Longitude and latitude of New Mexico county seats.

Description

A dataset containing the longitude and latitude of the county seats of New Mexico, except for Cibola county.

Usage

NM_geo

Format

A data frame with 33 rows and 7 variables:

county

Factor; the counties of New Mexico (no spaces).

seat

Character; the name of the county seat, i.e. the administrative center or seat of government.

area(km2)

Numeric; the area in square kilometers of each county.

seat_long

Numeric; the longitude of the county seat.

seat_lat

Numeric; the latitude of the county seat.

center_long

Numeric; the longitude of the geographical center of the county.

center_lat

Numeric; the latitude of the geographical center of the county.

Source

https://en.wikipedia.org/wiki/List_of_counties_in_New_Mexico

Data to plot the counties of New Mexico.

Description

Map data for New Mexico. Was created using ggplot2::map_data.

Usage

NM_map

Format

A data frame with 867 rows and 7 variables:

long

Numeric; longitude of county polygon corner.

lat

Numeric; latitude of county polygon corner.

group

Numeric; grouping by county.

order

Numeric; order of the polygon corners.

region

Character; region is "new mexico" for all rows.

subregion

Character; the county name (with spaces).

county

Factor; the county name (no spaces).

Population and brain cancer cases in New Mexico counties during 1973–1991.

Description

A dataset containing the population count and number of brain cancer cases in the counties of New Mexico during the years 1973–1991. The population numbers are interpolations from the censuses conducted in 1973, 1982, and 1991. Interpolations were done using a quadratic function of time. Thus the year-to-year changes are overly smooth but match the census numbers in the three years mentioned.

Usage

NM_popcas

Format

A data frame with 608 rows and 4 variables:

year

Integer; the year the cases were recorded.

county

Character; the name of the county (no spaces).

population

Integer; the population in that county and year.

count

Integer; the number of brain cancer cases in that county and year.

Set of increasing sets from left to right of input vector.

Description

Returns a set (list) of the increasing sets (integer vectors) of the input vector v, in the sense that the first set contains the first element of v, the second set the first and second elements of v, and so on.

Usage

closest_subsets(v)

Arguments

Value

A list of the same length as the input. The first element of the list is v[1], the second is sort(v[1:2]), the third sort(v[1:3]), and so on.

Find the connected sets for a location and its k nearest neighbors.

Description

Returns a set of sets, each set of the latter type containing the location itself and zero or more of its neighbors, if they are connected.

Usage

connected_neighbors(neighbors, adjacency_matrix)

Arguments

Value

Returns a set of sets, each set of the latter type containing the location itself and zero or more of its neighbors, if they are connected.

Return those elements in the second set which are connected to those in the first.

Description

Return those elements in the second set Z_1 which are connected to those in the first set Z_0, according to the adjacency matrix.

Usage

connected_to(Z_0, Z_1, adjacency_matrix)

Arguments

Value

A set, possibly empty, containing those locations in Z_1 that are connected to any of the locations in Z_0.

Get the k nearest neighbors for each location, given its coordinates.

Description

Get the k nearest neighbors for each location, including the location itself. This function calls dist, so the options for the distance measure used is the same as for that one. Distances are calculated between rows.

Usage

coords_to_knn(x, k = min(10, nrow(x)), method = "euclidean", p = 2)

Arguments

Value

An integer matrix of the k nearest neighbors for each location. Each row corresponds to a location, with the first element of each row being the location itself. Locations are encoded as integers.

Examples

x <- matrix(c(0, 0,
              1, 0,
              2, 1,
              0, 4,
              1, 3),
            ncol = 2, byrow = TRUE)
plot(x)
coords_to_knn(x)

Convert a long data frame to a wide matrix.

Description

Convert a long data frame to a wide matrix, with time along the row dimension and locations along the column dimension. Values in the matrix could be e.g. the observed counts or the population.

Usage

df_to_matrix(df, time_col = 1, location_col = 2, value_col = 3)

Arguments

Value

A matrix with time on rows and locations on columns.

Given a distance matrix, find the k nearest neighbors.

Description

Given a distance matrix, calculate the k nearest neighbors of each location, including the location itself. The matrix should contain only zeros on the diagonal, and all other elements should be positive.

Usage

dist_to_knn(x, k = min(10, nrow(x)))

Arguments

Value

A matrix of integers, row i containing the k nearest neighbors of location i, including itself.

Examples

x <- matrix(c(0, 0,
              1, 0,
              2, 1,
              0, 4,
              1, 3),
            ncol = 2, byrow = TRUE)
d <- dist(x, diag = TRUE, upper = TRUE)
dist_to_knn(d, k = 3)

Estimate baselines based on observed counts.

