subject:"\[R\] COVID\-19 datasets..."

Re: [R] COVID-19 datasets...

2020-05-07 Thread Thomas Petzoldt

On 07.05.2020 at 13:12 Deepayan Sarkar wrote:

On Thu, May 7, 2020 at 4:16 PM Thomas Petzoldt wrote:

On 07.05.2020 at 11:19 Deepayan Sarkar wrote:

On Thu, May 7, 2020 at 12:58 AM Thomas Petzoldt wrote:

Sorry if I'm joining a little bit late.

I've put some related links and scripts together a few weeks ago. Then I
stopped with this, because there is so much.

The data format employed by John Hopkins CSSE was sort of a big surprise
to me.

Why? I find it quite convenient to drop the first few columns and
extract the data as a matrix (using data.matrix()).

-Deepayan

Many thanks for the hint to use data.matrix

My aim was not to say that it is difficult, especially as R has all the
tools for data mangling.

My surprise was that "wide tables" and non-ISO dates as column names are
not the "data base way" that we in general teach to our students

Well, I am all for long format data when it makes sense, but I would
disagree that that is always the "right approach". In the case of
regular multiple time series, as in this context, a matrix-like
structure seems much more natural (and nicely handled by ts() in R),
and I wouldn't even bother reshaping the data in the first place.

See, for example,

https://github.com/deepayan/deepayan.github.io/blob/master/covid-19/deaths.rmd

and

https://deepayan.github.io/covid-19/deaths.html

-Deepayan

Great, thank you for the link with the comprehensive lattice graphs and
the explanations. I like your package very much and use it often, since
it appeared on CRAN (3 of my CRAN packages depend on it). As "dynamic
modeller", I consider time always as the first column, but I agree on
the other hand, that long tables are often, but not always the right
approach, let's think about gridded multi-dimensional netcdf data.

Many thanks for sharing your analysis publicly, I'll add your repo to my
link list.

Thomas

With reshape2::melt or tidyr::gather resp. pivot_longer, conversion is
quite easy, regardless if one wants to use tidyverse or not, see example
below.

Again, thanks, Thomas

library("dplyr")
library("readr")
library("tidyr")

file <-
"https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv;

dat <- read_delim(file, delim=",")
names(dat)[1:2] <- c("Province_State", "Country_Region")
dat2 <-
dat %>%
## summarize Country/Region duplicates
group_by(Country_Region) %>% summarise_at(vars(-(1:4)), sum) %>%
## make it a long table
pivot_longer(cols = -Country_Region, names_to = "time") %>%
## convert to ISO 8601 date
mutate(time = as.POSIXct(time, format="%m/%e/%y"))

An opposite approach was taken in Germany, that organized it as a
big JSON trees.

Fortunately, both can be "tidied" with R, and represent good didactic
examples for our students.

Here yet another repo linking to the data:

https://github.com/tpetzoldt/covid

Thomas

On 04.05.2020 at 20:48 James Spottiswoode wrote:

Sure. COVID-19 Data Repository by the Center for Systems Science and
Engineering (CSSE) at Johns Hopkins University is available here:

https://github.com/CSSEGISandData/COVID-19

All in csv fiormat.

On May 4, 2020, at 11:31 AM, Bernard McGarvey
wrote:

Just curious does anyone know of a website that has data available in a format
that R can download and analyze?

Thanks

Bernard McGarvey

Director, Fort Myers Beach Lions Foundation, Inc.

Retired (Lilly Engineering Fellow).

__
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.

James Spottiswoode
Applied Mathematics & Statistics
(310) 270 6220
jamesspottiswoode Skype
ja...@jsasoc.com

--
Dr. Thomas Petzoldt
senior scientist

Technische Universitaet Dresden
Faculty of Environmental Sciences
Institute of Hydrobiology
01062 Dresden, Germany

https://tu-dresden.de/Members/thomas.petzoldt

Re: [R] COVID-19 datasets...

