R Under development (unstable) (2024-10-01 r87205 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## 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 contact chain methods
> ##
> 
> ##
> ## Case 1
> ##
> 
> movements <- data.frame(
+     source = 1:7,
+     destination = c(4L, 5L, 5L, 6L, 8L, 8L, 8L),
+     t = structure(c(14849, 14846, 14847, 14850, 14848, 14851, 14852),
+                   class = "Date"))
> ct <- Trace(movements,
+             root = 8L,
+             inBegin = as.Date("2010-08-22"),
+             inEnd = as.Date("2010-10-01"),
+             outBegin = as.Date("2010-08-01"),
+             outEnd = as.Date("2010-08-31"))
> ct
Root: 8

<<< In contacts <<<
In begin date: 2010-08-22
In end date:   2010-10-01
In days: 40
In degree: 3
Ingoing contact chain: 7

8 <-- 5
      5 <-- 2
      5 <-- 3
8 <-- 6
      6 <-- 4
            4 <-- 1
8 <-- 7

>>> Out contacts >>>
Out begin date: 2010-08-01
Out end date:   2010-08-31
Out days: 30
Out degree: 0
Outgoing contact chain: 0

No outgoing contacts during the search period.

> stopifnot(identical(IngoingContactChain(ct)$ingoingContactChain, 7L))
> stopifnot(identical(OutgoingContactChain(ct)$outgoingContactChain, 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_))
> ct <- Trace(movements,
+             root = 4L,
+             inBegin = as.Date("2010-07-22"),
+             inEnd = as.Date("2010-08-21"),
+             outBegin = as.Date("2010-08-01"),
+             outEnd = as.Date("2010-08-31"))
> ct
Root: 4

<<< In contacts <<<
In begin date: 2010-07-22
In end date:   2010-08-21
In days: 30
In degree: 1
Ingoing contact chain: 3

4 <-- 3
      3 <-- 1
      3 <-- 2

>>> Out contacts >>>
Out begin date: 2010-08-01
Out end date:   2010-08-31
Out days: 30
Out degree: 0
Outgoing contact chain: 0

No outgoing contacts during the search period.

> stopifnot(identical(IngoingContactChain(ct)$ingoingContactChain, 3L))
> stopifnot(identical(OutgoingContactChain(ct)$outgoingContactChain, 0L))
> 
> ##
> ## Case 3
> ##
> 
> movements <- data.frame(
+     source = 1:2,
+     destination = c(2L, 1L),
+     t = structure(c(14834, 14834), class = "Date"),
+     individual = c(NA_character_, NA_character_),
+     n = c(NA_integer_, NA_integer_))
> ct <- Trace(movements,
+             root = 1L,
+             inBegin = as.Date("2010-08-02"),
+             inEnd = as.Date("2010-09-01"),
+             outBegin = as.Date("2010-09-01"),
+             outEnd = as.Date("2010-10-01"))
> ct
Root: 1

<<< In contacts <<<
In begin date: 2010-08-02
In end date:   2010-09-01
In days: 30
In degree: 1
Ingoing contact chain: 1

1 <-- 2

>>> Out contacts >>>
Out begin date: 2010-09-01
Out end date:   2010-10-01
Out days: 30
Out degree: 0
Outgoing contact chain: 0

No outgoing contacts during the search period.

> stopifnot(identical(IngoingContactChain(ct)$ingoingContactChain, 1L))
> stopifnot(identical(OutgoingContactChain(ct)$outgoingContactChain, 0L))
> 
> ##
> ## Case 4
> ##
> 
> movements <- data.frame(
+     source = c(1L, 2L, 2L, 1L, 3L, 7L, 1L),
+     destination = c(2L, 5L, 6L, 3L, 7L, 8L, 4L),
+     t = structure(c(14834, 14838, 14836, 14857, 14860, 14862, 14884),
+                   class = "Date"),
+     individual = c(NA_character_, NA_character_, NA_character_,
+                    NA_character_, NA_character_, NA_character_,
+                    NA_character_),
+     n = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_,
+           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("2010-11-09"))
> ct
Root: 1

<<< In contacts <<<
In begin date: 2010-08-02
In end date:   2010-09-01
In days: 30
In degree: 0
Ingoing contact chain: 0

No ingoing contacts during the search period.

