tag:blogger.com,1999:blog-8499895524521663926.post9130870073951877722..comments2024-03-27T07:13:39.236-04:00Comments on Phylogenetic Tools for Comparative Biology: Additional method for fitPagel to fit Pagel's (1994) model of correlated binary character evolutionLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-8499895524521663926.post-28542053797370798932017-05-24T09:23:16.878-04:002017-05-24T09:23:16.878-04:00Dear Liam,
thanks for your fast answer. Surprisin...Dear Liam,<br /><br />thanks for your fast answer. Surprisingly, I was able to conduct PagelTests if I download phytools from the Danish server but not from German (Göttingen, Münster) servers. <br /><br />Do you know a possibility to conduct a test with two factorial character of which one is not binary?<br /><br />Best<br /><br />StefanAnonymoushttps://www.blogger.com/profile/17147582678826326327noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-79473613874058311442017-05-22T14:53:50.773-04:002017-05-22T14:53:50.773-04:00I'm not sure why this would be the case. Have ...I'm not sure why this would be the case. Have you tried restarting your R session?Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-42146435764327620832017-05-22T11:18:46.327-04:002017-05-22T11:18:46.327-04:00Dear Liam,
I would like to use "fitPagel&quo...Dear Liam,<br /><br />I would like to use "fitPagel" to check for correlation between two binary traits. However, I always get the following message "could not find function "fitPagel"" even though I have the latest R version (3.4.0) and the libraries "phytools", "ape", "geiger", "rgl" installed and loaded.Do you have an idea why I get the error message?<br /><br />Best<br /><br />StefanAnonymoushttps://www.blogger.com/profile/17147582678826326327noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-67444534425610596682016-08-04T21:06:56.611-04:002016-08-04T21:06:56.611-04:00Dear Liam,
Is it possible to select a substitutio...Dear Liam,<br /><br />Is it possible to select a substitution model for one variable and other model for the other? (say ER for X and ARD for Y)<br /><br />Cheers,<br /><br />Guilhermenycterishttps://www.blogger.com/profile/07681927775969667237noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-80545362404572890782016-05-25T07:30:56.807-04:002016-05-25T07:30:56.807-04:00Thanks a lot. Now everything works perfectly.
Bes...Thanks a lot. Now everything works perfectly.<br /><br />Best<br />MarcinMaPhttps://www.blogger.com/profile/06269199215406608318noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-12872406747153770272016-05-24T10:02:39.561-04:002016-05-24T10:02:39.561-04:00Hi Marcin.
This is a known bug in the CRAN versio...Hi Marcin.<br /><br />This is a known bug in the CRAN version. I think it should be fixed if you update phytools from GitHub. To do that start a fresh R session & run:<br /><br />library(devtools) ## must have devtools installed<br />install_github("liamrevell/phytools")<br /><br />Let us know if that takes care of the issue.<br /><br />- LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-38074728680699847682016-05-24T06:41:38.570-04:002016-05-24T06:41:38.570-04:00Dear Liam,
I try to use fitPagel to check for cor...Dear Liam,<br /><br />I try to use fitPagel to check for correlation between two binary traits. However, I always get the following message when I'm using my data with fitMk method:<br /><br />"model does not have the right number of columns"<br /><br />Could you explain to me what this message exactly means?<br /><br />Best<br />Marcin<br />MaPhttps://www.blogger.com/profile/06269199215406608318noreply@blogger.com