Re: [R] [External Email] Re: [External] Re: access for free more than 500 essential Springer Nature textbooks
They can be downladed. I saved two of them to my desktop as pdf earlier. Sent from Yahoo Mail on Android On Fri, May 22, 2020 at 10:35 PM, Mark Leeds wrote: Hi: I'm not sure about the other link that was sent because I didn't try it but, in the case of the link that I sent, you can obtain the pdfs of a lot of the books shown. On Sat, May 23, 2020 at 12:16 AM Christopher W. Ryan wrote: > Am I interpreting this offer correctly, that it is for libraries to > obtain access to the e-books for free? It does not seem to me that an > invididual can download one--am I missing that part? > > Thanks > > --Chris Ryan > > Mark Leeds wrote: > > Abby: here's an easier link for seeing what you might like. > > > > > https://link.springer.com/search?facet-content-type=%22Book%22=mat-covid19_textbooks&%23038;facet-language=%22En%22&%23038;sortOrder=newestFirst&%23038;showAll=true > > > > On Fri, May 22, 2020 at 9:18 PM Richard O'Keefe > wrote: > > > >> the real pleasure comes from things you weren't looking for but > recognise > >> as just what you needed. > >> > >> On Sat, 23 May 2020 at 12:34, Jeff Newmiller > >> wrote: > >> > >>> You are bound to be disappointed if you invert the purpose of the list. > >>> This is marketing... think of it as a sale... stores rarely put their > >>> entire stock on sale... particularly if the sale price is zero. You > have > >> to > >>> start with the list and look for interesting titles. > >>> > >>> But don't let me dissuade you from adding to your killfile if that > seems > >>> more useful to you. > >>> > >>> On May 22, 2020 5:04:29 PM PDT, Abby Spurdle > >> wrote: > > The Excel file is what you need. > > Well, now I'm in a bad mood. > > I went to all the trouble of opening the thing... > And the first two Springer-published books I look for, aren't there. > > (1) Programming with Data, John Chambers > (2) Applied Econometrics with R, Z and co. > > Next time someone tells me to use an Excel document, I'm adding them > to the spam list. > > __ > 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. > >>> > >>> -- > >>> Sent from my phone. Please excuse my brevity. > >>> > >>> __ > >>> 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. > >>> > >> > >> [[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. > >> > > > > [[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. > > > [[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. Hi: I'm not sure about the other link that was sent because I didn't try it but, in the case of the link that I sent, you can obtain the pdfs of a lot of the books shown. On Sat, May 23, 2020 at 12:16 AM Christopher W. Ryan wrote: > Am I interpreting this offer correctly, that it is for libraries to > obtain access to the e-books for free? It does not seem to me that an > invididual can download one--am I missing that part? > > Thanks > > --Chris Ryan > > Mark Leeds wrote: > > Abby: here's an easier link for seeing what you might like. > > > > > https://link.springer.com/search?facet-content-type=%22Book%22=mat-covid19_textbooks&%23038;facet-language=%22En%22&%23038;sortOrder=newestFirst&%23038;showAll=true > > > > On Fri, May 22, 2020 at 9:18 PM Richard O'Keefe > wrote: > > > >> the real pleasure comes from things you weren't looking for but > recognise > >> as just what you needed. > >> > >> On Sat, 23 May 2020 at 12:34, Jeff Newmiller > >> wrote: > >> > >>> You are bound to be disappointed if you invert the
Re: [R] [External Email] Re: [External] Re: access for free more than 500 essential Springer Nature textbooks
Hi: I'm not sure about the other link that was sent because I didn't try it but, in the case of the link that I sent, you can obtain the pdfs of a lot of the books shown. On Sat, May 23, 2020 at 12:16 AM Christopher W. Ryan wrote: > Am I interpreting this offer correctly, that it is for libraries to > obtain access to the e-books for free? It does not seem to me that an > invididual can download one--am I missing that part? > > Thanks > > --Chris Ryan > > Mark Leeds wrote: > > Abby: here's an easier link for seeing what you might like. > > > > > https://link.springer.com/search?facet-content-type=%22Book%22=mat-covid19_textbooks&%23038;facet-language=%22En%22&%23038;sortOrder=newestFirst&%23038;showAll=true > > > > On Fri, May 22, 2020 at 9:18 PM Richard O'Keefe > wrote: > > > >> the real pleasure comes from things you weren't looking for but > recognise > >> as just what you needed. > >> > >> On Sat, 23 May 2020 at 12:34, Jeff Newmiller > >> wrote: > >> > >>> You are bound to be disappointed if you invert the purpose of the list. > >>> This is marketing... think of it as a sale... stores rarely put their > >>> entire stock on sale... particularly if the sale price is zero. You > have > >> to > >>> start with the list and look for interesting titles. > >>> > >>> But don't let me dissuade you from adding to your killfile if that > seems > >>> more useful to you. > >>> > >>> On May 22, 2020 5:04:29 PM PDT, Abby Spurdle > >> wrote: > > The Excel file is what you need. > > Well, now I'm in a bad mood. > > I went to all the trouble of opening the thing... > And the first two Springer-published books I look for, aren't there. > > (1) Programming with Data, John Chambers > (2) Applied Econometrics with R, Z and co. > > Next time someone tells me to use an Excel document, I'm adding them > to the spam list. > > __ > 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. > >>> > >>> -- > >>> Sent from my phone. Please excuse my brevity. > >>> > >>> __ > >>> 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. > >>> > >> > >> [[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. > >> > > > > [[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. > > > [[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.
