Hi,
you should be able to convert your date variables to integers (usually
viewed as the elapse between 1970/01/01 and today) by using date
conversion to integers:
TODAY="2020-05-22"
as.Date(TODAY)
[1] "2020-05-22"
> as.integer(as.Date(TODAY))
[1] 18404
Doing the same with your reference dates should do the job.
Yours.
Olivier.
On Fri, 22 May 2020
14:31:48 +0200 Luigi Marongiu <marongiu.lu...@gmail.com> wrote:
> In theory, it works
> ```
> > R0 = estimate.R(x1, t=d1, GT=mGT, begin=1, end=117,
> methods="EG",pop.size=pop, nsim=N)
> >R0
> Reproduction number estimate using Exponential Growth method.
> R : 0.7425278[ 0.7409297 , 0.7441229 ]
> ```
> but I am not happy because 1. I have to use numbers instead of
> variables and 2. numbers instead of dates (which are instead reported
> in the examples...).
> Even if I force to an integer, I still get an error:
> ```
> > R0 = estimate.R(x1, t=d1, GT=mGT, begin=1, end=length(x1),
> + methods="EG",pop.size=pop, nsim=N)
> Error in integrity.checks(epid, t, GT, begin, end, date.first.obs,
> time.step, :
> If both 'begin'= 1 and 'end'= 117 are provided, they must be of
> the same class (dates, character strings or integers).
> > int
> Error: object 'int' not found
> > R0 = estimate.R(x1, t=d1, GT=mGT, begin=1,
> > end=as.integer(length(x1)),
> + methods="EG",pop.size=pop, nsim=N)
> Error in integrity.checks(epid, t, GT, begin, end, date.first.obs,
> time.step, :
> If both 'begin'= 1 and 'end'= 117 are provided, they must be of
> the same class (dates, character strings or integers).
> ```
>
>
>
> On Fri, May 22, 2020 at 1:51 PM Eric Berger <ericjber...@gmail.com>
> wrote:
>
> > Hi Luigi,
> > how about begin=1L (to force it to be integer).
> > Also please keep the correspondence on the help list.
> >
> > Best,
> > Eric
> >
> > On Fri, May 22, 2020 at 2:40 PM Luigi Marongiu
> > <marongiu.lu...@gmail.com> wrote:
> > >
> > > Same error:
> > > ```
> > > > R0 = estimate.R(x1, t=d1, GT=mGT, begin=1, end=length(x1),
> > > methods="EG",pop.size=pop, nsim=N)
> > > Error in integrity.checks(epid, t, GT, begin, end,
> > > date.first.obs,
> > time.step, :
> > > If both 'begin'= 1 and 'end'= 117 are provided, they must be
> > > of the
> > same class (dates, character strings or integers).
> > > > str(length(x1))
> > > int 117
> > > ```
> > >
> > >
> > > On Fri, May 22, 2020 at 12:35 PM Eric Berger
> > > <ericjber...@gmail.com>
> > wrote:
> > >>
> > >> Hi Luigi,
> > >> I am not familiar with the R0 package but I took a quick look.
> > >> The example in the documentation sets begin and end to integers.
> > >> Try setting begin = 1, end = 121 and see if that works.
> > >>
> > >> HTH,
> > >> Eric
> > >>
> > >> On Fri, May 22, 2020 at 1:17 PM Luigi Marongiu <
> > marongiu.lu...@gmail.com> wrote:
> > >> >
> > >> > Hello,
> > >> > I am trying ot get the R0 from the incidence data from China
> > >> > for the COVID-19. I set the following:
> > >> > ```
> > >> > library("R0")
> > >> > x1 <- c(259, 457, 688, 769, 1771, 1459, 1737, 1981,
> > >> > 2099,
> > 2589,
> > >> > 2825, 3235, 3884, 3694, 3143,
> > >> > 3385, 2652, 2973, 2467, 2015, 14108, 5090,
> > >> > 2641, 2008, 2048, 1888, 1749, 391, 889, 823,
> > >> > 648, 214, 508, 406, 433, 327, 427,
> > >> > 573, 202,
> > 125,
> > >> > 119, 139, 143, 99, 44,
> > >> > 40, 19, 24, 15, 8, 11, 20,
> > >> > 0, 16,
> > 13,
> > >> > 13, 34, 39, 46, 39,
> > >> > 78, 47, 67, 55, 54, 45, 0,
> > >> > 79, 36,
> > 35,
> > >> > 31, 19, 30, 39, 32,
> > >> > 0, 63, 42, 46, 99, 108, 89, 46,
> > >> > 46,
> > 26,
> > >> > 325, 27, 16, 12, 11,
> > >> > 30, 10, 6, 12, 11, 3, 6,
> > >> > 22, 4,
> > 12,
> > >> > 1, 3, 3, 1, 2,
> > >> > 2, 1, 1, 14, 17, 1, 7,
> > >> > 3, 4,
> > 8,
> > >> > 6, 7)
> > >> > d1 = c("2020-01-23", "2020-01-24", "2020-01-25", "2020-01-26",
