On 09/16/2021 09:26 PM, H wrote:
> On 09/16/2021 09:00 PM, Jim Lemon wrote:
>> Okay, that was just my reading of the help page. I hope that I haven't
>> added to the confusion.
>>
>> Jim
>>
>> On Fri, Sep 17, 2021 at 10:50 AM H <age...@meddatainc.com> wrote:
>>> On 09/15/2021 09:40 PM, Jim Lemon wrote:
>>>> Oops, your plot
>>>>
>>>> On Thu, Sep 16, 2021 at 11:39 AM Jim Lemon <drjimle...@gmail.com> wrote:
>>>>> Hi H,
>>>>> Looking at your example and the help page, it looks to me as though
>>>>> the plot is consistent with the "A" matrix:
>>>>>
>>>>> Oz
>>>>> Rain Nice
>>>>> Rain 0.25 0.75
>>>>> Nice 0.60 0.40
>>>>>
>>>>> # help page
>>>>> A - square coefficient matrix, specifying the links (rows=to, cols=from).
>>>>>
>>>>> In your plot (attached):
>>>>> Rain (col) goes to Rain (row) 0.25
>>>>> Rain (col) goes to Nice (row) 0.6
>>>>> Nice (col) goes to Nice (row) 0.4
>>>>> Nice (col) goes to Rain (row) 0.75
>>>>>
>>>>> This is a bit confusing, but it seems to do what it says it does.
>>>>>
>>>>> Jim
>>>>>
>>>>> On Thu, Sep 16, 2021 at 10:40 AM H <age...@meddatainc.com> wrote:
>>>>>> I am using plotmat 1.6.5 (part of the diagram package) in R 3.6 to plot
>>>>>> Markov transition charts but have run into an issue that I was hoping
>>>>>> someone could shed light on here. I did e-mail the maintainer over a
>>>>>> month ago but have not received a reply.
>>>>>>
>>>>>> The issue is that the directional arrows point in the wrong direction. A
>>>>>> brief example:
>>>>>>
>>>>>> stateNames <- c("Rain", "Nice")
>>>>>> Oz <- matrix(c(0.25, 0.75, 0.6, 0.4), nrow = 2, byrow = TRUE)
>>>>>> rownames(Oz) <- stateNames; colnames(Oz) <- stateNames
>>>>>> plotmat(Oz, pos = c(1, 1), lwd = 1, box.lwd = 2, cex.txt = 0.8, box.size
>>>>>> = 0.1, box.type = "circle", box.prop = 0.5, box.col = "light yellow",
>>>>>> arr.length = 0.2, arr.width = 0.2, self.cex = 0.4, self.shifty = 0.01,
>>>>>> self.shiftx = 0.13, main = "")
>>>>>>
>>>>>> In the above example both arrows seem to point in the direction opposite
>>>>>> to what I expect. Has anyone encountered this and know how to fix it?
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> ______________________________________________
>>>>>> 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.
>>> I am sorry but I think you have it wrong. A transition probability matrix
>>> for the rain/nice scenario would be written:
>>>
>>> Rain, Nice
>>>
>>> Rain |0.25, 0.75|
>>>
>>> Nice |0.60, 0.40|
>>>
>>> If you sum the transition probabilities for rain or nice, they should each
>>> add to 1. Logic dictates if the only two states are rain and nice, and rain
>>> continues the next day with a probability of 0.25, nice must have a
>>> probability of 0.75. Likewise, the sum of probabilities for nice weather to
>>> change to rain, 0.6, and remain the same, 0.4 must add up to 1.
>>>
>>> I find that the arrow directions are the opposite of what I expect.
>>>
> I just realized you did identify what the problem was, it was not the arrow
> direction but that the matrix needed to be transposed before used in plotmat.
> I am used to transition probability matrices read row-wise where each row
> adds up to 1. Plotmat expects the transition matrix to be read column-wise
> where each column adds up to 1.
>
> Transposing the original matrix using t() before using it in plotmat() also
> resolved my own example which is considerably more complex.
>
> Thank you for your help!
>
> ______________________________________________
> 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.
Perhaps someone knows if it is possible to position the state boxes more
flexibly in plotmat()?
I have eight states I plot in four rows of 1-3-3-1 because it makes logical
sense to group them this way row-wise. There are transitions between some of
the states and the default positioning of the states, the transition arrows and
associated transition probabilities makes for not-so-clear figure...
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