Re: [R] [External Email] Re: [External] Re: access for free more than 500 essential Springer Nature textbooks
Am I interpreting this offer correctly, that it is for libraries to obtain access to the e-books for free? It does not seem to me that an invididual can download one--am I missing that part? Thanks --Chris Ryan Mark Leeds wrote: > Abby: here's an easier link for seeing what you might like. > > https://link.springer.com/search?facet-content-type=%22Book%22=mat-covid19_textbooks&%23038;facet-language=%22En%22&%23038;sortOrder=newestFirst&%23038;showAll=true > > On Fri, May 22, 2020 at 9:18 PM Richard O'Keefe wrote: > >> the real pleasure comes from things you weren't looking for but recognise >> as just what you needed. >> >> On Sat, 23 May 2020 at 12:34, Jeff Newmiller >> wrote: >> >>> You are bound to be disappointed if you invert the purpose of the list. >>> This is marketing... think of it as a sale... stores rarely put their >>> entire stock on sale... particularly if the sale price is zero. You have >> to >>> start with the list and look for interesting titles. >>> >>> But don't let me dissuade you from adding to your killfile if that seems >>> more useful to you. >>> >>> On May 22, 2020 5:04:29 PM PDT, Abby Spurdle >> wrote: > The Excel file is what you need. Well, now I'm in a bad mood. I went to all the trouble of opening the thing... And the first two Springer-published books I look for, aren't there. (1) Programming with Data, John Chambers (2) Applied Econometrics with R, Z and co. Next time someone tells me to use an Excel document, I'm adding them to the spam list. __ 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. >>> >>> -- >>> Sent from my phone. Please excuse my brevity. >>> >>> __ >>> 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. >>> >> >> [[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. >> > > [[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. > __ 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.
Re: [R] How to use R0 package?
Because the dates might not be consecutive. Or in ISO format.
On May 22, 2020 7:38:17 PM PDT, Jim Lemon 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
> 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
> 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
>> >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
>> >
>> >> 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
>> >
>> >> 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",
Re: [R] How to use R0 package?
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 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
> 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
> >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
> >
> >> 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
> >
> >> 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",
Re: [R] [External] Re: access for free more than 500 essential Springer Nature textbooks
Abby: here's an easier link for seeing what you might like. https://link.springer.com/search?facet-content-type=%22Book%22=mat-covid19_textbooks&%23038;facet-language=%22En%22&%23038;sortOrder=newestFirst&%23038;showAll=true On Fri, May 22, 2020 at 9:18 PM Richard O'Keefe wrote: > the real pleasure comes from things you weren't looking for but recognise > as just what you needed. > > On Sat, 23 May 2020 at 12:34, Jeff Newmiller > wrote: > > > You are bound to be disappointed if you invert the purpose of the list. > > This is marketing... think of it as a sale... stores rarely put their > > entire stock on sale... particularly if the sale price is zero. You have > to > > start with the list and look for interesting titles. > > > > But don't let me dissuade you from adding to your killfile if that seems > > more useful to you. > > > > On May 22, 2020 5:04:29 PM PDT, Abby Spurdle > wrote: > > >> The Excel file is what you need. > > > > > >Well, now I'm in a bad mood. > > > > > >I went to all the trouble of opening the thing... > > >And the first two Springer-published books I look for, aren't there. > > > > > >(1) Programming with Data, John Chambers > > >(2) Applied Econometrics with R, Z and co. > > > > > >Next time someone tells me to use an Excel document, I'm adding them > > >to the spam list. > > > > > >__ > > >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. > > > > -- > > Sent from my phone. Please excuse my brevity. > > > > __ > > 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. > > > > [[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. > [[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.
Re: [R] [External] Re: access for free more than 500 essential Springer Nature textbooks
the real pleasure comes from things you weren't looking for but recognise as just what you needed. On Sat, 23 May 2020 at 12:34, Jeff Newmiller wrote: > You are bound to be disappointed if you invert the purpose of the list. > This is marketing... think of it as a sale... stores rarely put their > entire stock on sale... particularly if the sale price is zero. You have to > start with the list and look for interesting titles. > > But don't let me dissuade you from adding to your killfile if that seems > more useful to you. > > On May 22, 2020 5:04:29 PM PDT, Abby Spurdle wrote: > >> The Excel file is what you need. > > > >Well, now I'm in a bad mood. > > > >I went to all the trouble of opening the thing... > >And the first two Springer-published books I look for, aren't there. > > > >(1) Programming with Data, John Chambers > >(2) Applied Econometrics with R, Z and co. > > > >Next time someone tells me to use an Excel document, I'm adding them > >to the spam list. > > > >__ > >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. > > -- > Sent from my phone. Please excuse my brevity. > > __ > 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. > [[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.
