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... ______________________________________________ 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.