[R-sig-eco] cozigam
Dear R users, I am analyzing data using a COZIGAM model The model is: res - cozigam(Clupeidae~s(temperature,salinity), constraint = proportional, family = gaussian) Clupeidae = abundance (from 132 observed 85 items=0 ), LDH = log of a distance that I am interested in, and SI3 = is a index of invasion severity, but these details are not important. The result: iteration = 2norm = 0.9998562 iteration = 3norm = 0.120129 iteration = 4norm = 0.01653977 iteration = 5norm = 0.000226035 == estimated alpha = -0.486186 ( 0.2076793 ) estimated delta = 0.01016082 ( 0.004780538 ) I am trying to plot for the effects of temperature and salinityindividually on Clupeidae through the code below: summary(res) Family: gaussian Link function: identity Formula: Clupeidae ~ s(temperature, salinity) Parametric coefficients: Estimate Std. Errort valuePr(|t|) (Intercept)-20.665505 13.904231 -1.486 0.1401 alpha-0.486186 0.207679-2.3410.0210 * delta10.010161 0.004781 2.1250.0358 * Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Approximate significance of smooth terms: Edf Est.rankF p-value s(temperature,salinity) 20.81 29 8.77 2e-16 *** Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Scale est. = 270.56n = 132 my problem is the interpret of the results ,is the result acceptable? For checking the good fitness of result, which code is used? For example :which code for plotting of the residuals and the plot of residuals vs. fitted Values is applied? Thanks a bunch for any suggestions that anyone can offer. -- Mahnaz [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] plot data on base of lonlat
Hi groups i want plot of phytoplankton density on base of Lon lat, as same as the description on the cozigam package. but the main problem is the form of matrix Lon parameters in the example on eggdata that is negative ,how changed the longitude to this form ? thanks all Mahnaz [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] plot data on base of lonlat
I don't completely understand your question, but is it perhaps that west longitude is often represented as negative? Otherwise, please provide a reproducible example, using data from the cogizam package if you'd like, or at least a clear guide to where you've found this example and how it differs from your own data. Sarah On Thu, Jul 5, 2012 at 11:38 AM, Mahnaz Rabbaniha rab.mah...@gmail.com wrote: Hi groups i want plot of phytoplankton density on base of Lon lat, as same as the description on the cozigam package. but the main problem is the form of matrix Lon parameters in the example on eggdata that is negative ,how changed the longitude to this form ? thanks all Mahnaz -- Sarah Goslee http://www.functionaldiversity.org ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] plot data on base of lonlat
Hello Mahnaz, Longitude is often expressed as distance or angle east of the prime meridian, so negative means it is west. If I am reading your question correctly, you are wondering how to change the longitude to make it negative? If so, you could create a new variable that is -1 times the original latitude for west coordinates, as in this example: newlongitude - -1 * oldlongitude If the coordinates are for the eastern hemisphere you should leave them as positive values. Jeff __ Jeffrey D. Holland Assoc. Prof. of Landscape Ecology Biodiversity Dept. of Entomology, Purdue University -Original Message- From: r-sig-ecology-boun...@r-project.org [mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of Mahnaz Rabbaniha Sent: Thursday, July 05, 2012 11:38 AM To: r-sig-ecology Subject: [R-sig-eco] plot data on base of lonlat Hi groups i want plot of phytoplankton density on base of Lon lat, as same as the description on the cozigam package. but the main problem is the form of matrix Lon parameters in the example on eggdata that is negative ,how changed the longitude to this form ? thanks all Mahnaz [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] plot data on base of lonlat