Re: [R] [External] Re: access for free more than 500 essential Springer Nature textbooks
You are bound to be disappointed if you invert the purpose of the list. This is marketing... think of it as a sale... stores rarely put their entire stock on sale... particularly if the sale price is zero. You have to start with the list and look for interesting titles. But don't let me dissuade you from adding to your killfile if that seems more useful to you. On May 22, 2020 5:04:29 PM PDT, Abby Spurdle wrote: >> The Excel file is what you need. > >Well, now I'm in a bad mood. > >I went to all the trouble of opening the thing... >And the first two Springer-published books I look for, aren't there. > >(1) Programming with Data, John Chambers >(2) Applied Econometrics with R, Z and co. > >Next time someone tells me to use an Excel document, I'm adding them >to the spam list. > >__ >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. -- Sent from my phone. Please excuse my brevity. __ 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.
Re: [R] [External] Re: access for free more than 500 essential Springer Nature textbooks
> The Excel file is what you need. Well, now I'm in a bad mood. I went to all the trouble of opening the thing... And the first two Springer-published books I look for, aren't there. (1) Programming with Data, John Chambers (2) Applied Econometrics with R, Z and co. Next time someone tells me to use an Excel document, I'm adding them to the spam list. __ 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.
Re: [R] how to show percentage of individuals for two groups on histogram?
Hi Ana,
I think this is what you want in the panel style of plot. Let me know
if not, or if I have calculated the wrong percentages. The overlaid
histograms definitely use a different calculation.
amsdf<-read.table("pheno_m1_plot",header=TRUE,stringsAsFactors=FALSE)
dim(amsdf)
# find the right breaks for your "cut"
casen<-table(cut(amsdf$HBA1C[amsdf$pheno==2],breaks=3:14))
controln<-table(cut(amsdf$HBA1C[amsdf$pheno==1],breaks=3:14))
# save yourself some typing
HBA1C2<-amsdf$HBA1C[amsdf$pheno==2]
HBA1C1<-amsdf$HBA1C[amsdf$pheno==1]
ncases<-length(HBA1C2)
ncontrols<-length(HBA1C1)
split.screen(matrix(c(0,1,0.6,1,0,1,0,0.6),nrow=2,byrow=TRUE))
par(mar=c(0,4,1,2))
barpos=barplot(100*casen/ncases,names.arg=NA,col="orange",
space=0,ylab="Percentage",xaxt="n",ylim=c(0,27))
case_text<-sprintf(
"Cases: n=%d, nulls=%d, median=%.1f, mean=%.1f, sd=%.1f",
length(HBA1C2),sum(is.na(HBA1C2)),round(median(HBA1C2,na.rm=TRUE),1),
round(mean(HBA1C2,na.rm=TRUE),1),round(sd(HBA1C2,na.rm=TRUE),1))
text(mean(barpos),25,case_text)
box()
screen(2)
par(mar=c(4,4,0,2))
barplot(100*controln/ncontrols,names.arg=NA,
space=0,ylab="Percentage",col="orange",ylim=c(0,34))
control_text<-sprintf(
"Cases: n=%d, nulls=%d, median=%.1f, mean=%.1f, sd=%.1f",
length(HBA1C1),sum(is.na(HBA1C1)),round(median(HBA1C1,na.rm=TRUE),1),
round(mean(HBA1C1,na.rm=TRUE),1),round(sd(HBA1C1,na.rm=TRUE),1))
text(mean(barpos),32,control_text)
box()
library(plotrix)
staxlab(1,at=barpos,labels=names(casen))
Jim
On Sat, May 23, 2020 at 9:01 AM Ana Marija wrote:
>
> Hi Jim,
>
> My data is attached. It is most kind of you for looking into this!
>
> Cheers,
> Ana
>
> On Fri, May 22, 2020 at 5:49 PM Jim Lemon wrote:
> >
> > Hi Ana,
> > As I had very little idea what your data looked like, what I made up
> > obviously didn't fit in the plot that well. If you can send the data I
> > can make a better attempt. The other thing is whether you want a plot
> > with two adjacent panels (what I sent) or overlaid histograms (what
> > Eric sent). Let me know.
> >
> > Jim
> >
> > On Sat, May 23, 2020 at 12:45 AM Ana Marija
> > wrote:
> > >
> > > HI Jim,
> > >
> > > Thank you so much for getting back to me I tried your codes and I got
> > > this in attach,
> > > I think the issue is in calculating percentage per groups (cases or
> > > controls)
> > > ...
> > > I can send you the whole dataset if you would like to try with it
> > > On Thu, May 21, 2020 at 11:14 PM Jim Lemon wrote:
__
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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.