2020-05-07 Thread Deepayan Sarkar

On Thu, May 7, 2020 at 4:16 PM Thomas Petzoldt  wrote:
>
> On 07.05.2020 at 11:19 Deepayan Sarkar wrote:
> > On Thu, May 7, 2020 at 12:58 AM Thomas Petzoldt  wrote:
> >>
> >> Sorry if I'm joining a little bit late.
> >>
> >> I've put some related links and scripts together a few weeks ago. Then I
> >> stopped with this, because there is so much.
> >>
> >> The data format employed by John Hopkins CSSE was sort of a big surprise
> >> to me.
> >
> > Why? I find it quite convenient to drop the first few columns and
> > extract the data as a matrix (using data.matrix()).
> >
> > -Deepayan
>
> Many thanks for the hint to use data.matrix
>
> My aim was not to say that it is difficult, especially as R has all the
> tools for data mangling.
>
> My surprise was that "wide tables" and non-ISO dates as column names are
> not the "data base way" that we in general teach to our students

Well, I am all for long format data when it makes sense, but I would
disagree that that is always the "right approach". In the case of
regular multiple time series, as in this context, a matrix-like
structure seems much more natural (and nicely handled by ts() in R),
and I wouldn't even bother reshaping the data in the first place.

See, for example,

https://github.com/deepayan/deepayan.github.io/blob/master/covid-19/deaths.rmd

and

https://deepayan.github.io/covid-19/deaths.html

-Deepayan

> With reshape2::melt or tidyr::gather resp. pivot_longer, conversion is
> quite easy, regardless if one wants to use tidyverse or not, see example
> below.
>
> Again, thanks, Thomas
>
>
> library("dplyr")
> library("readr")
> library("tidyr")
>
> file <-
> "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv;
>
> dat <- read_delim(file, delim=",")
> names(dat)[1:2] <- c("Province_State", "Country_Region")
> dat2 <-
>dat %>%
>## summarize Country/Region duplicates
>group_by(Country_Region) %>% summarise_at(vars(-(1:4)), sum) %>%
>## make it a long table
>pivot_longer(cols = -Country_Region, names_to = "time") %>%
>## convert to ISO 8601 date
>mutate(time = as.POSIXct(time, format="%m/%e/%y"))
>
>
>
> >
> >> An opposite approach was taken in Germany, that organized it as a
> >> big JSON trees.
> >>
> >> Fortunately, both can be "tidied" with R, and represent good didactic
> >> examples for our students.
> >>
> >> Here yet another repo linking to the data:
> >>
> >> https://github.com/tpetzoldt/covid
> >>
> >>
> >> Thomas
> >>
> >>
> >> On 04.05.2020 at 20:48 James Spottiswoode wrote:
> >>> Sure. COVID-19 Data Repository by the Center for Systems Science and 
> >>> Engineering (CSSE) at Johns Hopkins University is available here:
> >>>
> >>> https://github.com/CSSEGISandData/COVID-19
> >>>
> >>> All in csv fiormat.
> >>>
> >>>
>  On May 4, 2020, at 11:31 AM, Bernard McGarvey 
>   wrote:
> 
>  Just curious does anyone know of a website that has data available in a 
>  format that R can download and analyze?
> 
>  Thanks
> 
> 
>  Bernard McGarvey
> 
> 
>  Director, Fort Myers Beach Lions Foundation, Inc.
> 
> 
>  Retired (Lilly Engineering Fellow).
> 
>  __
>  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.
> 
> >>>
> >>> James Spottiswoode
> >>> Applied Mathematics & Statistics
> >>> (310) 270 6220
> >>> jamesspottiswoode Skype
> >>> ja...@jsasoc.com
> >>>
>
> --
> Dr. Thomas Petzoldt
> senior scientist
>
> Technische Universitaet Dresden
> Faculty of Environmental Sciences
> Institute of Hydrobiology
> 01062 Dresden, Germany
>
> https://tu-dresden.de/Members/thomas.petzoldt

__
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] COVID-19 datasets...

2020-05-07 Thread Thomas Petzoldt


On 07.05.2020 at 11:19 Deepayan Sarkar wrote:

On Thu, May 7, 2020 at 12:58 AM Thomas Petzoldt  wrote:


Sorry if I'm joining a little bit late.

I've put some related links and scripts together a few weeks ago. Then I
stopped with this, because there is so much.

The data format employed by John Hopkins CSSE was sort of a big surprise
to me.


Why? I find it quite convenient to drop the first few columns and
extract the data as a matrix (using data.matrix()).

-Deepayan


Many thanks for the hint to use data.matrix

My aim was not to say that it is difficult, especially as R has all the 
tools for data mangling.


My surprise was that "wide tables" and non-ISO dates as column names are 
not the "data base way" that we in general teach to our students


With reshape2::melt or tidyr::gather resp. pivot_longer, conversion is 
quite easy, regardless if one wants to use tidyverse or not, see example 
below.


