
Obs/Exp ratio to categorize and color the data areas. If TRUE. the location
ratios are used. If FALSE, the location Obs/Exp ratio is not used.
The default value is TRUE.
clusO_EMap
a logical variable. This parameter enables the use of the cluster
Obs/Exp ratio to categorize and color the data areas. If TRUE. the cluster
ratios are used. If FALSE, the cluster Obs/Exp ratio is not used.
The default value is FALSE.
Details
The satscanMapper function creates one or more maps for the SaTScan (TM) cluster analysis
results data. The following must be done to facilitate the use of SaTScan (TM) cluster
analysis and the satscanMapper package:
The coordinates file must be generated by the CreateGeo4SS function
in the package to ensure the area centroids used in the analysis match the
boundary projection used in the area mapping.
The Coordinates type must be set to "Cartesian". The centroid values
returned by the CreateGeo4SS function are based on an equal-area projection
and not Lat/Long coordinates.
Time Precision must be set to "Years". The mapping package only supports
time units of years.
Since mapping is spatial, only the Retrospective Purely Spatial and Space-Time
and the Prospective Space-Time analysis are supported.
There restrictions on the Probability Model used are imposed by the type of
analysis.
Time Aggregation is support for units of "years" for any number of years.
The default is 1 year. This parameter is generally not used.
Both the circular and elliptic Spatial Window Shapes are supported.
The Minimum Temporal Cluster Size is supported for any number of years. When
specified, maps are generated on a sliding time line for group of years.
The main results file and all Column Output files use the same "Main Results File"
name. This information is stored in the saved session *.PRM file. Any value
may be specified.
The Cluster Information dbase box must be checked.
The Location Information dbase box must be checked.
The Risk Estimate for Each Location dbase box must be checked.
IMPORTANT: Just before executing the SaTScan (TM) analysis, save the
session *.prm file in an appropriate directory. Menu -> File -> Save Session or Save Session as.
If you make changes to the analysis parameters make sure to re-save the
session file.
The saved session *.PRM file provides the main mapping function with
all of the information to generate the maps of the analysis results.
The saved session parameters are checked to ensure the mapping can
be done and any errors reported to the user.
The CreateGeo4SS function should be used to evaluate the location IDs
in the population and/or case data files and generate the coordinates(geo) file
for use in the SaTScan (TM) analysis.
The Location IDs used in the original population, case and coordinates(geo) input files
and the output results files must be in one of three formats based on
the mapping level desired: the 2 digit U. S. fips code for state data,
the 5 digit U. S. fips code for county data,
or 11 digit U. S. fips code for census tract data.
If the Location IDs for the census year being mapped, do not match the
boundary data, warnings will be generated to inform the user of the issue.
Check to make sure the correct census year was specified.
The boundary data and FIPS codes were pulled from the CENSUS.GOV web site
for the 2000 and 2010 census years and should be complete.
If 2 digit fips code IDs are used, the SaTScan (TM) results information
is mapped at the state, district and territory level. When states are mapped,
the boundaries for all of the states in the US will be drawn.
If 5 digit fips code IDs are used, the SaTScan (TM) results information
is mapped at the county level for the states containing the counties with data.
State boundaries are drawn around the counties as a reference. Only the county
boundaries in states with data will be drawn. Therefore, is the analysis results
contain counties in multiple states, all of the boundaries for the counties in these
states are drawn.
If 11 digit fips code IDs are used, the SaTScan (TM) location information is
mapped at the census tract level for the states containing the census tracts with data.
State and county boundaries are drawn for any state contain census tracts referenced
by an analysis.
The area categorization and coloring are based on either the location and cluster ODE ratios
reported in the results files. The ratio used is controlled by the locO_EMap and
clusO_EMap parameters.
The bndyCol parameter specifies the color used for the data area boundaries
(state, county or census tract). It's value must be a colors that is either from
the colors() name list or is a
#hhhhhh or #hhhhhhhh format as a character vector.
Only areas with data are mapped. To drawn all of the data level boundaries up
to the next level, specify fill = TRUE.
For example: All tract boundaries will be drawn up to
their county level for tract data. For county data, all counties will be drawn up
to the state boundary.