Description

Estimate the baselines (expected values) for the supplied counts.

Usage

estimate_baselines(counts, population = NULL)

Arguments

Value

A matrix of baselines of the same dimensions as counts.

Estimate variances based on observed counts.

Description

Estimate the variances for the supplied counts. It is assumed that variances are constant over time for each location.

Usage

estimate_variances(
  counts,
  baselines = NULL,
  population = NULL,
  constant_dim = 1
)

Arguments

Value

A matrix of variances of the same dimensions as counts.

Estimate the parameters of a ZIP distribution.

Description

Heuristically estimate the ZIP distribution Poisson mean parameters and the structural zero probabilities for each location and time point. Assumes the structural zero probability is constant over time for each location.

Usage

estimate_zip_params(counts, population = NULL, min_p = 0.001, min_mu = 0.3)

Arguments

Value

A list with two elements:

baselines

A matrix of the same dimensions as counts. If counts was a vector, a matrix with 1 row will be returned.

probs

A matrix of the same dimensions as counts. If counts was a vector, a matrix with 1 row will be returned.

Computes the flexibly shaped zones as in Tango (2005).

Description

Given a matrix of k nearest neighbors and an adjacency matrix for the locations involved, produces the set of flexibly shaped zones as a list of integer vectors. The locations in these zones are all connected, in the sense that any location in the zone can be reached from another by traveling through adjacent locations within the zone.

Usage

flexible_zones(k_nearest, adjacency_matrix)

Arguments

Value

A list of integer vectors.

References

Tango, T. & Takahashi, K. (2005), A flexibly shaped spatial scan statistic for detecting clusters, International Journal of Health Geographics 4(1).

Examples

A <- matrix(c(0,1,0,0,0,0,
              1,0,1,0,0,0,
              0,1,0,0,0,0,
              0,0,0,0,1,0,
              0,0,0,1,0,0,
              0,0,0,0,0,0), 
              nrow = 6, byrow = TRUE) == 1
nn <- matrix(as.integer(c(1,2,3,4,5,6,
                          2,1,3,4,5,6,
                          3,2,1,4,5,6,
                          4,5,1,6,3,2,
                          5,4,6,1,3,2,
                          6,5,4,1,3,2)),
                          nrow = 6, byrow = TRUE)
flexible_zones(nn, A)

Flip a matrix upside down

Description

Flip a matrix upside down

Usage

flipud(x)

Arguments

Value

A matrix, x with rows reversed.

Get indices of zero elements in a vector.

Description

Get indices of zero elements in a vector.

Usage

get_zero_indices(v)

Arguments

Value

A vector with the indices of elements equal to zero in v. Indices start at zero.

Extract a zone from the set of all zones.

Description

Extract zone number n from the set of all zones.

Usage

get_zone(n, zones)

Arguments

Value

An integer vector.

Examples

zones <- list(1L, 2L, 3L, 1:2, c(1L, 3L), c(2L, 3L))
get_zone(4, zones)

Calculate the Gumbel p-value for a scan statistic.

Description

Given an observed scan statistic \lambda^* and a vector of replicate scan statistics \lambda_i, i=1,\ldots,R, fit a Gumbel distribution to the replicates and calculate a p-value for the observed statistic based on the fitted distribution.

\frac{1 + \sum_{i=1}^R \mathrm{I}(\lambda_i > \lambda^*)}{1 + R}

The function is vectorized, so multiple p-values can be calculated if several scan statistics (e.g. statistics from secondary clusters) are supplied.

Usage

gumbel_pvalue(observed, replicates, method = "ML", ...)

Arguments

Value

The p-value or p-values corresponding to the observed scan statistic(s).

Is the relative error between two numbers is less than the given tolerance?

Description

Given two consecutive numbers in a sequence, return TRUE if the relative change is positive but less than the given tolerance.

Usage

has_converged(current, previous, tol = 0.01)

Arguments

Return a set of the location and its neighbors if they are connected, else return the empty set.

Description

If the location and its neighbors, not including itself, are connected, then return the set containing the location and its neighbors; otherwise, return the empty set

Usage

if_connected(distinct_neighbors, location, adjacency_matrix)

Arguments

Value

A set of the given location and the neighbors if they are connected, else returns the empty set.

Returns TRUE if the neighboring locations are connected to the given location, FALSE if not.

Description

Returns TRUE if the neighboring locations are connected to the given location, FALSE if not.

Usage

is_connected(neighbor_locations, location, adjacency_matrix)

Arguments

Value

Boolean: is the neighbors connected to the given location?

Find the increasing subsets of k nearest neighbors for all locations.

Description

Returns the set of increasing nearest neighbor sets for all locations, as a list of integer vectors. That is, for each location the list returned contains one vector containing the location itself, another containing the location and its nearest neighbor, and so on, up to the vector containing the location and its k-1 nearest neighbors.

Usage

knn_zones(k_nearest)

Arguments

Value

A list of integer vectors.

Examples

nn <- matrix(c(1L, 2L, 4L, 3L, 5L,
               2L, 1L, 3L, 4L, 5L, 
               3L, 2L, 4L, 1L, 5L,
               4L, 1L, 2L, 3L, 5L,
               5L, 3L, 4L, 2L, 1L),
               ncol = 5, byrow = TRUE)
knn_zones(nn[, 1:3])

Convert a matrix to a data frame.

Description

Convert a matrix to a data frame with columns time, location, and one more containing the elements of the input matrix.

Usage

matrix_to_df(mat, name, locations = NULL, times = NULL)

Arguments

Value

A matrix with columns time, location, name, where name is specified in the input.

Calculate the Monte Carlo p-value for a scan statistic.

Description

Given an observed scan statistic \lambda^* and a vector of replicate scan statistics \lambda_i, i=1,\ldots,R, calculate the Monte Carlo p-value as

\frac{1 + \sum_{i=1}^R \mathrm{I}(\lambda_i > \lambda^*)}{1 + R}

The function is vectorized, so multiple p-values can be calculated if several scan statistics (e.g. statistics from secondary clusters) are supplied.

Usage

mc_pvalue(observed, replicates)

Arguments

Value

The p-value or p-values corresponding to the observed scan statistic(s).

Permute the entries of the matrix, preserving row and column marginals.

Description

Permute the entries of the matrix, preserving row and column marginals.

Usage

permute_matrix(A)

Arguments

Value

An integer matrix.

Creates a set of all non-empty subsets of the integers from 1 to n.

Description

Creates a list of all 2^(n-1) non-empty subsets of the integers from 1 to n.

Usage

powerset_zones(n)

Arguments

Value

A list of integer vectors.

Print a scanstatistic object.

Description

Prints a scanstatistic object and returns it invisibly.

Usage

## S3 method for class 'scanstatistic'
print(x, ...)

Arguments

Value

x, invisibly

Run a scan statistic analysis.

Description

Run a scan statistic analysis with the given scan statistic and arguments.

Usage

run_scan(scanstat, args, gumbel = FALSE)

Arguments

Value

A list with components

observed

The table of observed statistics.

simulated

The table of simulated statistics.

MC_pvalue

The Monte Carlo P-value of the scan statistic.

Gumbel_pvalue

The Gumbel P-value of the scan statistic.

Calculate the negative binomial bayesian scan statistic..

Description

Calculate the "Bayesian Spatial Scan Statistic" by Neill et al. (2006), adapted to a spatio-temporal setting. The scan statistic assumes that, given the relative risk, the data follows a Poisson distribution. The relative risk is in turn assigned a Gamma distribution prior, yielding a negative binomial marginal distribution for the counts under the null hypothesis. Under the alternative hypothesis, the

Usage

scan_bayes_negbin(
  counts,
  zones,
  baselines = NULL,
  population = NULL,
  outbreak_prob = 0.05,
  alpha_null = 1,
  beta_null = 1,
  alpha_alt = alpha_null,
  beta_alt = beta_null,
  inc_values = seq(1, 3, by = 0.1),
  inc_probs = 1
)

Arguments

Value

A list which, in addition to the information about the type of scan statistic, has the following components: priors (list), posteriors (list), MLC (list) and marginal_data_prob (scalar). The list MLC has elements

zone

The number of the spatial zone of the most likely cluster (MLC).

duration

The most likely event duration.

log_posterior

The posterior log probability that an event is ongoing in the MLC.

log_bayes_factor

The logarithm of the Bayes factor for the MLC.

posterior

The posterior probability that an event is ongoing in the MLC.

locations

The locations involved in the MLC.

The list priors has elements

null_prior

The prior probability of no anomaly.

alt_prior

The prior probability of an anomaly.

inc_prior

A vectorof prior probabilities of each value in the argument inc_values.

window_prior

The prior probability of an outbreak in any of the space-time windows.

The list posteriors has elements

null_posterior

The posterior probability of no anomaly.

alt_posterior

The posterior probability of an anomaly.

inc_posterior

A data frame with columns inc_values and inc_posterior.

window_posteriors

A data frame with columns zone, duration, log_posterior and log_bayes_factor, each row corresponding to a space-time window.

space_time_posteriors

A matrix with the posterior anomaly probability of each location-time combination.

location_posteriors

A vector with the posterior probability of an anomaly at each location.