Again, thanks, Thomas


library("dplyr")
library("readr")
library("tidyr")

file <- 
"https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv;


dat <- read_delim(file, delim=",")
names(dat)[1:2] <- c("Province_State", "Country_Region")
dat2 <-
  dat %>%
  ## summarize Country/Region duplicates
  group_by(Country_Region) %>% summarise_at(vars(-(1:4)), sum) %>%
  ## make it a long table
  pivot_longer(cols = -Country_Region, names_to = "time") %>%
  ## convert to ISO 8601 date
  mutate(time = as.POSIXct(time, format="%m/%e/%y"))






An opposite approach was taken in Germany, that organized it as a
big JSON trees.

Fortunately, both can be "tidied" with R, and represent good didactic
examples for our students.

Here yet another repo linking to the data:

https://github.com/tpetzoldt/covid


Thomas


On 04.05.2020 at 20:48 James Spottiswoode wrote:

Sure. COVID-19 Data Repository by the Center for Systems Science and 
Engineering (CSSE) at Johns Hopkins University is available here:

https://github.com/CSSEGISandData/COVID-19

All in csv fiormat.



On May 4, 2020, at 11:31 AM, Bernard McGarvey  
wrote:

Just curious does anyone know of a website that has data available in a format 
that R can download and analyze?

Thanks


Bernard McGarvey


Director, Fort Myers Beach Lions Foundation, Inc.


Retired (Lilly Engineering Fellow).

__
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.



James Spottiswoode
Applied Mathematics & Statistics
(310) 270 6220
jamesspottiswoode Skype
ja...@jsasoc.com



--
Dr. Thomas Petzoldt
senior scientist

Technische Universitaet Dresden
Faculty of Environmental Sciences
Institute of Hydrobiology
01062 Dresden, Germany

https://tu-dresden.de/Members/thomas.petzoldt

__
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] COVID-19 datasets...

2020-05-07 Thread Deepayan Sarkar

On Thu, May 7, 2020 at 12:58 AM Thomas Petzoldt  wrote:
>
> Sorry if I'm joining a little bit late.
>
> I've put some related links and scripts together a few weeks ago. Then I
> stopped with this, because there is so much.
>
> The data format employed by John Hopkins CSSE was sort of a big surprise
> to me.

Why? I find it quite convenient to drop the first few columns and
extract the data as a matrix (using data.matrix()).

-Deepayan

> An opposite approach was taken in Germany, that organized it as a
> big JSON trees.
>
> Fortunately, both can be "tidied" with R, and represent good didactic
> examples for our students.
>
> Here yet another repo linking to the data:
>
> https://github.com/tpetzoldt/covid
>
>
> Thomas
>
>
> On 04.05.2020 at 20:48 James Spottiswoode wrote:
> > Sure. COVID-19 Data Repository by the Center for Systems Science and 
> > Engineering (CSSE) at Johns Hopkins University is available here:
> >
> > https://github.com/CSSEGISandData/COVID-19
> >
> > All in csv fiormat.
> >
> >
> >> On May 4, 2020, at 11:31 AM, Bernard McGarvey 
> >>  wrote:
> >>
> >> Just curious does anyone know of a website that has data available in a 
> >> format that R can download and analyze?
> >>
> >> Thanks
> >>
> >>
> >> Bernard McGarvey
> >>
> >>
> >> Director, Fort Myers Beach Lions Foundation, Inc.
> >>
> >>
> >> Retired (Lilly Engineering Fellow).
> >>
> >> __
> >> 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.
> >>
> >
> > James Spottiswoode
> > Applied Mathematics & Statistics
> > (310) 270 6220
> > jamesspottiswoode Skype
> > ja...@jsasoc.com
> >
> >
>
> __
> 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] COVID-19 datasets...

2020-05-06 Thread Thomas Petzoldt


Sorry if I'm joining a little bit late.

I've put some related links and scripts together a few weeks ago. Then I 
stopped with this, because there is so much.


The data format employed by John Hopkins CSSE was sort of a big surprise 
to me. An opposite approach was taken in Germany, that organized it as a 
big JSON trees.


Fortunately, both can be "tidied" with R, and represent good didactic 
examples for our students.