At the current time, the boundary data is based on the boundary data in the SeerMapper
and Seer2010Mapper packages. An additional parameter is required to specify which
census year is to be used: 2000 or 2010.
If a text report is required (report = TRUE), the package provides
a listing of the Cluster Information, Location Information and Risk data
in a tabular format for the user's review. The location information is listed
for each cluster in a tier format with the following levels:
State
County
PlaceName
Census Tract
If the locations are counties, county names are provided, but not the
Place names or the Census Tract IDs levels.
The critical SaTScan (TM) run options the must be set are:
StartDate = yyyy/mm/dd
EndDate = yyyy/mm/dd
AnalysisType = 4 (default)
Valid Types: 1 = Purely Spatial,
3 = Retrospective Space-time,
4 = Prospective Space-Time.
Not-Supported Types:
2 = Purely Temporal,
5 = Spatial Variation in Temporal Trends,
6 = Prospective Purely Temporal
IncludeRelativeRisksCensusAreasDBase = y # *.rr.dbf
CensusAreasReportedClustersDBase = y # *.col.dbf
MostLikelyClusterEachCentroidDBase = y # *.gis.dbf
MostLikelyClusterCaseInfoEachCentroidDBase = y # *.sci.dbf
The satscanMapper package uses the SeerMapper package to generate
all of the maps. Other R packages used by satscanMapper are: base, utils,
graphics, grDevices, stats, RColorBrewer, stringr, sp, and foreign.
Value
None
Author(s)
Jim Pearson and Linda Pickle of StatNet Consulting, LLC, Gaithersburg, MD
Examples
######
#
# These examples focus on mapping the SaTScan (TM) data after the analysis
# has been completed.
# See the section on the CreateGeo4SS function for an example of how
# to build a coordinates file (.geo) that matches the satscanMapper
# boundary data.
#
######
######
#
# Example # 1 - Mapping existing SaTScan (TM) results - "USStateLung" result files
# Make sure SaTScan (TM) results files are still located in the directories
# documented in the session saved (.prm) file.
#
# This example maps data for the US States containing circular clusters.
#
# Get location of .prm file and location to write mapping output files
#
## Not run:
tempdirOut <- tempdir()
cat("tempDirOut:",tempdirOut,"\n")
SSMInstDir <- system.file(package="satscanMapper", "extdata")
cat("SSMInstDir:",SSMInstDir,"\n")
TT =c("Contiguous US States All Lung Cancer Mortality, 2004")
satscanMapper(resDir = SSMInstDir, # path to .prm file location for output files.
prmFile = "stateLung.prm",
outDir = tempdirOut,
title = TT
)
## End(Not run)
## end of example # 1 Removed due to time constraints.
##
######
######
#
# Example # 2 - Mapping existing SaTScan (TM) results - "USCountyLung" result files
# named "inc_noadj_cir" files
# Make sure SaTScan (TM) results files are still located in the directories
# documented in the session saved (.prm) file.
## Not run:
tempdirOut <- tempdir()
cat("tempDirOut:",tempdirOut,"\n")
SSMInstDir <- system.file(package="satscanMapper", "extdata")
TT = "Contiguous US County Female Breast Cancer Incidence, 2009-2013"
satscanMapper(resDir=SSMInstDir, # path to .prm file location for output files.
prmFile = "inc_noadj_ellip_hilo_10_nosp.prm",
outDir = tempdirOut,
categ = 7,
title = TT,
censusYear = "2010"
)
## End(Not run)
#
# end of example # 2
#
#####
print("end of examples")
satscanMapper documentation built on Aug. 25, 2022, 9:09 a.m.
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| satscanMapper | R Documentation |
Function to map Results data produced by a SaTScan (TM) cluster analysis
Description
The satscanMapper creates maps based on the information and statistics data provide by in the SaTScan (TM) Results Files. The package can map the 50 U.S. states, District of Columbia and the Puerto Rico Territory at the state, county and census tract levels.
The locations are identified using the U. S. FIPS codes for the State (and DC/Territories), Counties with in a state, and Census Tracts with a state. The boundary data used by this package is based on the 2000 and 2010 U. S. Census and were pulled from the Census Bureau web site. The SeerMapper package is used for the mapping and the source of all boundary data.
