Comments for From the bottom of the heap

Comment on What’s wrong with LOESS for palaeo data? by Anand Jayakaran

Anand Jayakaran — Mon, 13 May 2013 14:50:52 +0000

I’d love to see an update on the h-block CV for temporal data too.

Comment on What is ordisurf() doing…? by ucfagls

ucfagls — Thu, 21 Mar 2013 04:38:18 +0000

No sorry; many other things including children, new job and emigration have all conspired against this happening. IIRC the very initial simulations I (we) did with random data seemed to indicate ordisurf() had broadly correct rejection levels.

Comment on What is ordisurf() doing…? by Erin

Erin — Thu, 21 Mar 2013 03:17:13 +0000

Thanks for the explanation! You mentioned that you were investigating trustworthiness of the p-values from mgcv, and possibly writing up a paper. Any news to report?

Comment on Decluttering ordination plots in vegan part 2: orditorp() by Siri L. O.

Siri L. O. — Mon, 25 Feb 2013 08:04:38 +0000

It worked! I just had to delete the two lines of code calling the axes. Again, thank you so much! Looking forward to your next post.

Comment on Decluttering ordination plots in vegan part 2: orditorp() by Siri L. O.

Siri L. O. — Mon, 25 Feb 2013 07:30:55 +0000

Thank you. I’ll give it a try.

Comment on Decluttering ordination plots in vegan part 2: orditorp() by ucfagls

ucfagls — Fri, 22 Feb 2013 17:33:09 +0000

It's hard coed in the vegan:::text.cca() function. The reason being I guess is that you need a scale of reference for the biplot arrows as the one used on the bottom and left is not appropriate for applying a quantitative scale to the biplot arrows. You'd need to study vegan:::text.cca() to see how it draws the arrows and then copy the essential bits into your own function that suppressed the two calls to axis() towards the end of the function.

Comment on Decluttering ordination plots in vegan part 2: orditorp() by Siri L. O.

Siri L. O. — Fri, 22 Feb 2013 11:30:21 +0000

Thank you for a very useful post. I have now successfully used orditorp() to make a nice and tidy plot of my RDA. However, when I use text() to add biplot arrows to the plot, tick marks automatically appear on the top and right axes. Do you know how I can remove these?

Comment on Customising vegan’s ordination plots by ucfagls

ucfagls — Sun, 27 Jan 2013 20:03:03 +0000

When you plot() the RDA object, include xlab = "", ylab = "" in the call.

Comment on Customising vegan’s ordination plots by Sarah Hicks

Sarah Hicks — Sun, 27 Jan 2013 19:11:28 +0000

Thanks! That worked for placement, but it overlays my custom text with the automatic labels “RDA1″ and “RDA2″. How do I get rid of those labels?

Comment on Customising vegan’s ordination plots by ucfagls

ucfagls — Sat, 26 Jan 2013 19:29:22 +0000

Have two calls to title() - you can't make arguments up! Something like

title(sub = "(Geum)", line = -27)
title(xlab = "X Axis Label", ylab = "Y Axis Label")