a) Keep the mailing list in the conversation... someone else may have useful
input, and others may benefit from reading the discussion.
b) If the issue can be reproduced on your end with something like a basic
plot(mpg~disk, data=mtcars) call, then you should use that instead of your
complicated example. If the problem only appears when you use certain plotting
functions hidden inside your plot1 through plot6 functions, we can't tell
that from here. Sorting that out is part of making your example minimal as the
Posting Guide requests.
c) If you can only reproduce with certain data, then you can use dput to give us
the necessary data.[1][2] It is up to you to determine what the minimal data
needed to demo the problem is, but we don't want to sift through some large
data blob only to find out that it was not relevant so you need to do that.
d) Interactions with data files are hard to make reproducible on someone
else's computer... saving data with different filenames will not help fix
that problem.
e) Note that this is the R-help mailing list, not the RStudio-help mailing list
nor the rmarkdown-package-help mailing list. We can and often do provide help on
using contributed packages anyway, but you should be aware that not everyone
here uses RStudio so doing your best to provide a reproducible example is in
your interest if you want readers to consider your question on topic.
There are many discussions online of how to communicate R examples, such as
[1][2][3]. In particular I think [3] is useful because it forces you to confirm
that the example will run in a fresh R environment which is the first step to
insuring it will run on our computers and we can dig into the problem. in this
case you could use it to help confirm that your R code should work for us
without the rmarkdown.
[1]
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
[2] http://adv-r.had.co.nz/Reproducibility.html
[3] https://cran.r-project.org/web/packages/reprex/index.html (read the
vignette)
On August 24, 2018 3:13:17 AM PDT, Patrick Connolly <p_connolly at
slingshot.co.nz> wrote:>On Thu, 23-Aug-2018 at 07:23AM -0700, Jeff Newmiller wrote:
>
>|> This is not reproducible because you have not provided the plot
>|> code or sample data. Output of sessionInfo would probably be
>|> appropriate as well.
>
>I took it as read that the plotting functions themselves aren't an
>issue since they operate as intended outside of the Rmarkdown
>space. Any function that uses the function plot() successfully will
>do. I was trying to ascertain how I should be setting up the scaling.
>
>|> As to whether needing to load objects is typical... yes, rmarkdown
>|> runs from a fresh environment to emphasize reproducibility, but
>|> your load command is bypassing that for us.
>
>The objects loaded from .RData took hours of simulating and it's out
>of the question to run them again inside Rmarkdown. Though the script
>used in the creation of .RData is reproducable, perhaps it would be
>clearer for me to have saved the objects to a file by a different
>name.
>
>Is there a better way to do that??
>
>
>
>|> On August 23, 2018 2:15:19 AM PDT, Patrick Connolly
><p_connolly at slingshot.co.nz> wrote:
>|> >I'm having difficulty getting plots into ioslides. It seems
to me
>|> >that the scale is completely out, but I can't figure out what
to do
>|> >about it. Whatever I try, I get the title slide, then a second
>with a
>|> >horizontal line and a vertical line in the bottom right corner.
It
>|> >looks like a badly scaled plot about 25 times the size of the
>plotting
>|> >area, so only a fragment is visible.
>|> >
>|> >This is the code I've tried:
>|> >
>|> >---
>|> >title: "Barking up the wrong tree"
>|> >author: "Patrick Connolly"
>|> >date: "`r format(Sys.time(), '%a %d/%m/%Y
%H:%M')`"
>|> >output: ioslides_presentation
>|> >---
>|> >
>|> >```{r global_options, echo=FALSE}
>|> >knitr::opts_chunk$set(tidy=TRUE,
>|> > warning=FALSE,
>|> > message=FALSE,
>|> > cache=FALSE,
>|> > dpi=600)
>|> >```
>|> >
>|> >```{r use these functions, echo= FALSE}
>|> > load(".RData") ## code for 6 plotting functions
>|> >
>|> >``
>|> >## 6 different Trees
>|> >
>|> >```{r 6 different Trees, echo = FALSE, messages=FALSE, fig.width
>7,
>|> >fig.height = 5}
>|> >
>|> >### par(mfrow = c(2, 3))
>|> >plot1()
>|> >plot2()
>|> >plot3()
>|> >plot4()
>|> >plot5()
>|> >plot6()
>|> >}
>|> >```
>|> >
>|> >If I run the plot functions in the Console, it all works and
>displays
>|> >correctly in Rstudiio's plot panel, even the mfrow bit. But I
>haven't
>|> >worked out how to include the code into Rmarkdown. I thought it
>might
>|> >be less taxing to not try putting the 6 plots on the same slide,
>but
>|> >it makes no difference when I commented out the mfrow bit.
>|> >
>|> >I'm not very familiar with the workings of Markdown or
Rstudio, but
>it
>|> >does seem strange to me that I need to specifically load the
global
>|> >environment otherwise it's not visible. Is that to be
expected?
>|> >
>|> >Ideas welcome, particularly about scaling.
>|>
>|> --
>|> Sent from my phone. Please excuse my brevity.
--
Sent from my phone. Please excuse my brevity.