References

Neill, D. B., Moore, A. W., Cooper, G. F. (2006). A Bayesian Spatial Scan Statistic. Advances in Neural Information Processing Systems 18.

Examples

set.seed(1)
# Create location coordinates, calculate nearest neighbors, and create zones
n_locs <- 50
max_duration <- 5
n_total <- n_locs * max_duration
geo <- matrix(rnorm(n_locs * 2), n_locs, 2)
knn_mat <- coords_to_knn(geo, 15)
zones <- knn_zones(knn_mat)

# Simulate data
baselines <- matrix(rexp(n_total, 1/5), max_duration, n_locs)
counts <- matrix(rpois(n_total, as.vector(baselines)), max_duration, n_locs)

# Inject outbreak/event/anomaly
ob_dur <- 3
ob_cols <- zones[[10]]
ob_rows <- max_duration + 1 - seq_len(ob_dur)
counts[ob_rows, ob_cols] <- matrix(
  rpois(ob_dur * length(ob_cols), 2 * baselines[ob_rows, ob_cols]), 
  length(ob_rows), length(ob_cols))
res <- scan_bayes_negbin(counts = counts,
                         zones = zones,
                         baselines = baselines)

Calculate the "Bayesian Spatial Scan Statistic" by Neill et al. (2006).

Description

Calculate the "Bayesian Spatial Scan Statistic" by Neill et al. (2006), adapted to a spatio-temporal setting. The scan statistic assumes that, given the relative risk, the data follows a Poisson distribution. The relative risk is in turn assigned a Gamma distribution prior, yielding a negative binomial marginal distribution for the counts.

Usage

scan_bayes_negbin_cpp(
  counts,
  baselines,
  zones,
  zone_lengths,
  outbreak_prob,
  alpha_null,
  beta_null,
  alpha_alt,
  beta_alt,
  inc_values,
  inc_probs
)

Arguments

Value

A list with elements priors (list), posteriors (list), and marginal_data_prob (scalar). The list priors has elements

null_prior

The prior probability of no anomaly.

alt_prior

The prior probability of an anomaly.

inc_prior

A vector (matrix with 1 row) of prior probabilities of each value in the argument m_values.

window_prior

The prior probability of an outbreak in any of the space-time windows.

The list posteriors has elements

null_posterior

The posterior probability of no anomaly.

alt_posterior

The posterior probability of an anomaly.

inc_posterior

A data frame with columns inc_values and inc_posterior.

window_posteriors

A data frame with columns zone, duration, log_posterior and log_bayes_factor, each row corresponding to a space-time window.

space_time_posteriors

A matrix with the posterior anomaly probability of each location-time combination.

location_posteriors

A vector (matrix with 1 row) with the posterior probability of an anomaly at each location.

Calculate the expectation-based negative binomial scan statistic.

Description

Calculate the expectation-based negative binomial scan statistic devised by Tango et al. (2011).

Usage

scan_eb_negbin(
  counts,
  zones,
  baselines = NULL,
  thetas = 1,
  type = c("hotspot", "emerging"),
  n_mcsim = 0,
  gumbel = FALSE,
  max_only = FALSE
)

Arguments

Value

A list which, in addition to the information about the type of scan statistic, has the following components:

MLC

A list containing the number of the zone of the most likely cluster (MLC), the locations in that zone, the duration of the MLC, and the calculated score. In order, the elements of this list are named zone_number, locations, duration, score.

observed

A data frame containing, for each combination of zone and duration investigated, the zone number, duration, and score. The table is sorted by score with the top-scoring location on top. If max_only = TRUE, only contains a single row corresponding to the MLC.

replicates

A data frame of the Monte Carlo replicates of the scan statistic (if any), and the corresponding zones and durations.

MC_pvalue

The Monte Carlo P-value.

Gumbel_pvalue

A P-value obtained by fitting a Gumbel distribution to the replicate scan statistics.

n_zones

The number of zones scanned.

n_locations

The number of locations.

max_duration

The maximum duration considered.

n_mcsim

The number of Monte Carlo replicates made.

References

Tango, T., Takahashi, K. & Kohriyama, K. (2011), A space-time scan statistic for detecting emerging outbreaks, Biometrics 67(1), 106–115.