Here yet another repo linking to the data:

https://github.com/tpetzoldt/covid


Thomas


On 04.05.2020 at 20:48 James Spottiswoode wrote:

Sure. COVID-19 Data Repository by the Center for Systems Science and 
Engineering (CSSE) at Johns Hopkins University is available here:

https://github.com/CSSEGISandData/COVID-19

All in csv fiormat.



On May 4, 2020, at 11:31 AM, Bernard McGarvey  
wrote:

Just curious does anyone know of a website that has data available in a format 
that R can download and analyze?
  
Thanks



Bernard McGarvey


Director, Fort Myers Beach Lions Foundation, Inc.


Retired (Lilly Engineering Fellow).

__
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.



James Spottiswoode
Applied Mathematics & Statistics
(310) 270 6220
jamesspottiswoode Skype
ja...@jsasoc.com




__
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] COVID-19 datasets...

2020-05-05 Thread James Spottiswoode

Sure. COVID-19 Data Repository by the Center for Systems Science and 
Engineering (CSSE) at Johns Hopkins University is available here:

https://github.com/CSSEGISandData/COVID-19

All in csv fiormat.

> On May 4, 2020, at 11:31 AM, Bernard McGarvey  
> wrote:
> 
> Just curious does anyone know of a website that has data available in a 
> format that R can download and analyze?
>  
> Thanks
> 
> 
> Bernard McGarvey
> 
> 
> Director, Fort Myers Beach Lions Foundation, Inc.
> 
> 
> Retired (Lilly Engineering Fellow).
> 
> __
> 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.
> 

James Spottiswoode
Applied Mathematics & Statistics
(310) 270 6220
jamesspottiswoode Skype
ja...@jsasoc.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] COVID-19 datasets...

2020-05-05 Thread PIKAL Petr

Another option is

https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide

Together with instruments from

https://www.repidemicsconsortium.org/

Cheers
Petr

Here is some simple code

library(EpiEstim)
library(ggplot2)
library(lubridate)
library(incidence)
library(distcrete)
library(epitrix)
library(readxl)

mena <- c("Austria", "Czechia", "Germany", "Italy", "Japan", "Russia", 
"South_Korea", 
"Spain", "Sweden", "Taiwan", "United_States_of_America", "United_Kingdom")

plot_Ri <- function(estimate_R_obj) {
p_I <- plot(estimate_R_obj, "incid") + ggtitle(staty[vyber][i])  # plots 
the incidence
p_SI <- plot(estimate_R_obj, "SI")  # plots the serial interval distribution
p_Ri <- plot(estimate_R_obj, "R") + ylim(c(0,5))
return(gridExtra::grid.arrange(p_I, p_Ri, ncol = 1))
}

data <- read_excel("covid.xlsx")
data <- as.data.frame(data)
staty <- levels(factor(data[,7]))
vyber <- which(staty %in% mena)
staty[vyber]

# covid.xlsx is downloaded data

vyber <- which(staty %in% mena)
vyber <- vyber[-6]
staty[vyber]
ddd <- vector("list", length=length(vyber))
pdf("grafy2.pdf")
for (i in 1:length(vyber)) {
temp <- data[data[,7]==staty[vyber][i],]
temp$cas <- ymd(temp$dateRep)
ooo <- order(temp$cas)
temp <- temp[ooo,]
temp<- temp[-1,]
temp <- temp[-(1:min(which(temp$cases>0))-1),]
head(temp)
test <- temp[, c(12,5)]
names(test) <- c("date", "I")
test$I <- abs(test$I)
inc <- rep(test$date, test$I)
inci <- incidence(inc)
peak <- find_peak(inci)
fit <- incidence::fit(inci, split=peak)
print(plot(inci, fit = fit)+ggtitle(staty[vyber][i]))
ddd[[i]] <- rbind(fit$before$info$doubling.conf, fit$after$info$halving.conf)
vysled <- estimate_R(test, method = "uncertain_si",
config = make_config(list(mean_si = 4, std_mean_si = 2,
min_mean_si = 1, max_mean_si = 8.4, std_si = 2.4, std_std_si = 1,
min_std_si = 0.5, max_std_si = 4, n1 = 1000, n2 = 1000)))
print(plot_Ri(vysled))
}
dev.off()
names(ddd) <- staty[vyber]
ddd


