Re: [R-sig-eco] Vegan metaMDS: unusual first run stress values with large data set

2012-12-12 Thread Jari Oksanen
Hello R-Community, First my thanks to Ewan Isherwood who turned our attention to this issue and sent his data file to us for analysing the situation. It seems that the default convergence criteria are too slack in monoMDS() that was the ordination engine of metaMDS() in this case. Good news ar

[R-sig-eco] Vegan metaMDS: unusual first run stress values with large data set

2012-12-05 Thread Ewan Isherwood
Hello, R-Community! This is the first time writing to this group and indeed the first time using a mailing list, so please bear with me if I’ve done something wrong. I have a large species x site matrix (89 x 4831) that I want to ordinate using metaMDS in the Vegan (2.0-5) package in R (2.15.2). I