>>> Out contacts >>>
Out begin date: 2010-08-01
Out end date:   2010-11-09
Out days: 100
Out degree: 3
Outgoing contact chain: 7

1 --> 2
      2 --> 5
      2 --> 6
1 --> 3
      3 --> 7
            7 --> 8
1 --> 4

> stopifnot(identical(IngoingContactChain(ct)$ingoingContactChain, 0L))
> stopifnot(identical(OutgoingContactChain(ct)$outgoingContactChain, 7L))
> 
> ##
> ## Case 5
> ##
> 
> movements <- data.frame(
+     source = 1:2,
+     destination = c(2L, 1L),
+     t = structure(c(14834, 14834), class = "Date"),
+     individual = c(NA_character_, NA_character_),
+     n = c(NA_integer_, NA_integer_))
> ct <- Trace(movements,
+             root = 1L,
+             inBegin = as.Date("2010-07-02"),
+             inEnd = as.Date("2010-08-01"),
+             outBegin = as.Date("2010-08-01"),
+             outEnd = as.Date("2010-08-31"))
> ct
Root: 1

<<< In contacts <<<
In begin date: 2010-07-02
In end date:   2010-08-01
In days: 30
In degree: 0
Ingoing contact chain: 0

No ingoing contacts during the search period.

>>> Out contacts >>>
Out begin date: 2010-08-01
Out end date:   2010-08-31
Out days: 30
Out degree: 1
Outgoing contact chain: 1

1 --> 2

> stopifnot(identical(IngoingContactChain(ct)$ingoingContactChain, 0L))
> stopifnot(identical(OutgoingContactChain(ct)$outgoingContactChain, 1L))
> 
> ##
> ## Case 6
> ##
> 
> movements <- data.frame(
+     source = c(1L, 2L, 1L, 2L, 1L, 3L, 1L),
+     destination = c(2L, 3L, 2L, 3L, 2L, 4L, 2L),
+     t = structure(c(1L, 2L, 3L, 4L, 7L, 6L, 5L),
+                   .Label = c("2010-10-01", "2010-10-05", "2010-10-10",
+                              "2010-10-15", "2010-10-20", "2010-10-25",
+                              "2010-10-30"),
+                   class = "factor"))
> ct <- Trace(movements,
+             root = 1L,
+             inBegin = as.Date("2010-10-10"),
+             inEnd = as.Date("2010-10-20"),
+             outBegin = as.Date("2010-10-10"),
+             outEnd = as.Date("2010-10-20"))
> ct
Root: 1

<<< In contacts <<<
In begin date: 2010-10-10
In end date:   2010-10-20
In days: 10
In degree: 0
Ingoing contact chain: 0

No ingoing contacts during the search period.

>>> Out contacts >>>
Out begin date: 2010-10-10
Out end date:   2010-10-20
Out days: 10
Out degree: 1
Outgoing contact chain: 2

1 --> 2
      2 --> 3

> stopifnot(identical(IngoingContactChain(ct)$ingoingContactChain, 0L))
> stopifnot(identical(OutgoingContactChain(ct)$outgoingContactChain, 2L))
> 
> ##
> ## Case 7
> ##
> 
> movements <- data.frame(
+     source = c(1L, 2L, 1L, 2L, 1L, 3L, 1L),
+     destination = c(2L, 3L, 2L, 3L, 2L, 4L, 2L),
+     t = structure(c(1L, 2L, 3L, 4L, 7L, 6L, 5L),
+                   .Label = c("2010-10-01", "2010-10-05", "2010-10-10",
+                              "2010-10-15", "2010-10-20", "2010-10-25",
+                              "2010-10-30"),
+                   class = "factor"))
> 
> ns <- NetworkSummary(movements, root = 1, tEnd = "2010-10-20", days = 10)
> 
> df <- data.frame(root = "1",
+                  inBegin = structure(14892, class = "Date"),
+                  inEnd = structure(14902, class = "Date"),
+                  inDays = 10L,
+                  outBegin = structure(14892, class = "Date"),
+                  outEnd = structure(14902, class = "Date"),
+                  outDays = 10L,
+                  inDegree = 0L,
+                  outDegree = 1L,
+                  ingoingContactChain = 0L,
+                  outgoingContactChain = 2L,
+                  stringsAsFactors = FALSE)
> ns
  root    inBegin      inEnd inDays   outBegin     outEnd outDays inDegree
1    1 2010-10-10 2010-10-20     10 2010-10-10 2010-10-20      10        0
  outDegree ingoingContactChain outgoingContactChain
1         1                   0                    2
> stopifnot(identical(ns, df))
> 
> proc.time()
   user  system elapsed 
   0.21    0.12    0.32