tag:blogger.com,1999:blog-8499895524521663926.post7858471376334127857..comments2024-03-27T07:13:39.236-04:00Comments on Phylogenetic Tools for Comparative Biology: New S3 print/plot methods & new functionality for phytools lttLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-8499895524521663926.post-68711589833669437692015-07-20T11:05:10.881-04:002015-07-20T11:05:10.881-04:00Hi, Liam,
Thank you for your quck responding! I ...Hi, Liam, <br /><br />Thank you for your quck responding! I think I do have the latest version. Do you think I need to source('ltt.R') when I'm running the latest version?<br /><br />> packageVersion("phytools")<br />[1] ‘0.4.60’<br /><br />Also, I have 100 of 9300 tips large tree, I used it like this:<br />Z100 <- ltt(trees, plot=FALSE)<br />plot(Z100,log.lineages=FALSE,log="y",<br /> main="lineage through time plot",<br /> col=rgb(0,0,1,0.1))<br />then it gave another error:<br />Warning message:<br />In plot.window(...) :<br /> nonfinite axis limits [GScale(-inf,3.96848,2, .); log=1]<br /><br />Sorry for the questions. I'm a brand-new beginner for R that can't handle any of error out side of script.<br /><br />Thanks!<br /><br />MiaoMiaohttps://www.blogger.com/profile/14349566285615714462noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-56264150226112868912015-07-19T16:17:13.465-04:002015-07-19T16:17:13.465-04:00Hi Miao. That error suggests to me that you do not...Hi Miao. That error suggests to me that you do not have the most recent version of phytools installed. It should be phytools >= 0.4-60.<br />You can find out your current package version by using:<br /><br />packageVersion("phytools")<br /><br />All the best, LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-45891377823848609632015-07-19T10:41:33.272-04:002015-07-19T10:41:33.272-04:00Hi Liam,
I guess the first comment did send out. ...Hi Liam,<br /><br />I guess the first comment did send out. So I do it again. This is really awesome package! I'm running your example scripts. Everything works fine, until I'm running:<br />"plot(obj,log.lineages=FALSE,<br /> main="lineage through time plots for 200 trees",<br /> col=rgb(0,0,1,0.1)) ## plot lines with transparency<br />"<br />It gave me error:<br />Error in xy.coords(x, y, xlabel, ylabel, log) : <br /> 'x' is a list, but does not have components 'x' and 'y'<br /><br />So it will gave me error as long as I use "plot" function. How to fix this? Thanks!Miaohttps://www.blogger.com/profile/14349566285615714462noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-19475761853149833322015-07-19T10:37:17.071-04:002015-07-19T10:37:17.071-04:00Hi again,
also this one:
> plot(obj,lwd=2,log....Hi again,<br />also this one:<br /><br />> plot(obj,lwd=2,log.lineages=FALSE,log="y",<br />+ main="lineage through time plot")<br />Error in xy.coords(x, y, xlabel, ylabel, log) : <br /> 'x' is a list, but does not have components 'x' and 'y'Miaohttps://www.blogger.com/profile/14349566285615714462noreply@blogger.com