scanstatistics: Space-Time Anomaly Detection using Scan Statistics

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Detection of anomalous space-time clusters using the scan statistics methodology. Focuses on prospective surveillance of data streams, scanning for clusters with ongoing anomalies. Hypothesis testing is made possible by the generation of Monte Carlo p-values.

Author
Benjamin Kjellson [aut, cre]
Date of publication
2016-09-29 11:37:32
Maintainer
Benjamin Kjellson <benjak@math.su.se>
License
GPL (>= 3)
Version
0.1.0
URLs

View on CRAN

Man pages

add_duration
Add a column 'duration' to a 'data.table' with column 'time'.
add_llr
Calculate the log-likelihood ratios from given...
calc_zipstat_over_duration
Calculate the ZIP window statistic over all durations, for a...
closest_subsets
Set of increasing sets from left to right of input vector.
column_to_int
Replaces a column with integers, its unique and sorted values...
connected_neighbors
Find the connected sets for a location and its k nearest...
connected_to
Return those elements in the second set which are connected...
convolute_denominator
Computes the sum in the increasing score denominator.
convolute_numerator
Computes the sum in the increasing score numerator.
coords_to_knn
Get the k nearest neighbors for each location, given its...
create_table
Create a 'data.table' with all combinations of the supplied...
cumsum_duration
Calculates the cumulative sum of columns over duration, by...
dist_to_knn
Given a distance matrix, find the k nearest neighbors.
enumerate_character
Enumerate the unique, sorted values of a column, returned as...
estimate_d
Estimate the indicators of excess zeros for a ZIP...
estimate_d_dagger
Estimate the ZIP excess zero indicators under null hypothesis...
estimate_zip_relrisk
Estimate the relative risk for an outbreak using a ZIP...
extract_mlc
Extract the most likely cluster (MLC) and the value of the...
extract_scanstatistic
Extract value of scan statistic from per-window statistics.
first_keys_match
Do the first few keys of the supplied table match the...
flexible_zones
Computes the flexibly shaped zones as in Tango (2005).
generate_poisson_counts
Randomly generate and add Poisson counts to a table.
generate_zip_counts
Randomly generate and add ZIP-distributed counts to a table.
gen_negbin_counts
Randomly generate and add negative binomial counts to a...
get_all_streams
Extract the sorted names of all data streams from a...
get_column_values
Extract the values of a 'data.table' column by the column...
get_enumerated_character
Get the name (as character) corresponding to the given...
getkeys
Get the keys from a data.table.
get_set
Get the set with the given index from an implicitly ordered...
get_zone
Extract a zone from the set of all zones.
has_converged
Is the relative error between two numbers is less than the...
haskeys
Determine if table has all the given keys.
if_connected
Return a set of the location and its neighbors if they are...
is_connected
Returns TRUE if the neighboring locations are connected to...
join_zones
Creates a new 'data.table' from a table containing locations,...
knn_zones
Find the increasing subsets of k nearest neighbors for all...
kulldorff_baseline
Estimate the _baselines_ (expected counts) by the Kulldorff...
mc_pvalue
Calculate the Monte Carlo p-value for a scan statistic.
negbin_calculations
Calculate the ordinary NegBin score for each space-time...
negbin_increasing_calculations
Calculate the increasing score for each space-time window.
negbin_increasing_score
Calculate the increasing score for each space-time window.
negbin_mcsim
Monte Carlo simulation of negative binomial score scan...
negbin_overdispersion
Computes the overdispersion parameter for a fitted negative...
negbin_score
Computes the ordinary score for each space-time window.
negbin_score_terms
Computes the numerator and denominator terms for the NegBin...
NM_geo
Longitude and latitude of New Mexico county seats.
NM_map
Data to plot the counties of New Mexico.
NM_popcas
Population and brain cancer cases in New Mexico counties...
partition_zones
Partition a set of zones.
poisson_calculations
Calculate the expectation-based Poisson statistic for each...
poisson_mcsim
Monte Carlo simulation of expectation-based Poisson scan...
poisson_relrisk
Add column for relative risk MLE to table with aggregate...
poisson_score_terms
Computes the numerator and denominator terms for the Poisson...
poisson_statistic
Calculate the expectation-based Poisson statistic for each...
powerset_zones
Creates a set of all non-empty subsets of the integers from 1...
print.scanstatistic
Print a scanstatistic object.
scan_negbin
Calculate the negative binomial scan statistic.
scan_poisson
Calculate the Poisson scan statistic.
scanstatistic_object
Creates an S3 object of class scanstatistic.
scanstatistics
scanstatistics: Space-time anomaly detection using scan...
scan_zip
Calculate the ZIP scan statistic.
score_locations
Score each location over zones and duration.
score_zone_sums
Sums the numerator and denominator terms over all locations...
sim_negbin_statistic
Simulate a single negative binomial score scan statistic.
simulate_poisson_scanstatistic
Simulate a single expectation-based Poisson scan statistic.
simulate_zip_scanstatistic
Simulate a single expectation-based ZIP-EM scan statistic.
times_and_durations
Creates a 'data.table' with columns 'time' and 'duration'.
top_clusters
Get the top (non-overlappig) clusters.
validate_colnames
Check that the input table has the right columns. Raises...
validate_scan
Check that input to scanstatistic function is valid.
validate_values
Check that the input table does not contain any missing...
validate_zones
Check that the zones argument is a list of integer or factor...
window_zip_statistic
Calculate the ZIP statistic for a single space-time window.
zip_calculations
Calculate the (logarithm of the) ZIP statistic for each...
zip_em_estimates
Estimates the ZIP relative risk and excess zero indicators...
zip_mcsim
Monte Carlo simulation of expectation-based Poisson scan...
zip_statistic
Calculates the ZIP statistic for each space-time window.
zip_statistic_factor
Factor(s) in the product of the EB-ZIP window statistic.
zip_statistic_term
Calculate a term in the sum of the logarithm of the ZIP...
zone_sum
Sum columns over all location in each zone, for each...
zone_table_creator
Converts a list of zones to a 'data.table' of zones and...