Examples

set.seed(1)
# Create location coordinates, calculate nearest neighbors, and create zones
n_locs <- 50
max_duration <- 5
n_total <- n_locs * max_duration
geo <- matrix(rnorm(n_locs * 2), n_locs, 2)
knn_mat <- coords_to_knn(geo, 15)
zones <- knn_zones(knn_mat)

# Simulate data
 baselines <- matrix(rexp(n_total, 1/5), max_duration, n_locs)
 thetas <- matrix(runif(n_total, 0.05, 3), max_duration, n_locs)
 counts <- matrix(rnbinom(n_total,  mu = baselines,  size = thetas), 
                  max_duration, n_locs)

# Inject outbreak/event/anomaly
ob_dur <- 3
ob_cols <- zones[[10]]
ob_rows <- max_duration + 1 - seq_len(ob_dur)
counts[ob_rows, ob_cols] <- matrix(
  rnbinom(ob_dur * length(ob_cols), 
          mu = 2 * baselines[ob_rows, ob_cols],
          size = thetas[ob_rows, ob_cols]),
  length(ob_rows), length(ob_cols))
res <- scan_eb_negbin(counts = counts,
                      zones = zones,
                      baselines = baselines,
                      thetas = thetas,
                      type = "hotspot",
                      n_mcsim = 99,
                      max_only = FALSE)

Calculate the expectation-based negative binomial scan statistic.

Description

Calculate the expectation-based negative binomial scan statistic and Monte Carlo replicates.

Usage

scan_eb_negbin_cpp(
  counts,
  baselines,
  overdisp,
  zones,
  zone_lengths,
  store_everything,
  num_mcsim,
  score_hotspot
)

Arguments

Value

A list with elements observed and simulated, each being a data frame with columns:

zone

The top-scoring zone (spatial component of MLC).

duration

The corresponding duration (time-length of MLC).

score

The value of the loglihood ratio statistic (the scan statistic).

relrisk

The estimated relative risk.

n_iter

The number of iterations performed by the EM algorithm.

Calculate the expectation-based Poisson scan statistic.

Description

Calculate the expectation-based Poisson scan statistic devised by Neill et al. (2005).

Usage

scan_eb_poisson(
  counts,
  zones,
  baselines = NULL,
  population = NULL,
  n_mcsim = 0,
  gumbel = FALSE,
  max_only = FALSE
)

Arguments

Value

A list which, in addition to the information about the type of scan statistic, has the following components:

MLC

A list containing the number of the zone of the most likely cluster (MLC), the locations in that zone, the duration of the MLC, the calculated score, and the relative risk. In order, the elements of this list are named zone_number, locations, duration, score, relative_risk.

observed

A data frame containing, for each combination of zone and duration investigated, the zone number, duration, score, relative risk. The table is sorted by score with the top-scoring location on top. If max_only = TRUE, only contains a single row corresponding to the MLC.

replicates

A data frame of the Monte Carlo replicates of the scan statistic (if any), and the corresponding zones and durations.

MC_pvalue

The Monte Carlo P-value.

Gumbel_pvalue

A P-value obtained by fitting a Gumbel distribution to the replicate scan statistics.

n_zones

The number of zones scanned.

n_locations

The number of locations.

max_duration

The maximum duration considered.

n_mcsim

The number of Monte Carlo replicates made.

References

Neill, D. B., Moore, A. W., Sabhnani, M. and Daniel, K. (2005). Detection of emerging space-time clusters. Proceeding of the eleventh ACM SIGKDD international conference on Knowledge discovery in data mining - KDD ’05, 218.

Examples

set.seed(1)
# Create location coordinates, calculate nearest neighbors, and create zones
n_locs <- 50
max_duration <- 5
n_total <- n_locs * max_duration
geo <- matrix(rnorm(n_locs * 2), n_locs, 2)
knn_mat <- coords_to_knn(geo, 15)
zones <- knn_zones(knn_mat)

# Simulate data
baselines <- matrix(rexp(n_total, 1/5), max_duration, n_locs)
counts <- matrix(rpois(n_total, as.vector(baselines)), max_duration, n_locs)

# Inject outbreak/event/anomaly
ob_dur <- 3
ob_cols <- zones[[10]]
ob_rows <- max_duration + 1 - seq_len(ob_dur)
counts[ob_rows, ob_cols] <- matrix(
  rpois(ob_dur * length(ob_cols), 2 * baselines[ob_rows, ob_cols]), 
  length(ob_rows), length(ob_cols))
res <- scan_eb_poisson(counts = counts,
                       zones = zones,
                       baselines = baselines,
                       n_mcsim = 99,
                       max_only = FALSE)

Calculate the expecation-based Poisson scan statistic.

Description

Calculate the expectation-based Poisson scan statistic and Monte Carlo replicates.

Usage

scan_eb_poisson_cpp(
  counts,
  baselines,
  zones,
  zone_lengths,
  store_everything,
  num_mcsim
)

Arguments

Value

A list with elements observed and simulated, each being a data frame with columns:

zone

The top-scoring zone (spatial component of MLC).

duration

The corresponding duration (time-length of MLC).

score

The value of the loglihood ratio statistic (the scan statistic).

relrisk_in

The estimated relative risk inside.

relrisk_in

The estimated relative risk outside.

