Hi all, a quick question: Does anyone know what vegan function was called to produce the following permutation test in this slide of Jari's: http://cc.oulu.fi/~jarioksa/opetus/metodi/ordination101.html#44 Cheers, Marc
permutation test for CCA variables
5 messages · Franz Krah, Marc Taylor, Jari Oksanen
Hi Marc, This is the example in the function envfit: library(vegan) data(varespec, varechem) library(MASS) ord <- metaMDS(varespec) (fit <- envfit(ord, varechem, perm = 999)) scores(fit, "vectors") plot(ord) plot(fit) Cheers, Franz ----------------------------------------------------- Franz-S. Krah (PhD student) Ecology and Evolution of mushroom-forming fungi RG Biodiversity of Plants Technical University of Munich (TUM) Mobile: 0170 5221189 Website: mycolab.de <http://mycolab.de/> Mail: franz.krah at tum.de <mailto:franz.krah at tum.de> ??????????????????????????
On 7. Dec 2018, at 07:30, Marc Taylor <marchtaylor at gmail.com> wrote: Hi all, a quick question: Does anyone know what vegan function was called to produce the following permutation test in this slide of Jari's: http://cc.oulu.fi/~jarioksa/opetus/metodi/ordination101.html#44 Cheers, Marc [[alternative HTML version deleted]]
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Thanks Franz! cheers, Marc
On Fri, Dec 7, 2018 at 7:44 AM Franz Krah <f.krah at mailbox.org> wrote:
Hi Marc, This is the example in the function envfit: library(vegan) data(varespec, varechem) library(MASS) ord <- metaMDS(varespec) (fit <- envfit(ord, varechem, perm = 999)) scores(fit, "vectors") plot(ord) plot(fit) Cheers, Franz ----------------------------------------------------- Franz-S. Krah (PhD student) Ecology and Evolution of mushroom-forming fungi RG Biodiversity of Plants Technical University of Munich (TUM) Mobile: 0170 5221189 Website: mycolab.de Mail: franz.krah at tum.de ?????????????????????????? On 7. Dec 2018, at 07:30, Marc Taylor <marchtaylor at gmail.com> wrote: Hi all, a quick question: Does anyone know what vegan function was called to produce the following permutation test in this slide of Jari's: http://cc.oulu.fi/~jarioksa/opetus/metodi/ordination101.html#44 Cheers, Marc [[alternative HTML version deleted]]
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Marc, the source code of those slides is in https://github.com/jarioksa/ordination101/. Look at the source code to see how the slide was generated. cheers, Jari Oksanen
On 7 Dec 2018, at 09:34, Marc Taylor <marchtaylor at gmail.com<mailto:marchtaylor at gmail.com>> wrote:
Thanks Franz! cheers, Marc
On Fri, Dec 7, 2018 at 7:44 AM Franz Krah <f.krah at mailbox.org<mailto:f.krah at mailbox.org>> wrote:
Hi Marc, This is the example in the function envfit: library(vegan) data(varespec, varechem) library(MASS) ord <- metaMDS(varespec) (fit <- envfit(ord, varechem, perm = 999)) scores(fit, "vectors") plot(ord) plot(fit) Cheers, Franz ----------------------------------------------------- Franz-S. Krah (PhD student) Ecology and Evolution of mushroom-forming fungi RG Biodiversity of Plants Technical University of Munich (TUM) Mobile: 0170 5221189 Website: mycolab.de<http://mycolab.de> Mail: franz.krah at tum.de<mailto:franz.krah at tum.de> ??????????????????????????
On 7. Dec 2018, at 07:30, Marc Taylor <marchtaylor at gmail.com<mailto:marchtaylor at gmail.com>> wrote:
Hi all, a quick question: Does anyone know what vegan function was called to produce the following permutation test in this slide of Jari's: http://cc.oulu.fi/~jarioksa/opetus/metodi/ordination101.html#44 Cheers, Marc _______________________________________________ R-sig-ecology mailing list R-sig-ecology at r-project.org<mailto:R-sig-ecology at r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology _______________________________________________ R-sig-ecology mailing list R-sig-ecology at r-project.org<mailto:R-sig-ecology at r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Many thanks Jari - I did see that afterwards and have already forked it :-) Thanks for the great resource. Cheers, Marc
On Fri, Dec 7, 2018 at 12:28 PM Jari Oksanen <jari.oksanen at oulu.fi> wrote:
Marc, the source code of those slides is in https://github.com/jarioksa/ordination101/. Look at the source code to see how the slide was generated. cheers, Jari Oksanen On 7 Dec 2018, at 09:34, Marc Taylor <marchtaylor at gmail.com> wrote: Thanks Franz! cheers, Marc On Fri, Dec 7, 2018 at 7:44 AM Franz Krah <f.krah at mailbox.org> wrote: Hi Marc, This is the example in the function envfit: library(vegan) data(varespec, varechem) library(MASS) ord <- metaMDS(varespec) (fit <- envfit(ord, varechem, perm = 999)) scores(fit, "vectors") plot(ord) plot(fit) Cheers, Franz ----------------------------------------------------- Franz-S. Krah (PhD student) Ecology and Evolution of mushroom-forming fungi RG Biodiversity of Plants Technical University of Munich (TUM) Mobile: 0170 5221189 Website: mycolab.de Mail: franz.krah at tum.de ?????????????????????????? On 7. Dec 2018, at 07:30, Marc Taylor <marchtaylor at gmail.com> wrote: Hi all, a quick question: Does anyone know what vegan function was called to produce the following permutation test in this slide of Jari's: http://cc.oulu.fi/~jarioksa/opetus/metodi/ordination101.html#44 Cheers, Marc [[alternative HTML version deleted]]
_______________________________________________ R-sig-ecology mailing list R-sig-ecology at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology