Help with ENFA in R
Le 04/09/2013 03:51 PM, JonathanAronson a ?crit :
Hi Mathieu
Thank you so much for your quick response. I really appreciate the effort
and thank you for your answers.
I am now using the AdehabitatHS package but still have some questions.
1) I am not sure what (renfa$expvar), (renfa$pvalue) and (renfa$obs) are
actually telling me in the output. I have copied the output below:
(renfa$expvar)
Std.Obs Expectation Variance
45.557688 7.316997 11.538948
$expvar gives you the expected value from the simulated set
('Expectation'), i.e. the mean of the simulated values, together with its
variance. 'Std.Obs' tells you how much the observed value differs from the
distribution: it is basically the ratio of the difference between the
observed and the mean of simulated values, over the standard deviation of
the simulated values. You expect a difference equal to the SD, i.e. a ratio
'Std.Obs' of 1.
(renfa$pvalue)
[1] 0.001
This is the p-value of the test. See ?randtest for the details of the computation.
(renfa$obs)
[1] 162.072
This is the observed value (here the first specialization eigenvalue). The best way to summarize the results is to simply print the object, by a direct call to 'renfa' in your case. Then, use 'plot(renfa)' for a very neat graphical display of the test.
2) because i am using AdehabitatHS do I not need the following line of code anymore: map<- as.kasc(list(bio_01 = var1, bio_12 = var2, Aridity = var3, altitude = var4, unpalatable = var5, thicket = var6, succulent = var7, shrubland = var8, rainforest = var9, mosaic = var10, mopane = var11, misavanna = var12, hydro = var13, fynbos = var14, desert = var15)) enfatest<- data2enfa(map, test)
No you don't. adehabitatHS uses 'sp' classes. Please have a look at the
vignette of both packages for more details:
vignette("intro_sp")
vignette("adehabitatHS")
3) I also got two error messages:
image(enfatest1)
Error in image.default(enfatest1) : 'z' must be a matrix
This is quite normal... Assuming 'enfatest1' is the result of the ENFA, there's no image function for such object... Check the section on the ENFA in the above cited vignette.
niche.test(map, test, nrepet = 999, o.include = FALSE)
Warning messages: 1: In hist.default(x, plot = FALSE, br = xbr, freq = FALSE) : argument ?freq? is not made use of 2: In hist.default(y, plot = FALSE, br = ybr, freq = FALSE) : argument ?freq? is not made use of
Not sure here, but I bet that the problem comes also from the class of 'map' and/or 'test'. Check the vignette and the example of the function. Mathieu.
Mathieu, could you please provide some assistance with these questions? Thank you Jonathan -- View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Help-with-ENFA-in-R-tp7583243p7583258.html Sent from the R-sig-geo mailing list archive at Nabble.com.
_______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
~$ whoami Mathieu Basille, PhD ~$ locate --details University of Florida \\ Fort Lauderdale Research and Education Center (+1) 954-577-6314 http://ase-research.org/basille ~$ fortune ? Le tout est de tout dire, et je manque de mots Et je manque de temps, et je manque d'audace. ? -- Paul ?luard