R Under development (unstable) (2024-10-01 r87205 ucrt) -- "Unsuffered Consequences"
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> ## 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)
> 
> ##
> ## Argument checking
> ##
> ## Check that the functions stop if not the expected arguments are
> ## given
> ##
> 
> ##
> ## Missing parameters in call to IngoingContactChain
> ##
> tools::assertError(IngoingContactChain(data.frame(source = 1L,
+                                                   destination = 2L,
+                                                   t = as.Date("2011-08-10")),
+                                        tEnd = "2005-10-31",
+                                        days = 90))
> 
> ##
> ## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in
> ## call to NetworkSummary
> ##
> tools::assertError(IngoingContactChain(data.frame(source = 1L,
+                                                   destination = 2L,
+                                                   t = as.Date("2011-08-10")),
+                                        root = 1,
+                                        days = 90))
> 
> ##
> ## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in
> ## call to IngoingContactChain
> ##
> tools::assertError(IngoingContactChain(data.frame(source = 1L,
+                                                   destination = 2L,
+                                                   t = as.Date("2011-08-10")),
+                                        root = 1,
+                                        tEnd = "2005-10-31"))
> 
> ##
> ## Missing parameters in call to OutgoingContactChain
> ##
> tools::assertError(OutgoingContactChain(data.frame(source = 1L,
+                                                    destination = 2L,
+                                                    t = as.Date("2011-08-10")),
+                                         tEnd = "2005-10-31",
+                                         days = 90))
> 
> ##
> ## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in
> ## call to NetworkSummary
> ##
> tools::assertError(OutgoingContactChain(data.frame(source = 1L,
+                                                    destination = 2L,
+                                                    t = as.Date("2011-08-10")),
+                                         root = 1,
+                                         days = 90))
> 
> ##
> ## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in
> ## call to NetworkSummary
> ##
> tools::assertError(OutgoingContactChain(data.frame(source = 1L,
+                                                    destination = 2L,
+                                                    t = as.Date("2011-08-10")),
+                                         root = 1,
+                                         tEnd = "2005-10-31"))
> 
> ##
> ## Missing parameters in call to InDegree
> ##
> tools::assertError(InDegree(data.frame(source = 1L,
+                                        destination = 2L,
+                                        t = as.Date("2011-08-10")),
+                             tEnd = "2005-10-31",
+                             days = 90))
> 
> ##
> ## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in
> ## call to NetworkSummary
> ##
> tools::assertError(InDegree(data.frame(source = 1L,
+                                        destination = 2L,
+                                        t = as.Date("2011-08-10")),
+                             root = 1,
+                             days = 90))
> 
> ##
> ## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in
> ## call to NetworkSummary
> ##
> tools::assertError(InDegree(data.frame(source = 1L,
+                                        destination = 2L,
+                                        t = as.Date("2011-08-10")),
+                             root = 1,
+                             tEnd = "2005-10-31"))
> 
> ##
> ## Missing parameters in call to OutDegree
> ##
> tools::assertError(OutDegree(data.frame(source = 1L,
+                                         destination = 2L,
+                                         t = as.Date("2011-08-10")),
+                              tEnd = "2005-10-31",
+                              days = 90))
> 
> ##
> ## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in
> ## call to NetworkSummary
> ##
> tools::assertError(OutDegree(data.frame(source = 1L,
+                                         destination = 2L,
+                                         t = as.Date("2011-08-10")),
+                              root = 1,
+                              days = 90))
> 
> ##
> ## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in
> ## call to NetworkSummary
> ##
> tools::assertError(OutDegree(data.frame(source = 1L,
+                                         destination = 2L,
+                                         t = as.Date("2011-08-10")),
+                              root = 1,
+                              tEnd = "2005-10-31"))
> 
> ##
> ## Missing parameters in call to Trace
> ##
> tools::assertError(Trace())
> 
> ##
> ## Missing parameters in call to Trace
> ##
> tools::assertError(Trace(movement = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10")),
+                          tEnd = "2005-10-31",
+                          days = 90))
> 
> ##
> ## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in
> ## call to Trace
> ##
> tools::assertError(Trace(movement = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10")),
+                          root = 1,
+                          days = 90))
> ##
> ## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in
> ## call to Trace
> ##
> tools::assertError(Trace(movement = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10")),
+                          root = 1,
+                          tEnd = "2005-10-31"))
> 
> ##
> ## movements must be a data.frame
> ##
> tools::assertError(Trace(movements = 1:3,
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## movements must contain the columns source, destination and t
> ##
> tools::assertError(Trace(movements = data.frame(destination = 1, t = 1),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## movements must contain the columns source, destination and t
> ##
> tools::assertError(Trace(movements = data.frame(source = 1, t = 1),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## movements must contain the columns source, destination and t
> ##
> tools::assertError(Trace(movements = data.frame(source = 1, destination = 1),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## invalid class of column t in movements
> ##
> tools::assertError(Trace(movements = data.frame(source = 1L,
+                                                 destination = 2L,
+                                                 t = 1),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## source in movements contains NA
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = c(1L, NA),
+                              destination = c(2L, 3L),
+                              t = c("2011-08-10", "2011-08-10")),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## destination in movements contains NA
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = c(1L, 2L),
+                              destination = c(2L, NA),
+                              t = c("2011-08-10", "2011-08-10")),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## t in movements contains NA
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = c(1L, 2L),
+                              destination = c(2L, 3L),
+                              t = c("2011-08-10", NA)),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## t in movements contains NA
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = c(1L, 2L),
+                              destination = c(2L, 3L),
+                              t = c("2011-08-10", NA)),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## invalid class of column n in movements
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10"),
+                              n = "3"),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## invalid class of column id in movements
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10"),
+                              n = 3L,
+                              id = 4),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## invalid class of column category in movements
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10"),
+                              n = 3L,
+                              id = 4L,
+                              category = 3),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## 'root' must be an integer or character
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10")),
+                          root = 1.1,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## 'inBegin' must be a Date vector
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10")),
+                          root = 1L,
+                          inBegin = 2011,
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## 'inEnd' must be a Date vector
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10")),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = 2011,
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## 'outBegin' must be a Date vector
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10")),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = 2011,
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## 'outEnd' must be a Date vector
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10")),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = 2011))
> 
> ##
> ## inEnd less than inBegin
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10")),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-07-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-08-10")))
> 
> ##
> ## outEnd less than outBegin
> ##
> tools::assertError(Trace(movements = data.frame(
+                              source = 1L,
+                              destination = 2L,
+                              t = as.Date("2011-08-10")),
+                          root = 1L,
+                          inBegin = as.Date("2011-08-10"),
+                          inEnd = as.Date("2011-08-10"),
+                          outBegin = as.Date("2011-08-10"),
+                          outEnd = as.Date("2011-07-10")))
> 
> proc.time()
   user  system elapsed 
   0.23    0.10    0.32