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]]
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.
In theory, it works ```> R0 = estimate.R(x1, t=d1, GT=mGT, begin=1, end=117,methods="EG",pop.size=pop, nsim=N)>R0Reproduction 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).> intError: 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 >-- Best regards, Luigi [[alternative HTML version deleted]]
class(length(x1)) "integer" Your problem is thinking that begin=1 means you are passing begin as an integer. class(1) "numeric" class(1L) "integer" You should pass: begin=1L, end=length(x1) Best, Eric On Fri, May 22, 2020 at 3:31 PM 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 > > > > -- > Best regards, > Luigi
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 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 > > > > > -- > 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.-- Olivier Crouzet, PhD http://olivier.ghostinthemachine.space /Ma?tre de Conf?rences/ @LLING - Laboratoire de Linguistique de Nantes UMR6310 CNRS / Universit? de Nantes /Guest Researcher/ @UMCG (University Medical Center Groningen) ENT department Rijksuniversiteit Groningen
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.