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- May 8, 2008 at 11:12 pm #430
I’m looking for some comment on an approach I have taken to reduce stress without taking out ‘noisy’ data.
In an analysis of vegetation plots that I have just completed I resulted in a stress level (SL) of 0.23, whcih is uncomforatably high. So I looked at the KW statistics to see what species I could remove to reduce the stress. I eliminated most with KW scores <1 (0.2May 9, 2008 at 4:50 am #510leeKeymaster
Mark, I think my post to your first post on Bray and Curtis vs Kulczynski addresses at least a fair part of this.
Stress of 0.2 is still too high for my comfort.
I’ll have to go over the fidelity stuff to remember the details but unsure if you are referring to my DOS PATN approach to constancy and fidelity (with presence/absence data) or Mike Bedwood’s fidel stuff. I think Mike extended my work.
LeeMay 9, 2008 at 4:57 am #512
I’ll check to see if it was Mikes fidelity work or yours.May 11, 2008 at 11:48 pm #513
It was Mike’s fidelity work.
OK I had another long session of reading, toggling and analysis on administering your advice and reduced stress to 0.1946. This is as low as I can get it.
I must admit to neglecting the value of the two way table. Never again. It was quite valuable in helping me gain a better understanding of the data. It is clear from the analysis that there is multiple sources of noise, with most of the noise coming from disturbance related factors (i.e. remnant size and vast array of past land uses including temporal variability). Unfortunately these factors represent truth in the area investigated, thus there is no escaping it.
The other noisy component of the data is the presence of a regional intergrade between at least 2 if not three vegetation communities. One could possibly interpret that as a signal, which is how I’m viewing it, as the presence of intergrades is natural and expected.
One last question. Should one report the resultant stress level? I would think that this is a responsible thing to do as it conveys to the reader the ‘strength’ of the analysis. It can also be used to demonstrate that the data patterns are quite complex, perhaps being an expected outcome?
Thanks for your pointers Lee and cheers till later.May 12, 2008 at 3:45 am #514leeKeymaster
You should take a look at 11. Austin, M.P., Williams, O.& Belbin, L.(1981). Grassland dynamics under sheep grazing in an Australian Mediterranean type Climate. Vegetatio 47, 201-211. This gives you an idea on how you could analyze temporal and disturbance factors in ‘noisy’ datasets.
If there are independent environmental/disturbance factors, then it is possible that more than 3d is required for the ordination. But an overlaid MST will also give a good indication of this. See my notes on it.
I would never publish an (MDS) ordination result without the stress value (or variance in a PCA/PCoA).
If you have very disjunct communities, then ordination is difficult. Take a look at the histogram of association measures and see the notes on this in the help. It will tell you if there are disjunctions. If there are, then there is a strong case for independent analysis of each disjunct group. BTW: Disjunctions = high stress.
LeeMay 12, 2008 at 7:40 am #515
Thanks again for your advice. I will seek out that paper and digest. It seems from its title to be most appropriate.
Yes, I will be publishing the stress value. I hope you didn’t get the impression that I wasn’t. The question was asked because I did not find the stress level for the PATN analysis that the regional vegetation study that relates to my area of interest. As such I had no way of comparitively measuring my data set with that ‘benchmark’ vegetation study. I felt like I was in a bit of a black hole.
None the less I reviewed the dendrogram of that regional study and ‘comapred’ it with mine, with the dichotmoy’s being relatively similar. On that basis I suspect the stress levels may very well be similar.
“disjunctions = high stress” hmmm food for thought and thanks.
Thanks again as I have really appreciated your assistance. Statistics has never been my strong suit, but none the less an interest to say the least.May 23, 2008 at 6:39 am #516
Lee and Mark,
Thanks for your posts I have used these comments to improve my stress problems on vegetation analysis as well with similar high stress levels as what you were experiencing. 😀
Mark were you able to export your data and run it through the Fidel program set up by Mike Bedwood using the windows verson of PATN? The program I found on the web at http://www.emilythecamel.com/projects/patn/ only uses the dos version files. As I would like to perform this anaylsis on my data.
DebbieMay 23, 2008 at 6:56 am #517
I have not attempted such a task as yet. I will probably experiment with this sometiome in the future, but based on the type of data I’ve got and the apparent variability in the PATN analysis for the regional vegetation study, I’m not sure if the Fidelity classifications would be all that informative.
I did perform a rather exhaustive google search for the Fidelity stuff and came up with the same link. I don’t think you can import the .ptn file, and yes Mike’s program uses the dos version. Talking with Lee I understand that there may be Fidelity classification built into the next version. That would be nice if it is truely a value adding tool.
Still a bit swamped by the whole thing atm, but from persisting with countless analysis and re analysis I suspect a better way forward would be to look really closely at the two way tables and box whisker plots rather than rely on the Fidelity classification. I could be wrong though and would be happy to be told so whilst I muddle on with my work in isolation ❗
I spent considerable time reading and re-reading the worked examples. After about the 10th time, it takes a while for my brain to switch on, I started to really get the jist of it. If you haven’t invested the time or thoroughly understand the worked examples, then I really recommend looking at them some more. I am still reading tehm on occassion, there is alot of insight in those examples!
have a good weekendMay 24, 2008 at 12:51 pm #518
Thanks for the info I will look more closely at my data, and the worked examples, to gain a better understanding of my data.
Thanks for replying so promptly and good luck with your regional vegetation study.
DebbieMay 25, 2008 at 5:18 am #519
No worries. Always happy to contribute – it helps me articulate my thoughts better and better still I get exposed to new ideas. Look forward to chatting re: application of PATN.
By the way I’m not actually doing a regional veg study. What I am doing is trying to fit my data analysis (regional data) with a published regional study/ associated map. It hasn’t been the most straight forward analysis – too many ‘factors’ to consider with perhaps the most difficult being the broad community transitions compounded by limited survey sites and disturbances.
I notice your in the lower hunter. Are you using PATN for work to or Uni research?
MarkMay 25, 2008 at 11:43 am #520
I am using the PATN analysis for work, and I am just using it to help guide me in delineating the vegetation communities. I have collected abundance data via quadrats and PATN has identified variations within the vegetation communities ie heathy understorey versus grassy understory which is real neat.
I had a closer look at the two-way table and KW stats today and the data is starting to make sense as the wet sclerophyll species are delineating out the wet sclerophyll from the dry sclerophyll vegetation communities in my data. However, I keep finding data entry errors so I have a bit of work to go before the data is up to scratch. I am also finding that limited survey sites are an issue, and on occasions I seemed to have put a plot in an ecotonal area and this puts the data in a spin. Fragmentation and possible regrowth as my veg has a young cohort of trees (lower biodiversity) in some areas and mature forests add fire to that and I’m sure all this is affecting the data.
But all this makes it fun to nut out so I will press on and keep chipping away to reduce the stress.
With the FIDEL analysis I think it tells you the unique, positive, constant and uninformative species which describe each community. I think this is the way Stephen Bell (Gosford, Wyong), Travis Peake (Upper Hunter), Lisa Hill (Maitland) and the like have in their regional mapping. Though I have to look into it in more detail to be sure.
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