Files in this package

scanstatistics
scanstatistics/inst
scanstatistics/inst/doc
scanstatistics/inst/doc/introduction.R
scanstatistics/inst/doc/introduction.html
scanstatistics/inst/doc/introduction.Rmd
scanstatistics/tests
scanstatistics/tests/testthat.R
scanstatistics/tests/testthat
scanstatistics/tests/testthat/test_utility_functions.R
scanstatistics/tests/testthat/test_zone_utility_functions.R
scanstatistics/tests/testthat/test_scan_zip.R
scanstatistics/tests/testthat/test_zones.R
scanstatistics/tests/testthat/test_scan_negbin.R
scanstatistics/tests/testthat/test_baseline_estimation.R
scanstatistics/tests/testthat/test_scan_poisson.R
scanstatistics/tests/testthat/test_aggregation_functions.R
scanstatistics/NAMESPACE
scanstatistics/NEWS.md
scanstatistics/data
scanstatistics/data/NM_geo.rda
scanstatistics/data/NM_map.rda
scanstatistics/data/NM_popcas.rda
scanstatistics/R
scanstatistics/R/scan_negbin.R
scanstatistics/R/baseline_estimation.R
scanstatistics/R/aggregation_functions.R
scanstatistics/R/scan_poisson.R
scanstatistics/R/data.R
scanstatistics/R/zones.R
scanstatistics/R/scanstatistics.R
scanstatistics/R/utility_functions.R
scanstatistics/R/datatable_utility_functions.R
scanstatistics/R/scanstatistics_general.R
scanstatistics/R/scan_zip.R
scanstatistics/R/zone_utility_functions.R
scanstatistics/vignettes
scanstatistics/vignettes/references.bib
scanstatistics/vignettes/introduction.Rmd
scanstatistics/README.md
scanstatistics/MD5
scanstatistics/build
scanstatistics/build/vignette.rds
scanstatistics/DESCRIPTION
scanstatistics/man
scanstatistics/man/scanstatistic_object.Rd
scanstatistics/man/if_connected.Rd
scanstatistics/man/negbin_calculations.Rd
scanstatistics/man/validate_values.Rd
scanstatistics/man/column_to_int.Rd
scanstatistics/man/connected_neighbors.Rd
scanstatistics/man/add_duration.Rd
scanstatistics/man/coords_to_knn.Rd
scanstatistics/man/simulate_zip_scanstatistic.Rd
scanstatistics/man/score_zone_sums.Rd
scanstatistics/man/convolute_denominator.Rd
scanstatistics/man/extract_mlc.Rd
scanstatistics/man/scanstatistics.Rd
scanstatistics/man/validate_zones.Rd
scanstatistics/man/scan_poisson.Rd
scanstatistics/man/closest_subsets.Rd
scanstatistics/man/poisson_statistic.Rd
scanstatistics/man/window_zip_statistic.Rd
scanstatistics/man/negbin_overdispersion.Rd
scanstatistics/man/times_and_durations.Rd
