R help - Aug 2020 - R Script Modification Questions

Okay, I can't help much with the ggplot stuff so forget the "lty="
argument for that is base graphics. However, you may get away with

ggtitle(paste0("COVID-19 Tests in Ohio
\n(",date[length(date]),")"))+

I don't know whether the tidy* stuff handles indexing in the same way as
base R.

Jim

On Wed, Aug 19, 2020 at 12:20 PM Stephen P. Molnar
<s.molnar at sbcglobal.net> wrote:
>
> Jim
>
> Thanks for your note.
>
> This is what didn't make it through:
>
> library(tidyverse)
> library(lubridate)
>
> datO <-
read.csv("https://api.covidtracking.com/v1/states/oh/daily.csv")
> <- line 14
> datO[ ,1] <- ymd(datO[ ,1])
>
> dfO <- tibble::as_tibble(data.frame(date = datO[ ,"date"],
>                                      positive = datO[
,"positive"],
>                                      negative = datO[
,"negative"],
>                                      total = datO[ ,"total"]))
>
> dfO %>%
>    pivot_longer(
>      cols = -date,
>      names_to = "cases",
>      values_to = "count"
>    ) %>%
>    mutate(cases = factor(cases, levels = c("positive",
"negative",
> "total"))) %>%
>    ggplot(aes(date, count, color = cases)) +
>    geom_line() +
>    scale_color_manual(name = "Test",
>                       labels = c("Positive",
"Negative", "Total"),
>                       values = c("red", "blue",
"green")) +
>    ylim(0, 2000000) +
>    labs(x = "Date", y = "Number of Tests")+
>    ggtitle("COVID-19 Tests in Ohio \n (8/17/20)")+   <- line
33
>    theme_bw() +
>    theme(axis.text.x = element_text(angle = 30, hjust = 1),
>          plot.title = element_text(hjust = 0.5))
>
>              Steve
>
> On 08/18/2020 07:55 PM, Jim Lemon wrote:
> > Hi Stephen,
> > I think something went amiss with your email as there are a few blank
> > lines where I think you meant to paste a code fragment. Line type is
> > specified by the "lty" argument and to stick things together
for your
> > plot title, you may want something like this:
> >
> > ..
> > main<-paste("My plot title for",dates[length(dates)]).
> > ..
> >
> > Jim
> >
> > On Wed, Aug 19, 2020 at 3:09 AM Stephen P. Molnar
> > <s.molnar at sbcglobal.net> wrote:
> >> Thanks to the kind folks on this list, this is an elegant
replacement
> >> for the clumsy R script that I that I wrote.
> >>
> >>
> >>
> >>
> >> However, I do have a few changes that I would like to make. The
problem
> >> is that while I know how to make changes in Python, I am still
bumbling
> >> around in R Code.
> >>
> >> The day-to-day changes in the data are in the cvs file downloaded
in
> >> line 11 of the code.
> >>
> >> What I would like to do is use linetype, rather than color, in
line 27.
> >>
> >> The date in the title of the plot , line 33, is the max value of
the
> >> date in in line 14 and I would like to use that rather than edit
the
> >> Script every time the date changes.
> >>
> >> I'd appreciate assistance in making these changes.
> >>
> >> Thanks in advance,.
> >>
> >> --
> >> Stephen P. Molnar, Ph.D.
> >> www.molecular-modeling.net
> >> 614.312.7528 (c)
> >> Skype:  smolnar1
> >>
> >> ______________________________________________
> >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
>
> --
> Stephen P. Molnar, Ph.D.
> www.molecular-modeling.net
> 614.312.7528 (c)
> Skype:  smolnar1
>

Dear Stephen,

I answer inline:

On 2020-08-19 12:57 +1000, Jim Lemon wrote:
| On Wed, Aug 19, 2020 at 3:09 AM Stephen P. Molnar <s.molnar at
sbcglobal.net> wrote:
| |
| | What I would like to do is use 
| | linetype, rather than color, in line 
| | 27.

You need to specify linetype instead of 
color in ggplot::aes, like so

	ggplot2::aes(
	  x=date,
	  y=count,
	  linetype=cases)

and change 
scale_color_manual to 
scale_linetype_manual and its values 
like so

	  ggplot2::scale_linetype_manual(
	    name = "Test",
	    labels = levels,
	    values 	      c("dotted",
	        "dashed",
	        "solid"))

| | The date in the title of the plot , 
| | line 33, is the max value of the 
| | date in in line 14 and I would like 
| | to use that rather than edit the 
| | Script every time the date changes.
| 
| Okay, I can't help much with the 
| ggplot stuff so forget the "lty=" 
| argument for that is base graphics. 
| However, you may get away with
| 
| ggtitle(paste0("COVID-19 Tests in Ohio
\n(",date[length(date]),")"))+
| 
| I don't know whether the tidy* stuff 
| handles indexing in the same way as 
| base R.

I added a format, which converts it to 
the date format you mentioned (but with 
a zero in the month part ...):

	  ggplot2::ggtitle(
	    paste0("COVID-19 Tests in Ohio \n(",
	           format(max(dfO$date), "%m/%d/%y"), ")")) +

Here is the whole script:

	datO <-
read.csv("https://api.covidtracking.com/v1/states/oh/daily.csv")
	
	cases <- c("positive", "negative", "total")
	levels <- paste0(
	  toupper(substr(cases, 1, 1)),
	  substr(cases, 2, nchar(cases)))
	
	dfO <- data.frame(
	  date	    rep(
	      x=lubridate::ymd(datO$date),
	      each=length(cases)),
	  cases=levels,
	  count=as.vector(t(datO[,cases])))
	dfO$cases <- factor(dfO$cases, levels=levels)
	
	file <- "/tmp/stephen.pdf"
	res <- .5
	width <- 9*res
	height <- 5*res
	pdf(file=file, width=width, height=height)
	
	mapping <- ggplot2::aes(
	  x=date,
	  y=count,
	  linetype=cases)
	
	p <- 
	  ggplot2::ggplot(
	    data=dfO,
	    mapping=mapping) +
	  ggplot2::geom_line() +
	  ggplot2::scale_linetype_manual(
	    name = "Test",
	    labels = levels,
	    values 	      c("dotted",
	        "dashed",
	        "solid")) +
	  ggplot2::ylim(0, 2e6) +
	  ggplot2::labs(
	    x = "Date",
	    y = "Number of Tests") +
	  ggplot2::ggtitle(
	    paste0("COVID-19 Tests in Ohio \n(",
	           format(max(dfO$date), "%m/%d/%y"), ")")) +
	  ggplot2::theme_bw() +
	  ggplot2::theme(
	    axis.text.x = 
	      ggplot2::element_text(
	        angle = 30, 
	        hjust = 1),
	    plot.title = 
	      ggplot2::element_text(
	        hjust = 0.5))
	
	p
	
	dev.off()

Best,
Rasmus

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