Calculate the expectation-based ZIP scan statistic.

Description

Calculates the expectation-based scan statistic. See details below.

Usage

scan_eb_zip(
  counts,
  zones,
  baselines = NULL,
  probs = NULL,
  population = NULL,
  n_mcsim = 0,
  gumbel = FALSE,
  max_only = FALSE,
  rel_tol = 0.001
)

Arguments

Details

For the expectation-based zero-inflated Poisson scan statistic (Allévius & Höhle 2017), the null hypothesis of no anomaly holds that the count observed at each location i and duration t (the number of time periods before present) has a zero-inflated Poisson distribution with expected value parameter \mu_{it} and structural zero probability p_{it}:

H_0 : Y_{it} \sim \textrm{ZIP}(\mu_{it}, p_{it}).

This holds for all locations i = 1, \ldots, m and all durations t = 1, \ldots,T, with T being the maximum duration considered. Under the alternative hypothesis, there is a space-time window W consisting of a spatial zone Z \subset \{1, \ldots, m\} and a time window D \subseteq \{1, \ldots, T\} such that the counts in that window have their Poisson expected value parameters inflated by a factor q_W > 1 compared to the null hypothesis:

H_1 : Y_{it} \sim \textrm{ZIP}(q_W \mu_{it}, p_{it}), ~~(i,t) \in W.

For locations and durations outside of this window, counts are assumed to be distributed as under the null hypothesis. The sets Z considered are those specified in the argument zones, while the maximum duration T is taken as the maximum value in the column duration of the input table.

For each space-time window W considered, (the log of) a likelihood ratio is computed using the distributions under the alternative and null hypotheses, and the expectation-based Poisson scan statistic is calculated as the maximum of these quantities over all space-time windows. The expectation-maximization (EM) algorithm is used to obtain maximum likelihood estimates.

Value

A list which, in addition to the information about the type of scan statistic, has the following components:

MLC

A list containing the number of the zone of the most likely cluster (MLC), the locations in that zone, the duration of the MLC, the calculated score, the relative risk, and the number of iterations until convergence for the EM algorithm. In order, the elements of this list are named zone_number, locations, duration, score, relative_risk, n_iter.

observed

A data frame containing, for each combination of zone and duration investigated, the zone number, duration, score, relative risk, number of EM iterations. The table is sorted by score with the top-scoring location on top. If max_only = TRUE, only contains a single row corresponding to the MLC.

replicates

A data frame of the Monte Carlo replicates of the scan statistic (if any), and the corresponding zones and durations.

MC_pvalue

The Monte Carlo P-value.

Gumbel_pvalue

A P-value obtained by fitting a Gumbel distribution to the replicate scan statistics.

n_zones

The number of zones scanned.

n_locations

The number of locations.

max_duration

The maximum duration considered.

n_mcsim

The number of Monte Carlo replicates made.

References

Allévius, B. and Höhle, M, An expectation-based space-time scan statistic for ZIP-distributed data, (Technical report), Link to PDF.

Examples

if (require("gamlss.dist")) {
  set.seed(1)
  # Create location coordinates, calculate nearest neighbors, and create zones
  n_locs <- 50
  max_duration <- 5
  n_total <- n_locs * max_duration
  geo <- matrix(rnorm(n_locs * 2), n_locs, 2)
  knn_mat <- coords_to_knn(geo, 15)
  zones <- knn_zones(knn_mat)
  
  # Simulate data
  baselines <- matrix(rexp(n_total, 1/5), max_duration, n_locs)
  probs <- matrix(runif(n_total) / 4, max_duration, n_locs)
  counts <- matrix(gamlss.dist::rZIP(n_total, baselines, probs), 
                   max_duration, n_locs)
  
  # Inject outbreak/event/anomaly
  ob_dur <- 3
  ob_cols <- zones[[10]]
  ob_rows <- max_duration + 1 - seq_len(ob_dur)
  counts[ob_rows, ob_cols] <- gamlss.dist::rZIP(
    ob_dur * length(ob_cols), 2 * baselines[ob_rows, ob_cols],
    probs[ob_rows, ob_cols])
  res <- scan_eb_zip(counts = counts,
                     zones = zones,
                     baselines = baselines,
                     probs = probs,
                     n_mcsim = 9,
                     max_only = FALSE,
                     rel_tol = 1e-3)
}

Calculate the highest-value EB ZIP loglihood ratio statistic.

Description

Calculate the expectation-based ZIP loglihood ratio statistic for each zone and duration, but only keep the zone and duration with the highest value (the MLC). The estimate of the relative risk is also calculated, along with the number of iterations the EM algorithm performed.