Hello Mahnaz, I have not used the cozigam package, but I would guess that if your longitude coordinates are for the western hemisphere you will want to have them negative. If they are for the eastern hemisphere then what you have is correct. You can check that they are displaying properly by examining the resulting plot. If the points are a mirror image of what you expect, then you need to change the sign of the longitude. Hope that helps. Jeff __ Jeffrey D. Holland Assoc. Prof. of Landscape Ecology Biodiversity Dept. of Entomology, Purdue University From: Mahnaz Rabbaniha [mailto:rab.mah...@gmail.com] Sent: Thursday, July 05, 2012 12:10 PM To: Holland, Jeffrey D Subject: Re: [R-sig-eco] plot data on base of lonlat excuse me it is necessary revised the my data matrix: phyto Temperature Salinity lat lon 6279.28 28.40206061 37.94621212 27. 2106 52.3402 25285.11667 28.70556522 37.55017391 27.1302 52.2808 34467.0 30.0357 37.5787 27.040852.2208 thanks On Thu, Jul 5, 2012 at 8:35 PM, Mahnaz Rabbaniha rab.mah...@gmail.commailto:rab.mah...@gmail.com wrote: thanks for answer but for question clearly i take a part of my data: phyto Temperature Salinity lat lon 6279.2833 28.40206 37.94621 27. 2106 52.3402 25285.117 28.70557 37.55017 27.1302 52.2808 34467.033 30.0357 37.5787 27.0408 52.2208 when i compare this with sample in cozigam pakage: i notice the lon in this matrix is different ( you can see in dawn) R head(eggdata) bottom lon lat catch j.day year 1 170 -147.7500 59.3 0 99 1987 2 620 -147.7500 59.01333 0 100 1987 3 160 -148.3000 59.0 0 100 1987 4 135 -148.3167 59.35000 0 100 1987 5 175 -149. 59.0 0 101 1987 6 115 -149.0333 58.3 0 101 1987 the question is: i have to change the lon in my matrix as sample or no? thanks On Thu, Jul 5, 2012 at 8:21 PM, Holland, Jeffrey D jdhol...@purdue.edumailto:jdhol...@purdue.edu wrote: Hello Mahnaz, Longitude is often expressed as distance or angle east of the prime meridian, so negative means it is west. If I am reading your question correctly, you are wondering how to change the longitude to make it negative? If so, you could create a new variable that is -1 times the original latitude for west coordinates, as in this example: newlongitude - -1 * oldlongitude If the coordinates are for the eastern hemisphere you should leave them as positive values. Jeff __ Jeffrey D. Holland Assoc. Prof. of Landscape Ecology Biodiversity Dept. of Entomology, Purdue University -Original Message- From: r-sig-ecology-boun...@r-project.orgmailto:r-sig-ecology-boun...@r-project.org [mailto:r-sig-ecology-boun...@r-project.orgmailto:r-sig-ecology-boun...@r-project.org] On Behalf Of Mahnaz Rabbaniha Sent: Thursday, July 05, 2012 11:38 AM To: r-sig-ecology Subject: [R-sig-eco] plot data on base of lonlat Hi groups i want plot of phytoplankton density on base of Lon lat, as same as the description on the cozigam package. but the main problem is the form of matrix Lon parameters in the example on eggdata that is negative ,how changed the longitude to this form ? thanks all Mahnaz [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.orgmailto:R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ R-sig-ecology mailing list R-sig-ecology@r-project.orgmailto:R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] adehabitat in R
Hi, everybody i´m new in this, I need help for work in ENFA anlyses and determine the habitat selection of a marine specie, i have a data matrix with oceanographic variables linked to specie presence and i have another matrix with the same variables but wihtout the presence of the specie (anchovy). Can someone help me on the step to follow for the analyses (a code for example). Any suggestion i will appreciate, regards, Carolina From Chile. -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/adehabitat-in-R-tp7577494.html Sent from the r-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] adehabitat in R
Dear Carolina, I already replied to your question on R-sig-Geo [1]. Please avoid cross-posting and continue there if any additional help is required. You may want to read the R posting guide [2], too. Mathieu. [1] https://stat.ethz.ch/pipermail/r-sig-geo/2012-July/015538.html [2] http://www.r-project.org/posting-guide.html Le 05/07/2012 17:45, carolang a écrit : Hi, everybody i´m new in this, I need help for work in ENFA anlyses and determine the habitat selection of a marine specie, i have a data matrix with oceanographic variables linked to specie presence and i have another matrix with the same variables but wihtout the presence of the specie (anchovy). Can someone help me on the step to follow for the analyses (a code for example). Any suggestion i will appreciate, regards, Carolina From Chile. -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/adehabitat-in-R-tp7577494.html Sent from the r-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- ~$ whoami Mathieu Basille, Post-Doc ~$ locate Laboratoire d'Écologie Comportementale et de Conservation de la Faune + Centre d'Étude de la Forêt Département de Biologie Université Laval, Québec ~$ info http://ase-research.org/basille ~$ fortune ``If you can't win by reason, go for volume.'' Calvin, by Bill Watterson. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
