[R-sig-eco] help

/mds.html) but i haven't done it, i think the main problem is the form of excel matrix for doing it and also i want to know about different between CLASSICAL MDS and isoMDS. please help me because this method is new in iran Thanks in advance -- *Mahnaz Rabbaniha* *Senior expert of m

[R-sig-eco] Fwd: help

-- Forwarded message -- From: Mahnaz Rabbaniha Date: Sat, 10 Dec 2011 08:31:10 +0330 Subject: Re: [R-sig-eco] help To: Sarah Goslee Dear Sarah thank you for your attention, I want to use PCA with supplementary variables due to correlation between the independent factor such

[R-sig-eco] hi

hi for doing the PCA with supplementary variables in FactoMIneR , is it necessary all dependent and independent variables tested with shapiro, in my project i check the data and they are non normal then i transformed them in ( density of plankton as DV) with log(x+1) and (salinity,temperature,...

[R-sig-eco] correlation

Dear r-sig-ecology group, > > I am trying to find correlation between two variables. whereas they are > non-normal used Spearman in this way: > cor.test(SiO4,density,method="spearman") Spearman's rank correlation rho data: SiO4 and density S = 5263.445, p-value = 0.1184 alternative hyp

[R-sig-eco] correlation

hi in base of your guide to solve my problem in how can draw line in correlation i have done these steps,rank (x,y),plot (x,y) and introduce graphics and done abline but unfortunately i revise mis message again: > cor.test(SiO4,density,method="spearman") Spearman's rank correlation rho

[R-sig-eco] nmds in vegan

0 0 0 0 0 *38* *18.6* 45 0 0 0 0 0 *21* * 21.7* 42 0 0 0 0 0 *3.3* *23.3* 43 0 0 0 0.491712 0 -- Mahnaz Rabbaniha Senior expert of marine ecology Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116 , P.Code: 1411816618* Tehran, IRAN Phone: +98 21 44580953 Fax: +98 21

[R-sig-eco] nmds

Dear all I have done nmds in PAST, but i have question? can we put independent and dependent variable in a data sheet for plot coordination? how can interpret the stress for example: 0.14 ,0.2.? thanks -- Mahnaz ___ R-sig-ecology mailing list R-sig

[R-sig-eco] (no subject)

hi all groups in calculate correlation ,i received this message: > cor.test(depth,abundance,method="spearman") Spearman's rank correlation rho data: depth and abundance S = 76554.61, p-value = 0.03969 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 0

[R-sig-eco] graph

Hi dear all who changed the format( size,font,,,) of graph text in r thanks -- 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] CA

Hi,i would like use CA code in my data it is a metrics with 16 column ( abundance of fish larva) and 84 raw, this raw in three groups: Coralline,non-coralline and creek habitat . the data are non-normal and i have to use non-parametric analyses ,i want to find similarity or dissimilarity between t

[R-sig-eco] gam

Dear all i have done GAM for data ( they are non- normal and i find regression between Sillaginidae with several hydrological factors),i done : [1] "depth""temperature" "salinity" "Sillaginidae" > pairs(sc,panel=function(x,y){points(x,y);lines(lowess(x,y))}) > model<-gam(Sillagini

[R-sig-eco] gam result

Dear all for finding the relation between this variable i use gam ( in base of non-normality) [1] "temperature" "salinity""depth" "Clupeidae" model<-gam(Clupeidae~s(temperature)+s(salinity)+s(depth)) the result: Parametric coefficients: EstimateSt

[R-sig-eco] Poisson regression

Dear all to find relation between non-normal response with independents variable i use this code: model1<-gam(Clupeidae~s(depth)+s(temperature)+s(salinity),poisson) the result shown is: There were 50 or more warnings (use warnings() to see the first 50) > warnings(model1) Warning messages: 1:

[R-sig-eco] cozigam

Dear all for finding the regression in base of my data with many zero in Clupeidae ,i used this code: res.tps <- cozigam(Clupeidae~s(temperature,salinity)+s(depth), constraint = "proportional", family=gaussian) but for checking of this model( find the goodfiness,,,) i have problem. i will

[R-sig-eco] cozigam

hi in data sheet (response variable) is included many zero and for finding the regression i have to use cozigam. is there necessary transformed response variable? thanks -- Mahnaz [[alternative HTML version deleted]] ___ R-sig-ecology maili