> -Original Message-
> From: R-help  On Behalf Of Bernard Comcast
> Sent: Monday, May 4, 2020 8:56 PM
> To: James Spottiswoode 
> Cc: r-help@r-project.org
> Subject: Re: [R] COVID-19 datasets...
> 
> Thanks, i will take a look
> 
> Bernard
> Sent from my iPhone so please excuse the spelling!"
> 
> > On May 4, 2020, at 2:49 PM, James Spottiswoode 
> wrote:
> >
> > Sure. COVID-19 Data Repository by the Center for Systems Science and
> Engineering (CSSE) at Johns Hopkins University is available here:
> >
> > https://github.com/CSSEGISandData/COVID-19
> >
> > All in csv fiormat.
> >
> >
> >> On May 4, 2020, at 11:31 AM, Bernard McGarvey
>  wrote:
> >>
> >> Just curious does anyone know of a website that has data available in a
> format that R can download and analyze?
> >>
> >> Thanks
> >>
> >>
> >> Bernard McGarvey
> >>
> >>
> >> Director, Fort Myers Beach Lions Foundation, Inc.
> >>
> >>
> >> Retired (Lilly Engineering Fellow).
> >>
> >> __
> >> 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.
> >>
> >
> > James Spottiswoode
> > Applied Mathematics & Statistics
> > (310) 270 6220
> > jamesspottiswoode Skype
> > ja...@jsasoc.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.
__
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] COVID-19 datasets...

2020-05-04 Thread Abby Spurdle

I don't know if this is useful of not.
But here's some dis-aggregated US data.
It's about 10 days old, and I need to improve the dis-aggregation algorithm.
--
age <- 0:80
rel.mort.rate <- c (0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
5.97119198173175e-14, 1.49279799543293e-12,
1.80329997848298e-11, 1.40323011570696e-10, 7.91302361419091e-10,
3.45021443896442e-09, 0.000121231319447505, 0.000353442018829079,
0.000874198628343878, 0.00186810950489511, 0.00350496608960251,
0.00586292710567257, 0.0088809586113832, 0.0123828572996647,
0.0161636339411418, 0.0200770373248443, 0.0240656741448015,
0.0281336507897391, 0.0323131179486445, 0.0366643530132155,
0.0412942874923419, 0.0463520698193433, 0.0519914074326175,
0.0583299029582447, 0.0654330938109396, 0.0733211405261902,
0.0819881232642656, 0.0914397689953956, 0.101752369848173,
0.113121562971092, 0.125849353938131, 0.140250299768815,
0.156519020717643, 0.174632527695486, 0.19434044086,
0.215255604245307, 0.237027683240887, 0.259554459399679,
0.283147468915187, 0.308551986409676, 0.336771894650306,
0.368753737436115, 0.405063605263262, 0.445688466005247,
0.490032796563514, 0.537118848883967, 0.585949512128272,
0.635935967055111, 0.687239859205501, 0.740884186923496,
0.798570919656766, 0.862259973389807, 0.933650267485426,
0.000101373734773254, 0.000110260898647345, 0.0001199575254273,
0.000130361177821875, 0.000141396704797265, 0.000153071840957868,
0.00016550903061107, 0.000178943792317475, 0.000193689554660746,
0.000210077052171998, 0.00022838282771009, 0.000248763951569319,
0.000271212123374848, 0.000295531695409173, 0.000321339382531619,
0.000348084036019435, 0.000375091815336575, 0.000401647747211891)

names (rel.mort.rate) <- age

options (scipen=4)
mar <- par ("mar")
mar [2] <- mar [2] + 1
p0 <- par (mar=mar)
barplot (rel.mort.rate [41:81], ylim = c (0, 0.0004), xlab="age",
ylab="relative mortality rate\n(ndeaths / npeople | age)")
par (p0)

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Re: [R] COVID-19 datasets...

2020-05-04 Thread Abby Spurdle

Yes, you're right.

Note that stack exchange is 10x more likely to flag my post as
off-topic, and I was looking for *interesting* applications of R.
There's only so many times one can use Fisher's iris data...

On Tue, May 5, 2020 at 8:42 AM Bert Gunter  wrote:
>
> Suggestion: Please stay on topic.
>
> This list is R-Help, not about scientific discussions or even what
> statistical procedures might be used for specific research questions.
> Perhaps https://stats.stackexchange.com/  for the latter.
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
> On Mon, May 4, 2020 at 12:55 PM Abby Spurdle  wrote:
> >
> > sorry, blood acidity probably wasn't the best choice of words
> >
> > __
> > 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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Re: [R] COVID-19 datasets...

2020-05-04 Thread Bert Gunter

Suggestion: Please stay on topic.