Usage
satscanMapper( resDir = NULL, # no default, must be provided
prmFile = NULL, # no default, must be provided
outDir = NULL, # default = NULL, uses value in resDir
censusYear = NULL, # default = census year 2000.
categ = NULL, # default = 5
title = NULL, # no default, optional
pValue = NULL, # default = 0.05
report = NULL, # default = TRUE
runId = NULL, # default = ""
bndyCol = NULL, # default = grey(0.9)
label = NULL, # default = TRUE
outline = NULL, # default = TRUE
locO_EMap = NULL, # default = TRUE
clusO_EMap = NULL # default = TRUE
)
Arguments
resDir |
is the name of the directory containing the SaTScan (TM) saved session parameter file (.PRM). This directory will be used to hold the output graphics (PDF) and text output report (.txt) files. |
prmFile |
is the file name of the SaTScan (TM) saved session parameter file (.PRM). The saved session parameter file contains all of the information about the SaTScan analysis to be mapped, including the location of the results cluster, location and RR files. The base of the .PRM filename (without extension) is used to create the filenames for the graphic and text output files. If the output filename already exists, a new name based on the original name is created and used. or you can specify the runId to prepend a few characters to the filenames to make them unique for each satscanMapper run. |
outDir |
is the name of the directory to write the PDF graphic map file and the TXT summary report file. Normally, the output files are written to the directory specified in the resDir parameter to keep the input and output information in the same location. However, if the output files need to be written to a different directory, the outDir parameter can be used to specify the different directory. If the outDir parameter is missing or NULL, the value of the resDir parameter is used as the output directory. If parameter is set to "", the current working directory will be used when the output files are written. If the parameter is set to a character string, it must be a valid/existing directory and will be used as the destination when the output files are written. The default value is NULL. |
censusYear |
This is a character value of the census year of the location IDs in the population and case data records or the SatScan (TM) results data files. The acceptable values for the censusYear parameter are "2000" and "2010". The default value is "2000" for the 2000 census year. |
categ |
This is an integer value specifying the number of categories to be used when coloring the locations in the cluster maps. A preset of Observed/Expected value break points is used based on the number of categories specified in the categ argument. categ can range from 3 to var10. The default categ value is 5. The breakpoints for each categ value from 3 to 10 are hard coded into the package as follows:
categ breakpoint list
3 -Inf, 0.9, 1.1, Inf
4 -Inf, 0.9, 1.1, 3.0, Inf
5 -Inf, 0.5, 0.9, 1.1, 3.0, Inf
6 -Inf, 0.5, 0.9, 1.1, 2.0, 3.0, Inf
7 -Inf, 0.33, 0.5, 0.9, 1.1, 2.0, 3.0, Inf
8 -Inf, 0.33, 0.5, 0.9, 1.1, 1.5, 2.0, 3.0, Inf
9 -Inf, 0.33, 0.5, 0.67, 0.9, 1.1, 1.5, 2.0, 3.0, Inf
10 -Inf, 0.33, 0.4, 0.5, 0.67, 0.9, 1.1, 1.5, 2.0, 3.0, Inf
Future plans include allowing the caller to specify their own set of break points. |
title |
A character string(vector) used as the main title for the cluster
maps. A title may be one or two lines. If two lines, code
|
pValue |
The package uses a default P Value of 0.05. Only cluster with a
P Value < 0.05 are colored on the resulting map by default.
If the P Value needs to be a different value, then the user
can specify the override P Value using the PValue argument.
