EpiContactTrace
Epidemiological Tool for Contact Tracing

Package index
Search the EpiContactTrace package
Vignettes
Functions
53
Source code
22
Man pages
16
Home
/
CRAN
/
EpiContactTrace
/
tests/arguments.R

tests/arguments.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)

##
## 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")))

Try the EpiContactTrace package in your browser

Any scripts or data that you put into this service are public.

EpiContactTrace documentation built on April 3, 2023, 5:22 p.m.

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close