I would like to put confidence intervals on a mantel corellogram
they are already calculated in the pmgram object but I am unsure how I
get the x value in order to plot them?
package(ecodist)
X<-1:100
Y<-rnorm(1:100)
Z<-rnorm(1:100)
XY<-dist(data.frame(X,Y))
YX<-dist(data.frame(Y,X))
my.mgram<-mgram(XY,XZ)
plot(my.mgram)
print(my.mgram)
> print(my.mgram)
$mgram
lag ngroup mantelr pval llim ulim
[1,] 3.770055 672 0.500012737 0.001 0.49689923 0.504301550
[2,] 11.310165 691 0.383960457 0.001 0.38000201 0.387324434
[3,] 18.850274 584 0.232086251 0.001 0.22670074 0.237501735
[4,] 26.390384 587 0.114097397 0.001 0.10243901 0.122973735
[5,] 33.930494 463 -0.003113351 0.835 -0.01928101 0.008839295
[6,] 41.470603 468 -0.106354446 0.001 -0.12682280 -0.089539628
[7,] 49.010713 357 -0.181250278 0.001 -0.20154017 -0.164863572
[8,] 56.550823 348 -0.266397615 0.001 -0.28498271 -0.251134864
[9,] 64.090933 252 -0.298705798 0.001 -0.31421396 -0.284154643
[10,] 71.631042 228 -0.353134525 0.001 -0.36468910 -0.341422330
[11,] 79.171152 147 -0.337181781 0.001 -0.34854961 -0.322161075
[12,] 86.711262 108 -0.334465576 0.001 -0.35500933 -0.309763543
[13,] 94.251371 43 -0.238965642 0.001 -0.26437371 -0.196038662
$resids
[1] NA
attr(,"class")
[1] "mgram"
Thanks
Nevil Amos
Hi, The x value you want is lag from my.mgram$mgram You can use lines() to add them to the plot. Sarah On Sun, Oct 16, 2011 at 7:10 PM, Nevil Amos <nevil.amos at gmail.com> wrote:> I would like to put confidence intervals on a mantel corellogram > they are already calculated in the pmgram object but I am unsure how I get > the x value in order to plot them? > > package(ecodist) > X<-1:100 > Y<-rnorm(1:100) > Z<-rnorm(1:100) > XY<-dist(data.frame(X,Y)) > YX<-dist(data.frame(Y,X)) > my.mgram<-mgram(XY,XZ) > plot(my.mgram) > print(my.mgram) >> print(my.mgram) > $mgram > ? ? ? ? ? ?lag ngroup ? ? ?mantelr ?pval ? ? ? ?llim ? ? ? ? ulim > ?[1,] ?3.770055 ? ?672 ?0.500012737 0.001 ?0.49689923 ?0.504301550 > ?[2,] 11.310165 ? ?691 ?0.383960457 0.001 ?0.38000201 ?0.387324434 > ?[3,] 18.850274 ? ?584 ?0.232086251 0.001 ?0.22670074 ?0.237501735 > ?[4,] 26.390384 ? ?587 ?0.114097397 0.001 ?0.10243901 ?0.122973735 > ?[5,] 33.930494 ? ?463 -0.003113351 0.835 -0.01928101 ?0.008839295 > ?[6,] 41.470603 ? ?468 -0.106354446 0.001 -0.12682280 -0.089539628 > ?[7,] 49.010713 ? ?357 -0.181250278 0.001 -0.20154017 -0.164863572 > ?[8,] 56.550823 ? ?348 -0.266397615 0.001 -0.28498271 -0.251134864 > ?[9,] 64.090933 ? ?252 -0.298705798 0.001 -0.31421396 -0.284154643 > [10,] 71.631042 ? ?228 -0.353134525 0.001 -0.36468910 -0.341422330 > [11,] 79.171152 ? ?147 -0.337181781 0.001 -0.34854961 -0.322161075 > [12,] 86.711262 ? ?108 -0.334465576 0.001 -0.35500933 -0.309763543 > [13,] 94.251371 ? ? 43 -0.238965642 0.001 -0.26437371 -0.196038662 > > $resids > [1] NA > > attr(,"class") > [1] "mgram" > > > Thanks > > Nevil Amos-- Sarah Goslee http://www.functionaldiversity.org
It is good to provide the code but please make sure it is reproducible? e.g. XZ is not defined in mgram(XY,XZ)? Weidong Gu On Sun, Oct 16, 2011 at 7:10 PM, Nevil Amos <nevil.amos at gmail.com> wrote:> I would like to put confidence intervals on a mantel corellogram > they are already calculated in the pmgram object but I am unsure how I get > the x value in order to plot them? > > package(ecodist) > X<-1:100 > Y<-rnorm(1:100) > Z<-rnorm(1:100) > XY<-dist(data.frame(X,Y)) > YX<-dist(data.frame(Y,X)) > my.mgram<-mgram(XY,XZ) > plot(my.mgram) > print(my.mgram) >> print(my.mgram) > $mgram > ? ? ? ? ? ?lag ngroup ? ? ?mantelr ?pval ? ? ? ?llim ? ? ? ? ulim > ?[1,] ?3.770055 ? ?672 ?0.500012737 0.001 ?0.49689923 ?0.504301550 > ?[2,] 11.310165 ? ?691 ?0.383960457 0.001 ?0.38000201 ?0.387324434 > ?[3,] 18.850274 ? ?584 ?0.232086251 0.001 ?0.22670074 ?0.237501735 > ?[4,] 26.390384 ? ?587 ?0.114097397 0.001 ?0.10243901 ?0.122973735 > ?[5,] 33.930494 ? ?463 -0.003113351 0.835 -0.01928101 ?0.008839295 > ?[6,] 41.470603 ? ?468 -0.106354446 0.001 -0.12682280 -0.089539628 > ?[7,] 49.010713 ? ?357 -0.181250278 0.001 -0.20154017 -0.164863572 > ?[8,] 56.550823 ? ?348 -0.266397615 0.001 -0.28498271 -0.251134864 > ?[9,] 64.090933 ? ?252 -0.298705798 0.001 -0.31421396 -0.284154643 > [10,] 71.631042 ? ?228 -0.353134525 0.001 -0.36468910 -0.341422330 > [11,] 79.171152 ? ?147 -0.337181781 0.001 -0.34854961 -0.322161075 > [12,] 86.711262 ? ?108 -0.334465576 0.001 -0.35500933 -0.309763543 > [13,] 94.251371 ? ? 43 -0.238965642 0.001 -0.26437371 -0.196038662 > > $resids > [1] NA > > attr(,"class") > [1] "mgram" > > > Thanks > > Nevil Amos > > ______________________________________________ > R-help at r-project.org mailing list > 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. >