[R] How to use R0 package?

Olivier Crouzet o||v|er@crouzet @end|ng |rom un|v-n@nte@@|r
Fri May 22 15:03:14 CEST 2020 

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.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
> >
> 
> 
> -- 
> 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.


-- 
  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

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