[R-sig-eco] cozigam

hi i try to find regression between clupeidae,with temperature,salinity and depth. the response variable is inclued many zero ( 86 from 133 observed) therefore i used this code : res <- cozigam(Clupeidae~s(temperature,salinity)+s(depth), constraint = "proportional", family = gaussian) the res

[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 inde

r-sig-ecology@r-project.org

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 [[

[R-sig-eco] cozigam

Dear all please accept my apologized if my question is very basically for finding the relation on fish larva and environmental factors i used cozigam; > res <- cozigam(Sillaginidae~s(temperature,salinity)+s(depth), constraint = "proportional", family = gaussian) the result: Error in smoo

[R-sig-eco] CCA

Dear sig-eco users, Hi I would like to do cca in vegan package,the main question is about the response variable, there are a variety from 0 to 1300, it is necessary transformed them before the analyses or used in original form. thank you in advance for answering -- Mahnaz Rabbaniha marine

[R-sig-eco] anova

quot;~", xx), data = mf) : non-factors ignored: STATION > -- Mahnaz Rabbaniha marine ecology PhD Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116 , P.Code: 1411816618* Tehran, IRAN Phone: +98 21 44580953 Fax: +98 21 44580583 Mobile: +98 912 5790377 [[a

[R-sig-eco] monte carlo

Dear all i want to find the variation of zooplankton on some abiotic factors such as: temperature,salinity, nutrient by monte carlo in r . which one code in which package is the better selection. thanks -- Mahnaz Rabbaniha marine ecology PhD Iranian Fisheries Research Organization (IFRO

[R-sig-eco] GLM

Dear all I want to find regression between fish larva abundance and some abiotic factor ,i used this code: glm(formula = mychto ~ po4 + No3 + Si + Tn) result: Deviance Residuals: Min 1Q Median 3Q Max -26.586 -18.262 -12.296 -2.949 226.229 Coefficients: E

[R-sig-eco] AIC

HI DEAR ALL maybe my question is basically but I will be so glad for answer : in the result of GLM in base of family = poisson, AIC: Inf , What is the meaning? thanks all -- Mahnaz Rabbaniha marine ecology PhD Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116 , P.Code

[R-sig-eco] rda.

Dear all how i open file in rda. form? thanks -- Mahnaz Rabbaniha [[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] neuralnet

Dear all i have problem in interprate of neuralnet plot, i attached this plot could you please help me thanks -- Mahnaz Rabbaniha marine ecology PhD Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116 , P.Code: 1411816618* Tehran, IRAN Phone: +98 21 44580953 Fax: +98 21

[R-sig-eco] cozigam

.4626 -3.407 0.000658 *** delta10.4176 0.2826 1.478 0.139540 delta20. 0. NA NA or Warning message: In sqrt(diag(V.theta)[2:(n.delta + 1)]) : NaNs produced what are meaning? could you please explain them. thanks all -- Mahnaz Rabbaniha marine ecolo

[R-sig-eco] neural net work

Dear all I have a continuous response with a series of independent variables, i would like to nnt, which package and code is more useful for calculating? thanks -- Mahnaz Rabbaniha marine Ecologist, PhD Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116 Tehran, IRAN Phone

[R-sig-eco] pca in ade4

is meaning of this error thanks -- Mahnaz Rabbaniha marine Ecologist, PhD Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116 Tehran, IRAN Phone: +98 21 44580953 Fax: +98 21 44580583 [[alternative HTML version dele

[R-sig-eco] cca

t also show the names of zooplankton groups? regards -- Mahnaz Rabbaniha marine Ecologist, PhD Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116 Tehran, IRAN Phone: +98 21 44580953 Fax: +98 21 44580583 [[alternative HTML version d

[R-sig-eco] help

-- Mahnaz Rabbaniha marine Ecologist, PhD Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116 Tehran, IRAN Phone: +98 21 44580953 Fax: +98 21 44580583 ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch

[R-sig-eco] neural net work

Dear all for nnt on continues variable response,please inform which package or code is appropriate? thanks mahnaz -- Mahnaz Rabbaniha marine Ecologist, PhD Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116 Tehran, IRAN Phone: +98 21 44580953 Fax: +98 21 44580583

[R-sig-eco] error in install packge

Dear all for installing of new packages i select the country but i have gotten the error message any times: Warning: unable to access index for repository http://mirrors.softliste.de/cran/bin/windows/contrib/3.0 Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bi