Usage

scan_eb_zip_cpp(
  counts,
  baselines,
  probs,
  zones,
  zone_lengths,
  rel_tol,
  store_everything,
  num_mcsim
)

Arguments

Value

A list with elements observed and simulated, each being a data frame with columns:

zone

The top-scoring zone (spatial component of MLC).

duration

The corresponding duration (time-length of MLC).

score

The value of the loglihood ratio statistic (the scan statistic).

relrisk

The estimated relative risk.

n_iter

The number of iterations performed by the EM algorithm.

Calculate the space-time permutation scan statistic.

Description

Calculate the space-time permutation scan statistic (Kulldorff 2005) and Monte Carloo replicates.

Usage

scan_pb_perm_cpp(
  counts,
  baselines,
  zones,
  zone_lengths,
  store_everything,
  num_mcsim
)

Arguments

Value

A list with elements observed and simulated, each being a data frame with columns:

zone

The top-scoring zone (spatial component of MLC).

duration

The corresponding duration (time-length of MLC).

score

The value of the loglihood ratio statistic (the scan statistic).

relrisk_in

The estimated relative risk inside.

relrisk_in

The estimated relative risk outside.

Calculate the population-based Poisson scan statistic.

Description

Calculate the population-based Poisson scan statistic devised by Kulldorff (1997, 2001).

Usage

scan_pb_poisson(
  counts,
  zones,
  population = NULL,
  n_mcsim = 0,
  gumbel = FALSE,
  max_only = FALSE
)

Arguments

Value

A list which, in addition to the information about the type of scan statistic, has the following components:

MLC

A list containing the number of the zone of the most likely cluster (MLC), the locations in that zone, the duration of the MLC, the calculated score, and the relative risk inside and outside the cluster. In order, the elements of this list are named zone_number, locations, duration, score, relrisk_in, relrisk_out.

observed

A data frame containing, for each combination of zone and duration investigated, the zone number, duration, score, relative risks. The table is sorted by score with the top-scoring location on top. If max_only = TRUE, only contains a single row corresponding to the MLC.

replicates

A data frame of the Monte Carlo replicates of the scan statistic (if any), and the corresponding zones and durations.

MC_pvalue

The Monte Carlo P-value.

Gumbel_pvalue

A P-value obtained by fitting a Gumbel distribution to the replicate scan statistics.

n_zones

The number of zones scanned.

n_locations

The number of locations.

max_duration

The maximum duration considered.

n_mcsim

The number of Monte Carlo replicates made.

References

Kulldorff, M. (1997). A spatial scan statistic. Communications in Statistics - Theory and Methods, 26, 1481–1496.

Kulldorff, M. (2001). Prospective time periodic geographical disease surveillance using a scan statistic. Journal of the Royal Statistical Society, Series A (Statistics in Society), 164, 61–72.

Examples

set.seed(1)
# Create location coordinates, calculate nearest neighbors, and create zones
n_locs <- 50
max_duration <- 5
n_total <- n_locs * max_duration
geo <- matrix(rnorm(n_locs * 2), n_locs, 2)
knn_mat <- coords_to_knn(geo, 15)
zones <- knn_zones(knn_mat)

# Simulate data
population <- matrix(rnorm(n_total, 100, 10), max_duration, n_locs)
counts <- matrix(rpois(n_total, as.vector(population) / 20), 
                 max_duration, n_locs)

# Inject outbreak/event/anomaly
ob_dur <- 3
ob_cols <- zones[[10]]
ob_rows <- max_duration + 1 - seq_len(ob_dur)
counts[ob_rows, ob_cols] <- matrix(
  rpois(ob_dur * length(ob_cols), 2 * population[ob_rows, ob_cols] / 20), 
  length(ob_rows), length(ob_cols))
res <- scan_pb_poisson(counts = counts,
                       zones = zones,
                       population = population,
                       n_mcsim = 99,
                       max_only = FALSE)

Calculate the population-based Poisson scan statistic.

Description

Calculate the population-based Poisson scan statistic and Monte Carlo replicates.

Usage

scan_pb_poisson_cpp(
  counts,
  baselines,
  zones,
  zone_lengths,
  store_everything,
  num_mcsim
)

Arguments

Value

A list with elements observed and simulated, each being a data frame with columns:

zone

The top-scoring zone (spatial component of MLC).

duration

The corresponding duration (time-length of MLC).

score

The value of the loglihood ratio statistic (the scan statistic).

relrisk_in

The estimated relative risk inside.

relrisk_in

The estimated relative risk outside.

Calculate the space-time permutation scan statistic.

Description

Calculate the space-time permutation scan statistic devised by Kulldorff (2005).