This list is R-Help, not about scientific discussions or even what
statistical procedures might be used for specific research questions.
Perhaps https://stats.stackexchange.com/  for the latter.

Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Mon, May 4, 2020 at 12:55 PM Abby Spurdle  wrote:
>
> sorry, blood acidity probably wasn't the best choice of words
>
> __
> 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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Re: [R] COVID-19 datasets...

2020-05-04 Thread Abby Spurdle

sorry, blood acidity probably wasn't the best choice of words

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Re: [R] COVID-19 datasets...

2020-05-04 Thread Abby Spurdle

While we're on this topic...

I was interested in testing hypotheses (plural) that acid base
chemistry (blood H+/HCO3/PCO2) or closely-related metabolic processes
could influence the rate of viral replication, possibly by having some
sort of effect on the acidity of phagocytes, vesicles or other
cellular/intracellular-level "host" environments.

There appears to be a relationship between age and blood pH, with a
possibility of a change point around retirement age. This could (being
somewhat speculative) be related to the differences we see in
mortality rates by age.

However, I've got no idea how to test the second part of the
hypotheses, that blood acidity (or any other metabolic process) could
influence the acidity of phagocytes or vesicles.

Suggestions welcome...

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Re: [R] COVID-19 datasets...

2020-05-04 Thread Bernard Comcast

Thanks, i will take a look

Bernard
Sent from my iPhone so please excuse the spelling!"

> On May 4, 2020, at 2:49 PM, James Spottiswoode  wrote:
> 
> Sure. COVID-19 Data Repository by the Center for Systems Science and 
> Engineering (CSSE) at Johns Hopkins University is available here:
> 
> https://github.com/CSSEGISandData/COVID-19
> 
> All in csv fiormat.
> 
> 
>> On May 4, 2020, at 11:31 AM, Bernard McGarvey  
>> wrote:
>> 
>> Just curious does anyone know of a website that has data available in a 
>> format that R can download and analyze?
>>  
>> Thanks
>> 
>> 
>> Bernard McGarvey
>> 
>> 
>> Director, Fort Myers Beach Lions Foundation, Inc.
>> 
>> 
>> Retired (Lilly Engineering Fellow).
>> 
>> __
>> 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.
>> 
> 
> James Spottiswoode
> Applied Mathematics & Statistics
> (310) 270 6220
> jamesspottiswoode Skype
> ja...@jsasoc.com
> 
> 
> 

[[alternative HTML version deleted]]

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Re: [R] COVID-19 datasets...

2020-05-04 Thread Hasan Diwan

On Mon, 4 May 2020 at 11:32, Bernard McGarvey 
wrote:

> Just curious does anyone know of a website that has data available in a
> format that R can download and analyze?
>

https://hd1-units.herokuapp.com/covid has a days parameter one can adjust
to go back in time and a suffix parameter to obtain json, yml, or csv. -- H

-- 
OpenPGP:
https://sks-keyservers.net/pks/lookup?op=get=0xFEBAD7FFD041BBA1
If you wish to request my time, please do so using
*bit.ly/hd1AppointmentRequest
*.
Si vous voudrais faire connnaisance, allez a *bit.ly/hd1AppointmentRequest
*.

Sent
from my mobile device
Envoye de mon portable

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Re: [R] COVID-19 datasets...

2020-05-04 Thread Ben Tupper

This works very well https://github.com/covid19datahub/COVID19

Cheers,
Ben

On Mon, May 4, 2020 at 2:32 PM Bernard McGarvey <
mcgarvey.bern...@comcast.net> wrote:

> Just curious does anyone know of a website that has data available in a
> format that R can download and analyze?
>
> Thanks
>
>
> Bernard McGarvey
>
>
> Director, Fort Myers Beach Lions Foundation, Inc.
>
>
> Retired (Lilly Engineering Fellow).
>
> __
> 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.
>


-- 
Ben Tupper
Bigelow Laboratory for Ocean Science
East Boothbay, Maine
http://www.bigelow.org/
https://eco.bigelow.org

[[alternative HTML version deleted]]

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[R] COVID-19 datasets...

2020-05-04 Thread Bernard McGarvey

Just curious does anyone know of a website that has data available in a format 
that R can download and analyze?
 
Thanks


Bernard McGarvey


Director, Fort Myers Beach Lions Foundation, Inc.


Retired (Lilly Engineering Fellow).

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