Re: [R] [External] Re: access for free more than 500 essential Springer Nature textbooks
On Fri, 22 May 2020 at 21:15, Richard M. Heiberger wrote: > The Excel file is what you need. > As Fabio remarked, the downloadable links are in column R > > I normally read (and write) Excel files into R using library(openxlsx) > There are also several other packages on CRAN for reading and writing > Excel. > > I opened the .xlxs file in LibreOffice Calc. I pasted the links in column S into my browser and was offered a download in pdf and /or epub. This worked very well. Apologies for the double posting John C Frain 3 Aranleigh Park Rathfarnham Dublin 14 Ireland www.tcd.ie/Economics/staff/frainj/home.html mailto:fra...@tcd.ie mailto:fra...@gmail.com > > [[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.
Re: [R] [External] Re: access for free more than 500 essential Springer Nature textbooks
The Excel file is what you need. As Fabio remarked, the downloadable links are in column R I normally read (and write) Excel files into R using library(openxlsx) There are also several other packages on CRAN for reading and writing Excel. MARC stands for MAchine-Readable Cataloging. Information is at the Library of Congress https://www.loc.gov/marc/faq.html Rich On Fri, May 22, 2020 at 2:24 PM Abby Spurdle wrote: > > That sounds like progress. > > However, I was unable to use their website. > All I can find is Excel documents (which I can't open) and MARC (?), > which I don't have time to look into. > > Your post might have more value, if you provide a list of the titles > (or a link to a list, in an easy to read open access format), ideally > with a note on where to find open access copies of those texts, > without spending a long time searching. > > On Sat, May 23, 2020 at 4:29 AM Richard M. Heiberger wrote: > > > > Springer has just made available free access to many books through July. > > This is part of their global program to support educators, students > > and academics > > affected by coronavirus lockdown. > > > > Their list includes about 20 statistics books in English and 2 in > > German. Several, including mine, have R in the title or subtitle. > > > > This link describes the program: > > https://www.springernature.com/gp/librarians/news-events/all-news-articles/industry-news-initiatives/free-access-to-textbooks-for-institutions-affected-by-coronaviru/17855960?sap-outbound-id=07923935E132AFCC90201BAEA7D6755EC6C597DE_source=hybris-campaign_medium=email_campaign=000_BARZ01_001531_AEXS_AWA_CB02_GL_txt_covid_content=EN_internal_5917_20200522=42010A0550671EDA9BA73AC34F576EF6 > > > > My book is > > Statistical Analysis and Data Display, Richard M. Heiberger, Burt > > Holland, 2nd ed. 2015 > > It is supported by the HH package available from CRAN. > > > > Rich > > > > __ > > 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. __ 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.
Re: [R] How to only show two numbers on bar_plot with ggplot
Hello,
Why not remove aes(x = ESRD,...) from the call to geom_bar and instead do
ed <- ggplot(e, aes(x = factor(ESRD)) + etc?
If you are using an aesthetic throughout the plot, put it in the call to
ggplot().
Hope this helps,
Rui Barradas
Às 20:22 de 22/05/20, Ana Marija escreveu:
I resolved it not elegantly with:
d=as.numeric(as.character(e$pheno))
ed<-ggplot(e) +
geom_bar(aes(x = ESRD, fill =
factor(pheno,labels=c("control","case"+scale_fill_manual(values=c("#56B4E9","#E7B800"))+labs(fill="pheno")+scale_x_continuous(breaks
= unique(d))
ed
where:
head(e)
ESRD pheno
11 1
21 1
31 2
41 1
51 1
sapply(e,class)
ESRD pheno
"integer" "factor"
On Fri, May 22, 2020 at 1:52 PM Ana Marija wrote:
Hello,
I made the plot in attach via:
ed<-ggplot(e) +
geom_bar(aes(x = ESRD, fill =
factor(pheno,labels=c("control","case"+scale_fill_manual(values=c("#56B4E9","#E7B800"))+labs(fill="pheno")
ed
How do I show only 1 and 2 on x axis?
Thanks
Ana
__
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and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to only show two numbers on bar_plot with ggplot
I resolved it not elegantly with:
d=as.numeric(as.character(e$pheno))
ed<-ggplot(e) +
geom_bar(aes(x = ESRD, fill =
factor(pheno,labels=c("control","case"+scale_fill_manual(values=c("#56B4E9","#E7B800"))+labs(fill="pheno")+scale_x_continuous(breaks
= unique(d))
ed
where:
> head(e)
ESRD pheno
11 1
21 1
31 2
41 1
51 1
> sapply(e,class)
ESRD pheno
"integer" "factor"
On Fri, May 22, 2020 at 1:52 PM Ana Marija wrote:
>
> Hello,
>
> I made the plot in attach via:
>
> ed<-ggplot(e) +
> geom_bar(aes(x = ESRD, fill =
> factor(pheno,labels=c("control","case"+scale_fill_manual(values=c("#56B4E9","#E7B800"))+labs(fill="pheno")
>
> ed
>
> How do I show only 1 and 2 on x axis?