The |
report |
This is logical value. If TRUE a text report of the statistics from each cluster and location in a tier format by State, County, Place, and Location (Census Tract) will be created. If varFALSE, a summary report is generated. The default is TRUE for a full report. |
runId |
If a user is creating multiple mappings of the same SaTScan (TM) Results Data Files, but with different arguments and options, they will want to save the PDF and report text files for each run. Normally the PDF and report text files would be overlaid. The runId argument provides a way to modify the output PDF and text filenames to make a unique filename for the output. The runId string is inserted near the end of the output filename. This allows multiple mapping runs against the same data and a collection of resulting maps. If runId is not specified, the package will append to the '.prm' filename the string of "-Rnn", where 'nn' is a number from 01 to 99. If an output set already exists, 'nn' is increased by 1 until an unused output file name is discovered. |
label |
This is a logical argument that indicates whether or not the outlines of each cluster on a map is labeled with the cluster number from the SaTScan (TM) data. If a cluster spans multiple years, the number of years is added to the label. For example: "1-2", this is cluster number 1 and the cluster existing over a two year period including the current year being mapped. The default value for label is varTRUE. |
outline |
This is a logical value specifying whether or not draw the outline of the
cluster on the cluster map. If |
bndyCol |
is a character string that defines the color to use for the area boundaries. The default color value is grey50. The value provided is verified against the values returned from the colors() function. |
locO_EMap |
a logical variable. This parameter enables the use of the location Obs/Exp ratio to categorize and color the data areas. If TRUE. the location ratios are used. If FALSE, the location Obs/Exp ratio is not used. The default value is TRUE. |
clusO_EMap |
a logical variable. This parameter enables the use of the cluster Obs/Exp ratio to categorize and color the data areas. If TRUE. the cluster ratios are used. If FALSE, the cluster Obs/Exp ratio is not used. The default value is FALSE. |
Details
The satscanMapper function creates one or more maps for the SaTScan (TM) cluster analysis results data. The following must be done to facilitate the use of SaTScan (TM) cluster analysis and the satscanMapper package:
The coordinates file must be generated by the CreateGeo4SS function in the package to ensure the area centroids used in the analysis match the boundary projection used in the area mapping.
The Coordinates type must be set to "Cartesian". The centroid values returned by the CreateGeo4SS function are based on an equal-area projection and not Lat/Long coordinates.
Time Precision must be set to "Years". The mapping package only supports time units of years.
Since mapping is spatial, only the Retrospective Purely Spatial and Space-Time and the Prospective Space-Time analysis are supported.
There restrictions on the Probability Model used are imposed by the type of analysis.
Time Aggregation is support for units of "years" for any number of years. The default is 1 year. This parameter is generally not used.
Both the circular and elliptic Spatial Window Shapes are supported.
The Minimum Temporal Cluster Size is supported for any number of years. When specified, maps are generated on a sliding time line for group of years.
The main results file and all Column Output files use the same "Main Results File" name. This information is stored in the saved session *.PRM file. Any value may be specified.
The Cluster Information dbase box must be checked.
The Location Information dbase box must be checked.
The Risk Estimate for Each Location dbase box must be checked.
IMPORTANT: Just before executing the SaTScan (TM) analysis, save the session *.prm file in an appropriate directory. Menu -> File -> Save Session or Save Session as. If you make changes to the analysis parameters make sure to re-save the session file.
The saved session *.PRM file provides the main mapping function with all of the information to generate the maps of the analysis results. The saved session parameters are checked to ensure the mapping can be done and any errors reported to the user.
The CreateGeo4SS function should be used to evaluate the location IDs in the population and/or case data files and generate the coordinates(geo) file for use in the SaTScan (TM) analysis.
The Location IDs used in the original population, case and coordinates(geo) input files and the output results files must be in one of three formats based on the mapping level desired: the 2 digit U. S. fips code for state data, the 5 digit U. S. fips code for county data, or 11 digit U. S. fips code for census tract data. If the Location IDs for the census year being mapped, do not match the boundary data, warnings will be generated to inform the user of the issue. Check to make sure the correct census year was specified. The boundary data and FIPS codes were pulled from the CENSUS.GOV web site for the 2000 and 2010 census years and should be complete.
If 2 digit fips code IDs are used, the SaTScan (TM) results information is mapped at the state, district and territory level. When states are mapped, the boundaries for all of the states in the US will be drawn.
If 5 digit fips code IDs are used, the SaTScan (TM) results information is mapped at the county level for the states containing the counties with data. State boundaries are drawn around the counties as a reference. Only the county boundaries in states with data will be drawn. Therefore, is the analysis results contain counties in multiple states, all of the boundaries for the counties in these states are drawn.
If 11 digit fips code IDs are used, the SaTScan (TM) location information is mapped at the census tract level for the states containing the census tracts with data. State and county boundaries are drawn for any state contain census tracts referenced by an analysis.