[R-sig-eco] cca

0 0 0 TOM0.63367 -0.6390 0.4239 0 0 0 *silt is not in the summary part??/* Please inform me what is problem all the best -- Mahnaz Rabbaniha Marine Ecologist, PhD Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116 Tehran, IRAN Phone: +98 21 44580953 Fax:

[R-sig-eco] Neural Networks

Dear all could you please to introduce: which code in which package use for nnt on continuous response? thanks mahnaz [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailma

[R-sig-eco] Correlogram

hi Dear all member in the advance graph i see the Correlogram and have done one of them plot: *corrgram(mtcars, order=TRUE, lower.panel=panel.shade, upper.panel=panel.pie, text.panel=panel.txt, main="Car Milage Data in PC2/PC1 Order")* could you please how to interprate the plot and find t

[R-sig-eco] gis

Dear all in using of GIS codes after the install the packages and add the (FieldSamples.csv): *samps <- read.csv("FieldSamples.csv") * I revised this message: Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'Fie

[R-sig-eco] RDA

Dear all I want to apply RDA in vegan package on my data ( fish larva , hydrological factors). After the coding: mod1 <- rda(bi~Depth+Transparency+Salinity+Temperature+PH+Chlorophyll, data=mo) > plot(mod1) > summary(mod1) I have taken this answer: Call: rda(formula = bi ~ Depth + Transparency +

[R-sig-eco] gis

or example: 1: 25000, ? thanks mahnaz -- *Mahnaz Rabbaniha* *Marine Ecologist, PhD* *Executive manager of IJFS* *Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116Tehran, IRAN Phone: +98 21 44580953Fax: +98 21 44580583* [[alternative HTML version deleted]] _

[R-sig-eco] gis2

colour="red"),data=geot,cex=3) all the best mahnaz -- *Mahnaz Rabbaniha* *Marine Ecologist, PhD* *Executive manager of IJFS* *Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116Tehran, IRAN Phone: +98 21 44580953Fax: +98 21 445

[R-sig-eco] Fwd: gis2

-- Forwarded message -- From: Mahnaz Rabbaniha Date: Wed, Oct 28, 2015 at 11:31 AM Subject: gis2 To: r-sig-ecology Dear all which code is used for adding the characters of point for example abundance ( in attach file i send the excel ) I have done this code: library(ggmap

[R-sig-eco] boxplot

Dear all, maybe my question is very simple and basically.please accept my apologize. for coding of box plot i send this order on my data with two column: month (May-09,.Dec-10) and temperature. boxplot(Temprature~month) but in plot the X shown Dec-10 to the May-09, it is just convert.what i

[R-sig-eco] xlsx load

Dear all I want to load the xlsx package and ,the R version is 3.3.1 (2016-06-21) . but i cant and have taken this message: > local({pkg <- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE) + if(nchar(pkg)) library(pkg, character.only=TRUE)}) Loading required package: rJava Error :

[R-sig-eco] CCA INTERPRATE

analyses acceptable or no? all the best -- *Mahnaz Rabbaniha* *Marine Ecologist, PhD* *Executive manager of IJFS* *Iranian Fisheries Research Organization (IFRO) P.O.Box: 14155-6116Tehran, IRAN Phone: +98 21 44580953Fax: +98 21 44580583* [[alternative HTML version deleted

[R-sig-eco] ordinal regration

you please send your suggestion or any link for that. for more inform, I have attached the text in exam.it is necessary to point that the independent variables are average of five questions in the Likert scale (rating scale is 1,2,3,4,5). best mahnaz -- *Mahnaz Rabbaniha* *Marine Ecologist, PhD

[R-sig-eco] Fwd: ordinal regration

-- Forwarded message -- From: *Mahnaz Rabbaniha* Date: Tuesday, July 16, 2019 Subject: ordinal regration To: r-sig-ecology Dear all, I have some data in the social study: Right to the city ( dependent variable ) and 6 independent variables (appropriation, participation

[R-sig-eco] PCA–GAM

method such as PCA-GAM. best regards *Mahnaz Rabbaniha* [[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] predict in decision tree

Dear all, I have done the rf and gbm in R packages between response continue variable and independent variables, My main request about the predicted plot in R, could you please introduce the package in this field? best regards, *Mahnaz * [[alternative HTML version deleted]] _