>
> Thanks
> Ana
__
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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.
[R] How to only show two numbers on bar_plot with ggplot
Hello,
I made the plot in attach via:
ed<-ggplot(e) +
geom_bar(aes(x = ESRD, fill =
factor(pheno,labels=c("control","case"+scale_fill_manual(values=c("#56B4E9","#E7B800"))+labs(fill="pheno")
ed
How do I show only 1 and 2 on x axis?
Thanks
Ana
__
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.
Re: [R] access for free more than 500 essential Springer Nature textbooks
That sounds like progress. However, I was unable to use their website. All I can find is Excel documents (which I can't open) and MARC (?), which I don't have time to look into. Your post might have more value, if you provide a list of the titles (or a link to a list, in an easy to read open access format), ideally with a note on where to find open access copies of those texts, without spending a long time searching. On Sat, May 23, 2020 at 4:29 AM Richard M. Heiberger wrote: > > Springer has just made available free access to many books through July. > This is part of their global program to support educators, students > and academics > affected by coronavirus lockdown. > > Their list includes about 20 statistics books in English and 2 in > German. Several, including mine, have R in the title or subtitle. > > This link describes the program: > https://www.springernature.com/gp/librarians/news-events/all-news-articles/industry-news-initiatives/free-access-to-textbooks-for-institutions-affected-by-coronaviru/17855960?sap-outbound-id=07923935E132AFCC90201BAEA7D6755EC6C597DE_source=hybris-campaign_medium=email_campaign=000_BARZ01_001531_AEXS_AWA_CB02_GL_txt_covid_content=EN_internal_5917_20200522=42010A0550671EDA9BA73AC34F576EF6 > > My book is > Statistical Analysis and Data Display, Richard M. Heiberger, Burt > Holland, 2nd ed. 2015 > It is supported by the HH package available from CRAN. > > Rich > > __ > 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. __ 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.
[R] access for free more than 500 essential Springer Nature textbooks
Springer has just made available free access to many books through July. This is part of their global program to support educators, students and academics affected by coronavirus lockdown. Their list includes about 20 statistics books in English and 2 in German. Several, including mine, have R in the title or subtitle. This link describes the program: https://www.springernature.com/gp/librarians/news-events/all-news-articles/industry-news-initiatives/free-access-to-textbooks-for-institutions-affected-by-coronaviru/17855960?sap-outbound-id=07923935E132AFCC90201BAEA7D6755EC6C597DE_source=hybris-campaign_medium=email_campaign=000_BARZ01_001531_AEXS_AWA_CB02_GL_txt_covid_content=EN_internal_5917_20200522=42010A0550671EDA9BA73AC34F576EF6 My book is Statistical Analysis and Data Display, Richard M. Heiberger, Burt Holland, 2nd ed. 2015 It is supported by the HH package available from CRAN. Rich __ 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.
Re: [R] How to use R0 package?
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 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
>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
>
>> 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
>
>> 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",
Re: [R] how to show percentage of individuals for two groups on histogram?
Hi Eric,
Thank you for getting back to me, I tried those solutions but they
don't do percentage per groups, so if I do
ggplot(data=subset(a, !is.na(pheno)), aes(x=HBA1C, fill=pheno)) +
geom_histogram(aes(y =
stat(density)), binwidth = 0.5) +
scale_y_continuous(labels = scales::percent_format())
I am getting the plot in attach, while my results should be more in
this range like on the plot here:
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/variable.cgi?study_id=phs18.v2.p1=19980=154=2864=62=1==1
On Fri, May 22, 2020 at 12:18 AM Eric Berger wrote:
>
> Hi Ana,
> This is a very common question about ggplot.
> A quick search turns up lots of hits that answer your question. Here
> are a couple
> https://community.rstudio.com/t/trouble-scaling-y-axis-to-percentages-from-counts/42999
> https://stackoverflow.com/questions/3695497/show-instead-of-counts-in-charts-of-categorical-variables
>
> From reading those discussions, the following should work (untested)
>
> ggplot(a, aes(x = HBA1C, fill=pheno)) + geom_histogram(aes(y =
> stat(density)), binwidth = 0.5) +
> scale_y_continuous(labels = scales::percent_format())
>
> HTH,
> Eric
>
>
> On Fri, May 22, 2020 at 7:18 AM Jim Lemon wrote:
> >
> > Hi Ana,
> > Just noticed a typo from a hasty cut-paste. Two lines should read:
> >
> > casehist<-table(cut(aafd$HBAIC[aafd$pheno=="case"],breaks=0:15))
> > controlhist<-table(cut(aafd$HBAIC[aafd$pheno=="control"],breaks=0:15))
> >
> > Jim
> >
> > On Fri, May 22, 2020 at 2:08 PM Jim Lemon wrote:
> > >
> > > Hi Ana,
> > > My apologies for the pedestrian graphics, but it may help.