The area categorization and coloring are based on either the location and cluster ODE ratios reported in the results files. The ratio used is controlled by the locO_EMap and clusO_EMap parameters.
The bndyCol parameter specifies the color used for the data area boundaries (state, county or census tract). It's value must be a colors that is either from the colors() name list or is a #hhhhhh or #hhhhhhhh format as a character vector.
Only areas with data are mapped. To drawn all of the data level boundaries up to the next level, specify fill = TRUE. For example: All tract boundaries will be drawn up to their county level for tract data. For county data, all counties will be drawn up to the state boundary.
At the current time, the boundary data is based on the boundary data in the SeerMapper and Seer2010Mapper packages. An additional parameter is required to specify which census year is to be used: 2000 or 2010.
If a text report is required (report = TRUE), the package provides a listing of the Cluster Information, Location Information and Risk data in a tabular format for the user's review. The location information is listed for each cluster in a tier format with the following levels:
State
County
PlaceName
Census Tract
If the locations are counties, county names are provided, but not the Place names or the Census Tract IDs levels.
The critical SaTScan (TM) run options the must be set are:
StartDate = yyyy/mm/dd
EndDate = yyyy/mm/dd
AnalysisType = 4 (default)
Valid Types: 1 = Purely Spatial,
3 = Retrospective Space-time,
4 = Prospective Space-Time.
Not-Supported Types:
2 = Purely Temporal,
5 = Spatial Variation in Temporal Trends,
6 = Prospective Purely Temporal
IncludeRelativeRisksCensusAreasDBase = y # *.rr.dbf
CensusAreasReportedClustersDBase = y # *.col.dbf
MostLikelyClusterEachCentroidDBase = y # *.gis.dbf
MostLikelyClusterCaseInfoEachCentroidDBase = y # *.sci.dbf
The satscanMapper package uses the SeerMapper package to generate all of the maps. Other R packages used by satscanMapper are: base, utils, graphics, grDevices, stats, RColorBrewer, stringr, sp, and foreign.
Value
None
Author(s)
Jim Pearson and Linda Pickle of StatNet Consulting, LLC, Gaithersburg, MD
Examples
######
#
# These examples focus on mapping the SaTScan (TM) data after the analysis
# has been completed.
# See the section on the CreateGeo4SS function for an example of how
# to build a coordinates file (.geo) that matches the satscanMapper
# boundary data.
#
######
######
#
# Example # 1 - Mapping existing SaTScan (TM) results - "USStateLung" result files
# Make sure SaTScan (TM) results files are still located in the directories
# documented in the session saved (.prm) file.
#
# This example maps data for the US States containing circular clusters.
#
# Get location of .prm file and location to write mapping output files
#
## Not run:
tempdirOut <- tempdir()
cat("tempDirOut:",tempdirOut,"\n")
SSMInstDir <- system.file(package="satscanMapper", "extdata")
cat("SSMInstDir:",SSMInstDir,"\n")
TT =c("Contiguous US States All Lung Cancer Mortality, 2004")
satscanMapper(resDir = SSMInstDir, # path to .prm file location for output files.
prmFile = "stateLung.prm",
outDir = tempdirOut,
title = TT
)
## End(Not run)
## end of example # 1 Removed due to time constraints.
##
######
######
#
# Example # 2 - Mapping existing SaTScan (TM) results - "USCountyLung" result files
# named "inc_noadj_cir" files
# Make sure SaTScan (TM) results files are still located in the directories
# documented in the session saved (.prm) file.
## Not run:
tempdirOut <- tempdir()
cat("tempDirOut:",tempdirOut,"\n")
SSMInstDir <- system.file(package="satscanMapper", "extdata")
TT = "Contiguous US County Female Breast Cancer Incidence, 2009-2013"
satscanMapper(resDir=SSMInstDir, # path to .prm file location for output files.
prmFile = "inc_noadj_ellip_hilo_10_nosp.prm",
outDir = tempdirOut,
categ = 7,
title = TT,
censusYear = "2010"
)
## End(Not run)
#
# end of example # 2
#
#####
print("end of examples")
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