> > >> > "2020-01-27", "2020-01-28", "2020-01-29",
> > >> > "2020-01-30", "2020-01-31", "2020-02-01", "2020-02-02",
> > >> > "2020-02-03", "2020-02-04", "2020-02-05",
> > >> > "2020-02-06", "2020-02-07", "2020-02-08", "2020-02-09",
> > >> > "2020-02-10", "2020-02-11", "2020-02-12",
> > >> > "2020-02-13", "2020-02-14", "2020-02-15", "2020-02-16",
> > >> > "2020-02-17", "2020-02-18", "2020-02-19",
> > >> > "2020-02-20", "2020-02-21", "2020-02-22", "2020-02-23",
> > >> > "2020-02-24", "2020-02-25", "2020-02-26",
> > >> > "2020-02-27", "2020-02-28", "2020-02-29", "2020-03-01",
> > >> > "2020-03-02", "2020-03-03", "2020-03-04",
> > >> > "2020-03-05", "2020-03-06", "2020-03-07", "2020-03-08",
> > >> > "2020-03-09", "2020-03-10", "2020-03-11",
> > >> > "2020-03-12", "2020-03-13", "2020-03-14", "2020-03-15",
> > >> > "2020-03-16", "2020-03-17", "2020-03-18",
> > >> > "2020-03-19", "2020-03-20", "2020-03-21", "2020-03-22",
> > >> > "2020-03-23", "2020-03-24", "2020-03-25",
> > >> > "2020-03-26", "2020-03-27", "2020-03-28", "2020-03-29",
> > >> > "2020-03-30", "2020-03-31", "2020-04-01",
> > >> > "2020-04-02", "2020-04-03", "2020-04-04", "2020-04-05",
> > >> > "2020-04-06", "2020-04-07", "2020-04-08",
> > >> > "2020-04-09", "2020-04-10", "2020-04-11", "2020-04-12",
> > >> > "2020-04-13", "2020-04-14", "2020-04-15",
> > >> > "2020-04-16", "2020-04-17", "2020-04-18", "2020-04-19",
> > >> > "2020-04-20", "2020-04-21", "2020-04-22",
> > >> > "2020-04-23", "2020-04-24", "2020-04-25", "2020-04-26",
> > "2020-04-27"
> > >> > ,"2020-04-28", "2020-04-29",
> > >> > "2020-04-30", "2020-05-01", "2020-05-02", "2020-05-03",
> > >> > "2020-05-04", "2020-05-05", "2020-05-06",
> > >> > "2020-05-07", "2020-05-08", "2020-05-09", "2020-05-10",
> > >> > "2020-05-11", "2020-05-12", "2020-05-13",
> > >> > "2020-05-14", "2020-05-15", "2020-05-16", "2020-05-17",
> > "2020-05-18")
> > >> > names(x1) <- d1
> > >> > pop = 1438443864
> > >> > Ts_mean = 5.16
> > >> > Ts_sd = 1.49
> > >> > N=10000
> > >> > TODAY = Sys.Date()
> > >> > mGT = generation.time("gamma", c(Ts_mean, Ts_sd))
> > >> > R0 = estimate.R(x1, t=d1, GT=mGT, begin=as.Date(d1[1]),
> > >> > end=TODAY, methods="EG",pop.size=pop, nsim=N)
> > >> > ```
> > >> > but when I run I get:
> > >> > ```
> > >> > Error in if (end.nb <= begin.nb) stop("'begin' and 'end' are
> > >> > not consistent.") :
> > >> > argument is of length zero
> > >> > > as.Date(d1[1])
> > >> > [1] "2020-01-23"
> > >> > > TODAY
> > >> > [1] "2020-05-22"
> > >> > > str(TODAY)
> > >> > Date[1:1], format: "2020-05-22"
> > >> > > str(as.Date(d1[1]))
> > >> > Date[1:1], format: "2020-01-23"
> > >> > ```
> > >> > Since I provided both start and end in the same format, I don't
> > understand
> > >> > the error.
> > >> > Any tips?
> > >> > Thank you
> > >> > --
> > >> > Best regards,
> > >> > Luigi
> > >> >
> > >> > [[alternative HTML version deleted]]
> > >> >
> > >> > ______________________________________________
> > >> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more,
> > >> > see https://stat.ethz.ch/mailman/listinfo/r-help
> > >> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > >> > and provide commented, minimal, self-contained, reproducible
> > >> > code.
> > >
> > >
> > >
> > > --
> > > Best regards,
> > > Luigi
> >
>
>
> --
> Best regards,
> Luigi
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html and provide commented,
> minimal, self-contained, reproducible code.
--
Olivier Crouzet, PhD
http://olivier.ghostinthemachine.space
/Maître de Conférences/
@LLING - Laboratoire de Linguistique de Nantes
UMR6310 CNRS / Université de Nantes
/Guest Researcher/
@UMCG (University Medical Center Groningen)
ENT department
Rijksuniversiteit Groningen
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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