> > >
> > > # a bit of fake data
> > > aafd<-data.frame(FID=paste0("fam",1000:2739),
> > > IID=paste0("G",1000,2739),FLASER=rep(1,1740),
> > > PLASER=c(rep(1,892),rep(2,848)),
> > > DIABDUR=sample(10:50,1740,TRUE),
> > > HBAIC=rnorm(1740,mean=7.45,sd=2),ESRD=rep(1,1740),
> > > pheno=c(rep("control",892),rep("case",848)))
> > > par(mfrow=c(2,1))
> > > casepct<-table(cut(aafd$HBAIC[aafd$pheno=="case"],breaks=0:15))
> > > controlpct<-table(cut(aafd$HBAIC[aafd$pheno=="control"],breaks=0:15))
> > > par(mar=c(0,4,1,2))
> > > barpos=barplot(100*casehist,names.arg=names(casepct),col="orange",
> > > space=0,ylab="Percentage",xaxt="n",ylim=c(0,25))
> > > text(mean(barpos),23,
> > > "Cases: n=848, nulls=26, median=7.3, mean=7.45, sd=1.96")
> > > box()
> > > par(mar=c(3,4,0,2))
> > > barplot(100*controlhist,names.arg=names(controlpct),
> > > space=0,ylab="Percentage",col="orange",ylim=c(0,25))
> > > text(mean(barpos),23,
> > > "Controls: n=892, nulls=7, median=7.3, mean=7.45, sd=1.12")
> > > box()
> > >
> > > Jim
> > >
> > > On Fri, May 22, 2020 at 9:08 AM Ana Marija
> > > wrote:
> > > >
> > > > the result would basically look something like this on in attach or
> > > > the overlay of those two plots
> > > >
> > > >
> > > > On Thu, May 21, 2020 at 5:23 PM Ana Marija
> > > > wrote:
> > > > >
> > > > > Hello,
> > > > >
> > > > > I have a data frame like this:
> > > > > > head(a)
> > > > > FID IID FLASER PLASER DIABDUR HBA1C ESRD pheno
> > > > > 1 fam1000-03 G1000 1 1 38 10.21 control
> > > > > 2 fam1001-03 G1001 1 1 15 7.31 control
> > > > > 3 fam1003-03 G1003 1 2 17 7.01case
> > > > > 4 fam1005-03 G1005 1 1 36 7.71 control
> > > > > 5 fam1009-03 G1009 1 1 23 7.61 control
> > > > > 6 fam1052-03 G1052 1 1 32 7.31 control
> > > > >
> > > > > > dim(a)
> > > > > [1] 16988
> > > > >
> > > > > I am doing histogram plot via:
> > > > > ggplot(a, aes(x=HBA1C, fill=pheno)) + geom_histogram(binwidth=.5,
> > > > > position="dodge")
> > > > >
> > > > > there is 848 who have "case" in pheno column and 892 who have
> > > > > "control" in pheno column.
> > > > >
> > > > > I would like to have on y-axis shown percentage of individuals which
> > > > > have either "case" or "control" in pheno instead of count.
> > > > >
> > > > > Please advise,
> > > > > Ana
> > > > __
> > > > 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.
> >
> > __
> > 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.
__
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,
Re: [R] how to show percentage of individuals for two groups on histogram?
HI Jim,
Thank you so much for getting back to me I tried your codes and I got
this in attach,
I think the issue is in calculating percentage per groups (cases or controls)
par(mfrow=c(2,1))
casehist<-table(cut(a$HBA1C[a$pheno=="case"],breaks=0:15))
controlhist<-table(cut(a$HBA1C[a$pheno=="control"],breaks=0:15))
par(mar=c(0,4,1,2))
barpos=barplot(100*casehist,names.arg=names(casehist),col="orange",
space=0,ylab="Percentage",xaxt="n",ylim=c(0,25))
text(mean(barpos),23,
"Cases: n=848, nulls=26, median=7.3, mean=7.45, sd=1.96")
box()
par(mar=c(3,4,0,2))
barplot(100*controlhist,names.arg=names(controlhist),
space=0,ylab="Percentage",col="orange",ylim=c(0,25))
text(mean(barpos),23,
"Controls: n=892, nulls=7, median=7.3, mean=7.45, sd=1.12")
box()
I can send you the whole dataset if you would like to try with it
On Thu, May 21, 2020 at 11:14 PM Jim Lemon wrote:
>
> Hi Ana,
> Just noticed a typo from a hasty cut-paste. Two lines should read:
>
> casehist<-table(cut(aafd$HBAIC[aafd$pheno=="case"],breaks=0:15))
> controlhist<-table(cut(aafd$HBAIC[aafd$pheno=="control"],breaks=0:15))
>
> Jim
>
> On Fri, May 22, 2020 at 2:08 PM Jim Lemon wrote:
> >
> > Hi Ana,
> > My apologies for the pedestrian graphics, but it may help.
