[R] How to use R0 package?
Jim Lemon
drj|m|emon @end|ng |rom gm@||@com
Sat May 23 04:38:17 CEST 2020
So what if you treat a nuisance as a feature and import your dates as
factors? as.numeric(dates) would have the correct structure or am I,
as usual, missing something?
Jim
On Sat, May 23, 2020 at 1:00 AM Jeff Newmiller <jdnewmil using dcn.davis.ca.us> wrote:
>
> This is getting off-topic here but R0 is a mathematical parameter unrelated to calendar dates. It arises when analyzing case counts (integers) as a function of the numerical measure of time since some non-trivial number of cases has occurred (conventionally this measure is in days)..
>
> dta$days <- as.numeric( dta$date - startdate, units="days" )
>
> On May 22, 2020 5:31:48 AM PDT, Luigi Marongiu <marongiu.luigi using 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 <ericjberger using 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.luigi using 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
> ><ericjberger using 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.luigi using 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 using 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
> >>
>
> --
> Sent from my phone. Please excuse my brevity.
>
> ______________________________________________
> R-help using 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
> and provide commented, minimal, self-contained, reproducible code.
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