tests/degree.R

In EpiContactTrace: Epidemiological Tool for Contact Tracing

## Copyright 2013-2020 Stefan Widgren and Maria Noremark,
## National Veterinary Institute, Sweden
##
## Licensed under the EUPL, Version 1.1 or - as soon they
## will be approved by the European Commission - subsequent
## versions of the EUPL (the "Licence");
## You may not use this work except in compliance with the
## Licence.
## You may obtain a copy of the Licence at:
##
## http://ec.europa.eu/idabc/eupl
##
## Unless required by applicable law or agreed to in
## writing, software distributed under the Licence is
## distributed on an "AS IS" basis,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either
## express or implied.
## See the Licence for the specific language governing
## permissions and limitations under the Licence.

library(EpiContactTrace)

##
## Check in- and outgoing degree methods
##

##
## Case 1
##
movements <- data.frame(
    source = c(1L, 2L, 3L, 3L),
    destination = c(3L, 3L, 4L, 4L),
    t = structure(c(14834, 14838, 14836, 14841), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_))

ct <- Trace(movements,
            root = 4L,
            inBegin = as.Date("2010-08-02"),
            inEnd = as.Date("2010-09-01"),
            outBegin = as.Date("2010-08-01"),
            outEnd = as.Date("2010-08-31"))

stopifnot(identical(InDegree(ct)$inDegree, 1L))
stopifnot(identical(OutDegree(ct)$outDegree, 0L))

##
## Case 2
##
movements <- data.frame(
    source = c(1L, 2L, 3L, 3L),
    destination = c(3L, 3L, 4L, 4L),
    t = structure(c(14834, 14838, 14836, 14841), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_))

ns <- NetworkSummary(movements, root = 4, tEnd = "2010-09-01", days = 30)
stopifnot(identical(ns$inDegree, 1L))

##
## Case 3
##
movements <- data.frame(
    source = c(1L, 2L, 3L, 3L),
    destination = c(3L, 3L, 4L, 4L),
    t = structure(c(14834, 14838, 14836, 14841), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_))

ns <- NetworkSummary(movements, root = 4, tEnd = "2010-08-31", days = 30)
stopifnot(identical(ns$outDegree, 0L))

##
## Case 4
##
movements <- data.frame(
    source = c(1L, 2L, 3L, 3L),
    destination = c(3L, 3L, 4L, 4L),
    t = structure(c(14834, 14838, 14836, 14841), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_))

ct <- Trace(movements,
            root = 4L,
            inBegin = as.Date("2010-08-27"),
            inEnd = as.Date("2010-09-01"),
            outBegin = as.Date("2010-08-01"),
            outEnd = as.Date("2010-08-31"))

stopifnot(identical(InDegree(ct)$inDegree, 0L))
stopifnot(identical(OutDegree(ct)$outDegree, 0L))

##
## Case 5
##
movements <- data.frame(
    source = c(1L, 2L, 3L, 3L),
    destination = c(3L, 3L, 4L, 4L),
    t = structure(c(14834, 14838, 14836, 14841), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_))

ns <- NetworkSummary(movements, root = 4, tEnd = "2010-09-01", days = 5)
stopifnot(identical(ns$inDegree, 0L))

##
## Case 6
##
movements <- data.frame(
    source = c(1L, 2L, 3L, 3L),
    destination = c(3L, 3L, 4L, 4L),
    t = structure(c(14834, 14838, 14836, 14841), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_))

ns <- NetworkSummary(movements, root = 4, tEnd = "2010-08-31", days = 30)
stopifnot(identical(ns$outDegree, 0L))

##
## Case 7
##
movements <- data.frame(
    source = c("1", "1", "1"),
    destination = c("2", "3", "4"),
    t = structure(c(14834, 14838, 14836), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_))

ct <- Trace(movements,
            root = 1L,
            inBegin = as.Date("2010-08-02"),
            inEnd = as.Date("2010-09-01"),
            outBegin = as.Date("2010-08-01"),
            outEnd = as.Date("2010-08-31"))

stopifnot(identical(InDegree(ct)$inDegree, 0L))
stopifnot(identical(OutDegree(ct)$outDegree, 3L))

##
## Case 8
##
movements <- data.frame(
    source = c("1", "1", "1"),
    destination = c("2", "3", "4"),
    t = structure(c(14834, 14838, 14836), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_))

ns <- NetworkSummary(movements, root = 1, tEnd = "2010-09-01", days = 30)
stopifnot(identical(ns$inDegree, 0L))

##
## Case 9
##
movements <- data.frame(
    source = c("1", "1", "1"),
    destination = c("2", "3", "4"),
    t = structure(c(14834, 14838, 14836), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_))

ns <- NetworkSummary(movements, root = 1, tEnd = "2010-08-31", days = 30)
stopifnot(identical(ns$outDegree, 3L))

##
## Case 10
##
movements <- data.frame(
    source = c("1", "1", "1"),
    destination = c("2", "3", "4"),
    t = structure(c(14834, 14838, 14836), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_))

ct <- Trace(movements,
            root = 1L,
            inBegin = as.Date("2010-08-02"),
            inEnd = as.Date("2010-09-01"),
            outBegin = as.Date("2010-08-01"),
            outEnd = as.Date("2010-08-16"))

stopifnot(identical(InDegree(ct)$inDegree, 0L))
stopifnot(identical(OutDegree(ct)$outDegree, 2L))

##
## Case 11
##
movements <- data.frame(
    source = c("1", "1", "1"),
    destination = c("2", "3", "4"),
    t = structure(c(14834, 14838, 14836), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_))

ns <- NetworkSummary(movements, root = 1, tEnd = "2010-09-01", days = 30)
stopifnot(identical(ns$inDegree, 0L))

##
## Case 12
##
movements <- data.frame(
    source = c("1", "1", "1"),
    destination = c("2", "3", "4"),
    t = structure(c(14834, 14838, 14836), class = "Date"),
    individual = c(NA_character_, NA_character_, NA_character_),
    n = c(NA_integer_, NA_integer_, NA_integer_))

ns <- NetworkSummary(movements, root = 1, tEnd = "2010-08-16", days = 15)
stopifnot(identical(ns$outDegree, 2L))