scanstatistics/man/validate_scan.Rd
scanstatistics/man/top_clusters.Rd
scanstatistics/man/is_connected.Rd
scanstatistics/man/negbin_score.Rd
scanstatistics/man/zip_mcsim.Rd
scanstatistics/man/create_table.Rd
scanstatistics/man/scan_zip.Rd
scanstatistics/man/get_all_streams.Rd
scanstatistics/man/zip_statistic_term.Rd
scanstatistics/man/haskeys.Rd
scanstatistics/man/convolute_numerator.Rd
scanstatistics/man/NM_popcas.Rd
scanstatistics/man/calc_zipstat_over_duration.Rd
scanstatistics/man/poisson_relrisk.Rd
scanstatistics/man/negbin_increasing_score.Rd
scanstatistics/man/poisson_score_terms.Rd
scanstatistics/man/partition_zones.Rd
scanstatistics/man/connected_to.Rd
scanstatistics/man/first_keys_match.Rd
scanstatistics/man/kulldorff_baseline.Rd
scanstatistics/man/has_converged.Rd
scanstatistics/man/negbin_mcsim.Rd
scanstatistics/man/negbin_increasing_calculations.Rd
scanstatistics/man/score_locations.Rd
scanstatistics/man/zip_em_estimates.Rd
scanstatistics/man/negbin_score_terms.Rd
scanstatistics/man/extract_scanstatistic.Rd
scanstatistics/man/zip_statistic.Rd
scanstatistics/man/zone_sum.Rd
scanstatistics/man/powerset_zones.Rd
scanstatistics/man/NM_map.Rd
scanstatistics/man/knn_zones.Rd
scanstatistics/man/getkeys.Rd
scanstatistics/man/cumsum_duration.Rd
scanstatistics/man/get_zone.Rd
scanstatistics/man/poisson_calculations.Rd
scanstatistics/man/scan_negbin.Rd
scanstatistics/man/generate_poisson_counts.Rd
scanstatistics/man/mc_pvalue.Rd
scanstatistics/man/simulate_poisson_scanstatistic.Rd
scanstatistics/man/join_zones.Rd
scanstatistics/man/dist_to_knn.Rd
scanstatistics/man/enumerate_character.Rd
scanstatistics/man/zip_statistic_factor.Rd
scanstatistics/man/get_enumerated_character.Rd
scanstatistics/man/NM_geo.Rd
scanstatistics/man/estimate_zip_relrisk.Rd
scanstatistics/man/zip_calculations.Rd
scanstatistics/man/add_llr.Rd
scanstatistics/man/estimate_d.Rd
scanstatistics/man/sim_negbin_statistic.Rd
scanstatistics/man/get_column_values.Rd
scanstatistics/man/poisson_mcsim.Rd
scanstatistics/man/estimate_d_dagger.Rd
scanstatistics/man/flexible_zones.Rd
scanstatistics/man/get_set.Rd
scanstatistics/man/zone_table_creator.Rd
scanstatistics/man/print.scanstatistic.Rd
scanstatistics/man/gen_negbin_counts.Rd
scanstatistics/man/generate_zip_counts.Rd
scanstatistics/man/validate_colnames.Rd