> >
> > # a bit of fake data
> > aafd<-data.frame(FID=paste0("fam",1000:2739),
> > IID=paste0("G",1000,2739),FLASER=rep(1,1740),
> > PLASER=c(rep(1,892),rep(2,848)),
> > DIABDUR=sample(10:50,1740,TRUE),
> > HBAIC=rnorm(1740,mean=7.45,sd=2),ESRD=rep(1,1740),
> > pheno=c(rep("control",892),rep("case",848)))
> > par(mfrow=c(2,1))
> > casepct<-table(cut(aafd$HBAIC[aafd$pheno=="case"],breaks=0:15))
> > controlpct<-table(cut(aafd$HBAIC[aafd$pheno=="control"],breaks=0:15))
> > par(mar=c(0,4,1,2))
> > barpos=barplot(100*casehist,names.arg=names(casepct),col="orange",
> > space=0,ylab="Percentage",xaxt="n",ylim=c(0,25))
> > text(mean(barpos),23,
> > "Cases: n=848, nulls=26, median=7.3, mean=7.45, sd=1.96")
> > box()
> > par(mar=c(3,4,0,2))
> > barplot(100*controlhist,names.arg=names(controlpct),
> > space=0,ylab="Percentage",col="orange",ylim=c(0,25))
> > text(mean(barpos),23,
> > "Controls: n=892, nulls=7, median=7.3, mean=7.45, sd=1.12")
> > box()
> >
> > Jim
> >
> > On Fri, May 22, 2020 at 9:08 AM Ana Marija
> > wrote:
> > >
> > > the result would basically look something like this on in attach or
> > > the overlay of those two plots
> > >
> > >
> > > On Thu, May 21, 2020 at 5:23 PM Ana Marija
> > > wrote:
> > > >
> > > > Hello,
> > > >
> > > > I have a data frame like this:
> > > > > head(a)
> > > > FID IID FLASER PLASER DIABDUR HBA1C ESRD pheno
> > > > 1 fam1000-03 G1000 1 1 38 10.21 control
> > > > 2 fam1001-03 G1001 1 1 15 7.31 control
> > > > 3 fam1003-03 G1003 1 2 17 7.01case
> > > > 4 fam1005-03 G1005 1 1 36 7.71 control
> > > > 5 fam1009-03 G1009 1 1 23 7.61 control
> > > > 6 fam1052-03 G1052 1 1 32 7.31 control
> > > >
> > > > > dim(a)
> > > > [1] 16988
> > > >
> > > > I am doing histogram plot via:
> > > > ggplot(a, aes(x=HBA1C, fill=pheno)) + geom_histogram(binwidth=.5,
> > > > position="dodge")
> > > >
> > > > there is 848 who have "case" in pheno column and 892 who have
> > > > "control" in pheno column.
> > > >
> > > > I would like to have on y-axis shown percentage of individuals which
> > > > have either "case" or "control" in pheno instead of count.
> > > >
> > > > Please advise,
> > > > Ana
> > > __
> > > 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.
__
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.
Re: [R] How to install R 4.0 on chromebook?
Hi, You appear to have installed Debian on a Chromebook, presumably to overcome the limitations otherwise present in Chrome OS. Since the questions you pose are specific to Debian, there is an R e-mail list focused on the use of R on Debian based computers: https://stat.ethz.ch/mailman/listinfo/r-sig-debian You should subscribe to that list and post your queries there to avail yourself of a focused audience, which may include folks that have installed a Debian based Linux distribution on a Chromebook. Regards, Marc Schwartz > On May 22, 2020, at 9:49 AM, Luigi Marongiu wrote: > > Hello, > I have tried to upgrade R to 4.0. I have added `deb > http://cloud.r-project.org/bin/linux/debian buster-cran40/` to > `/etc/apt/sources.list` > (but I removed cran35). Btu when I run `apt-get update; apt-get install > r-base r-base-dev` I get an error. I think it depends on r-base-core, since > it depends on these obsolete libraries: > ``` > $ sudo apt-get install r-base-core > Reading package lists... Done > Building dependency tree > Reading state information... Done > Some packages could not be installed. This may mean that you have > requested an impossible situation or if you are using the unstable > distribution that some required packages have not yet been created > or been moved out of Incoming. > The following information may help to resolve the situation: > > The following packages have unmet dependencies: > r-base-core : Depends: libc6 (>= 2.27) but 2.24-11+deb9u4 is to be > installed > Depends: libcurl4 (>= 7.28.0) but it is not installable > Depends: libgfortran5 (>= 8) but it is not installable > Depends: libicu63 (>= 63.1-1~) but it is not installable > Depends: libpcre2-8-0 (>= 10.32) but it is not going to be > installed > Recommends: r-recommended but it is not going to be installed > Recommends: r-base-dev but it is not going to be installed > Recommends: r-doc-html but it is not going to be installed > E: Unable to correct problems, you have held broken packages. > ``` > How can I upgrade these libraries on Chromebook? > Thank you > > -- > Best regards, > Luigi __ 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.
[R] How to install R 4.0 on chromebook?