Usage

scan_permutation(
  counts,
  zones,
  population = NULL,
  n_mcsim = 0,
  gumbel = FALSE,
  max_only = FALSE
)

Arguments

Value

A list which, in addition to the information about the type of scan statistic, has the following components:

MLC

A list containing the number of the zone of the most likely cluster (MLC), the locations in that zone, the duration of the MLC, the calculated score, and the relative risk inside and outside the cluster. In order, the elements of this list are named zone_number, locations, duration, score, relrisk_in, relrisk_out.

observed

A data frame containing, for each combination of zone and duration investigated, the zone number, duration, score, relative risks. The table is sorted by score with the top-scoring location on top. If max_only = TRUE, only contains a single row corresponding to the MLC.

replicates

A data frame of the Monte Carlo replicates of the scan statistic (if any), and the corresponding zones and durations.

MC_pvalue

The Monte Carlo P-value.

Gumbel_pvalue

A P-value obtained by fitting a Gumbel distribution to the replicate scan statistics.

n_zones

The number of zones scanned.

n_locations

The number of locations.

max_duration

The maximum duration considered.

n_mcsim

The number of Monte Carlo replicates made.

References

Kulldorff, M., Heffernan, R., Hartman, J., Assunção, R. M., Mostashari, F. (2005). A space-time permutation scan statistic for disease outbreak detection. PLoS Medicine, 2(3), 0216-0224.

Examples

set.seed(1)
# Create location coordinates, calculate nearest neighbors, and create zones
n_locs <- 50
max_duration <- 5
n_total <- n_locs * max_duration
geo <- matrix(rnorm(n_locs * 2), n_locs, 2)
knn_mat <- coords_to_knn(geo, 15)
zones <- knn_zones(knn_mat)

# Simulate data
population <- matrix(rnorm(n_total, 100, 10), max_duration, n_locs)
counts <- matrix(rpois(n_total, as.vector(population) / 20), 
                 max_duration, n_locs)

# Inject outbreak/event/anomaly
ob_dur <- 3
ob_cols <- zones[[10]]
ob_rows <- max_duration + 1 - seq_len(ob_dur)
counts[ob_rows, ob_cols] <- matrix(
  rpois(ob_dur * length(ob_cols), 2 * population[ob_rows, ob_cols] / 20), 
  length(ob_rows), length(ob_cols))
res <- scan_permutation(counts = counts,
                           zones = zones,
                           population = population,
                           n_mcsim = 99,
                           max_only = FALSE)

scanstatistics: Space-time anomaly detection using scan statistics.

Description

The scanstatistics package provides two categories of important functions: data preparation functions, and the scan statistics themselves.

Data preparation functions

These functions prepare your data for use. In particular, it helps you define the zones which will be considered by the scan statistics.

Scan statistics

These are the functions used for space-time anomaly detection. Scan statistic functions for univariate space-time data have a name that begins with scan_ and functions for multivariate space-time data have a name that begins with mscan_.

Score each location over zones and duration.

Description

For each location, compute the average of the statistic calculated for each space-time window that the location is included in, i.e. average the statistic over both zones and the maximum duration.

Usage

score_locations(x, zones)

Arguments

Value

A data.table with the following columns:

location

The locations (as integers).

total_score

For each location, the sum of all window statistics that the location appears in.

n_zones

The number of spatial zones that the location appears in.

score

The total score divided by the number of zones and the maximum duration.

relative_score

The score divided by the maximum score.

Examples

# Simple example
set.seed(1)
table <- data.frame(zone = 1:5, duration = 1, score = 5:1)
zones <- list(1:2, 1:3, 2:5, 4:5, c(1, 5))
x <- list(observed = table, n_locations = 5, max_duration = 1, n_zones = 5)
score_locations(x, zones)

Get the top (non-overlappig) clusters.

Description

Get the top k space-time clusters according to the statistic calculated for each cluster (the maximum being the scan statistic). The default is to return the spatially non-overlapping clusters, i.e. those that do not have any locations in common.

Usage

top_clusters(
  x,
  zones,
  k = 5,
  overlapping = FALSE,
  gumbel = FALSE,
  alpha = NULL,
  ...
)

Arguments

Value

A data frame with at most k rows, with columns zone, duration, score and possibly MC_pvalue, Gumbel_pvalue and critical_value.

Examples

set.seed(1)
counts <- matrix(rpois(15, 3), 3, 5)
zones <- list(1:2, 1:3, 2:5, c(1, 3), 4:5, c(1, 5))
scanres <- scan_permutation(counts, zones, n_mcsim = 5)
top_clusters(scanres, zones, k = 4, overlapping = FALSE)