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 at 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 at 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 at 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 at 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 at 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 at 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.
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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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.
Because the dates might not be consecutive. Or in ISO format. On May 22, 2020 7:38:17 PM PDT, Jim Lemon <drjimlemon at gmail.com> wrote:>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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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.-- Sent from my phone. Please excuse my brevity.