Hello, I have tried to upgrade R to 4.0. I have added `deb http://cloud.r-project.org/bin/linux/debian buster-cran40/` to `/etc/apt/sources.list` (but I removed cran35). Btu when I run `apt-get update; apt-get install r-base r-base-dev` I get an error. I think it depends on r-base-core, since it depends on these obsolete libraries: ``` $ sudo apt-get install r-base-core Reading package lists... Done Building dependency tree Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: r-base-core : Depends: libc6 (>= 2.27) but 2.24-11+deb9u4 is to be installed Depends: libcurl4 (>= 7.28.0) but it is not installable Depends: libgfortran5 (>= 8) but it is not installable Depends: libicu63 (>= 63.1-1~) but it is not installable Depends: libpcre2-8-0 (>= 10.32) but it is not going to be installed Recommends: r-recommended but it is not going to be installed Recommends: r-base-dev but it is not going to be installed Recommends: r-doc-html but it is not going to be installed E: Unable to correct problems, you have held broken packages. ``` How can I upgrade these libraries on Chromebook? 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.
Re: [R] How to use R0 package?
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 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
> 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
> > 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
> > >
> > 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",
> > >> >
Re: [R] How to use R0 package?
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 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 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
>> 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 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
>> >> 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",
>> >> >
Re: [R] How to use R0 package?
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 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
> 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
> 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",
Re: [R] iterators : checkFunc with ireadLines
Hi Ivan,
Endeed, it is a good idea. I am under MSwindows but I can use the
bash command I use with git. I will see how to do that with the unix
command lines.
Le 20/05/2020 à 09:46, Ivan Krylov a écrit :
Hi Laurent,
I am not saying this will work every time and I do recognise that this
is very different from a more general solution that you had envisioned,
but if you are on an UNIX-like system or have the relevant utilities
installed and on the %PATH% on Windows, you can filter the input file
line-by-line using a pipe and an external program:
On Sun, 17 May 2020 15:52:30 +0200
Laurent Rhelp wrote:
# sensors to keep
sensors <- c("N053", "N163")
# filter on the beginning of the line
i <- pipe("grep -E '^(N053|N163)' test.txt")
# or:
# filter on the beginning of the given column
# (use $2 for the second column, etc.)
i <- pipe("awk '($1 ~ \"^(N053|N163)\")' test.txt")
# or:
# since your message is full of Unicode non-breaking spaces, I have to
# bring in heavier machinery to handle those correctly;
# only this solution manages to match full column values
# (here you can also use $F[1] for second column and so on)
i <- pipe("perl -CSD -F'\\s+' -lE \\
'print join qq{\\t}, @F if $F[0] =~ /^(N053|N163)$/' \\
test.txt
")
lines <- read.table(i) # closes i when done
The downside of this approach is having to shell-escape the command
lines, which can become complicated, and choosing between use of regular
expressions and more wordy programs (Unicode whitespace in the input
doesn't help, either).
--
L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel
antivirus Avast.
https://www.avast.com/antivirus
__
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.
Re: [R] How to use R0 package?
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 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=1
> 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.
__
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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.
[R] How to use R0 package?
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=1
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]]
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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.
Re: [R] Problem with checks on R/4.0.0
> Jeff Newmiller > on Thu, 21 May 2020 13:30:26 -0700 writes: > Do read the Posting Guide... you are on the wrong mailing list for this question. > On May 20, 2020 6:46:01 PM PDT, Simon Michnowicz via R-help wrote: >> Dear R Group, >> I can build a simple R/4.0.0 OK using gcc/8.1.0, but when I tried to >> link >> it with the Intel MKL, 'make check' produced this error >> >> tail tests/reg-tests-1d.Rout.fail >> >>> (m <- cbind(0, c(NA, 0), 0:-1)) >> [,1] [,2] [,3] >> [1,]0 NA0 >> [2,]00 -1 >>> nTypes <- eval(formals(base::norm)$type) # "O" "I" "F" "M" "2" >>> stopifnot(is.na( print(vapply(nTypes, norm, 0., x = m)) )) # print(): >> show NA *or* NaN >> O I F M 2 >> NA NA 1 NA NA >> Error: is.na(print(vapply(nTypes, norm, 0, x = m))) are not all TRUE >> Execution halted >> >> Is this a significant error? >> There may be differences in how NaN are treated between GNU and MKL >> that >> caused this. Yes, there are such differences. This one is indeed new bug in that version of Lapack which in the mean time has been fixed AFAIK... definitely has been fixed in R's builtin version of Lapack. Martin Maechler ETH Zurich and R Core Team >> regards >> >> >> *---Simon Michnowicz * >> Senior Application Specialist, High-Performance Computing >> >> *Research Support Services - eSolutions* >> *Monash eResearch Centre* >> Monash University >> 15 Innovation Walk, Building 75, Clayton Campus >> Wellington Road, VIC 3800 >> Australia >> >> T: +61 3 9902 0794 >> M: +61 3 0418 302 046 >> E: simon.michnow...@monash.edu >> monash.edu >> >> [[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. > -- > Sent from my phone. Please excuse my brevity. > __ > 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. __ 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.
