Re: [R-sig-eco] plot confidence interval binomial glm

HTML version deleted]] > > ___ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre U

Re: [R-sig-eco] [EXTERNAL] Time to Independence in R

ampling frequency than empirical estimation form a "continuous" > datastream of limited duration. That approach also helps me think about > the spatial concordance of the correlated errors: which are site-specific, > which are concordant across all of the sites. > > Tom >

[R-sig-eco] Time to Independence in R

to take into account the temporal autocorrelation of the data, but I am asking to optimize the data collection, before modeling. Thank you very much in advance. Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado

[R-sig-eco] Appropriate model parameterization in lme4 for spatio-temporal structured data

(1 | location) + (1 | day/hour/min), data = my_data) Thank you very much in advance. Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.cr mspinol...@gmail.com Teléfono: (

Re: [R-sig-eco] Ecological datasets for teaching statistics

ion of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body of data. > ~ John Tukey > > /////////// > > <https://www.inbo.be>

Re: [R-sig-eco] Ecological datasets for teaching statistics

Thank you very much Mollie. Manuel El jue., 18 jun. 2020 a las 14:12, Mollie Brooks () escribió: > > > On 18Jun 2020, at 19:58, Manuel Spínola wrote: > > Thank you very much Rich. > > Yes, you are right, is a very broad spectrum. > > I teach mainly to wildlife ecolog

Re: [R-sig-eco] Ecological datasets for teaching statistics

812-8842 | mike.mahoney....@gmail.com > > > On Thu, Jun 18, 2020 at 2:14 PM Manuel Spínola > wrote: > >> Thank you very much Rich. >> >> Manuel >> >> El jue., 18 jun. 2020 a las 12:11, Rich Shepard (< >> rshep...@appl-ecosys.com>) >

Re: [R-sig-eco] Ecological datasets for teaching statistics

Thank you very much Rich. Manuel El jue., 18 jun. 2020 a las 12:11, Rich Shepard () escribió: > On Thu, 18 Jun 2020, Manuel Spínola wrote: > > > I teach mainly to wildlife ecology students. > > Manuel, > > I'm a stream ecologist/fluvial geomorphologist but hav

Re: [R-sig-eco] Ecological datasets for teaching statistics

Behalf Of > Rich Shepard > Sent: Thursday, June 18, 2020 10:38 AM > To: r-sig-ecology@r-project.org > Subject: [EXTERNAL] Re: [R-sig-eco] Ecological datasets for teaching > statistics > > On Thu, 18 Jun 2020, Manuel Spínola wrote: > > > I teach statistics to stude

Re: [R-sig-eco] Ecological datasets for teaching statistics

0 a las 11:41, Rich Shepard () escribió: > On Thu, 18 Jun 2020, Manuel Spínola wrote: > > > I teach statistics to students in ecology and environmental sciences > > fields and I would like to know if you could point me in the right > > direction of sources of ecological

Re: [R-sig-eco] Ecological datasets for teaching statistics

demy of Science > http://www.bugsmapsandmath.com > > ---*/ > > ________ > From: R-sig-ecology on behalf of > Manuel Spínola > Sent: Thursday, June 18, 2020 1:20 PM > To: r-sig-ecology@r-proj

[R-sig-eco] Ecological datasets for teaching statistics

multivariate statistics. Manuel Spínola -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.cr mspinol...@gmail.com Teléfono: (506) 8706 - 4662 Personal website: Lobito de río

[R-sig-eco] Mixed model in R

following model parameterization appropriate in the lme4 package: mod_adi_01 <- lmer(ADI ~ Season*CoverType + (1 | Point) + (1 | Month) + (1 | Day) + (1 | Hour), data = df_01, REML = FALSE) Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silves

Re: [R-sig-eco] UK.AdvancingInRForEcologists.Dec4-8

> PR statistics > > 2017 publications - > > Ecosystem size predicts eco-morphological variability in post-glacial > diversification. Ecology and Evolution. In press. > > The physiological costs of prey switching reinforce foraging > specialization. Journal of animal

Re: [R-sig-eco] UK.AdvancingInRForEcologists.Dec4-8

A USING > R #MVSP > Prof. Pierre Legendre, Dr. Olivier Gauthier - Date and location to be > confirmed > > > -- > Oliver Hooker PhD. > PR statistics > > 2017 publications - > > Ecosystem size predicts eco-morphological variability in post-glacial > diver

Re: [R-sig-eco] How to include math symbols in a data frame

olumn3 <- paste("<= ", c(0.5, 0.6, 0.9)) > > table <- data.frame(column1, column2, column3) > > table > > > " > > > > Watch out not to mix English with Spanish while scripting fast. > > > Pura Vida! > > > Yaïr Levy > >

[R-sig-eco] How to include math symbols in a data frame

0.6, 0.9) table <- data.frame(columna1, columna2, columna3) kable(table) How can I include the math symbol in the table? Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una

Re: [R-sig-eco] mvpart alternatives and machine learning multivariate analysis

s datasets methods base >> > >> > other attached packages: >> > [1] mvpart_1.6-2 >> > >> > loaded via a namespace (and not attached): >> > [1] compiler_3.4.0 >> >> >> However, there are certainly other packages that c

Re: [R-sig-eco] mvpart alternatives and machine learning multivariate analysis

t; >> > other attached packages: >> > [1] mvpart_1.6-2 >> > >> > loaded via a namespace (and not attached): >> > [1] compiler_3.4.0 >> >> >> However, there are certainly other packages that can partition >> multivariate ecologi

Re: [R-sig-eco] mvpart alternatives and machine learning multivariate analysis

t; > Manuel > > -- > *Manuel Sp?nola, Ph.D.* > Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre > Universidad Nacional > Apartado 1350-3000 > Heredia > COSTA RICA > mspin...@una.cr > mspinol...@gmail.com > Tel?fono: (506) 8706 - 4662 > Personal w

[R-sig-eco] mvpart alternatives and machine learning multivariate analysis

relationships? Thank you very much in advance, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.cr mspinol...@gmail.com Teléfono: (506) 8706 - 4662 Personal website: Lobito de río

[R-sig-eco] How to compare 2 independent estimates in R

effect size (the difference between estimates) with the 95% confidence limits. Is there any package that allow me to do that? Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin

[R-sig-eco] Machine learning in R for ecology

-- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.cr mspinol...@gmail.com Teléfono: (506) 8706 - 4662 Personal website: Lobito de río <https://sites.google.com/site/lobitode

[R-sig-eco] Repeated mesaures mixed model in R

ble ~ occasion * treatment + (occasion | plot/subplot) Is the model parameterization correct? Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.cr mspinol...@gmail.

Re: [R-sig-eco] Package to analyse population time series (trend analysis)

en't yet dealt with. > > A bit more information about what you have in terms of data, and about the > questions you are interested within the broad definition of "trend" might > get you informed answers. > > Tom 2 > > > > On Wed, Oct 19, 2016 at 5:47 AM, Man

[R-sig-eco] Package to analyse population time series (trend analysis)

Dear list members, What is the appropriate package to analyze population time series (trend analysis) when you have one count per year. Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia

Re: [R-sig-eco] Question on unexpected regression results

Dear Bruce, Besides any other problems I can see that you consider FA as a factor and that could be a problem with your data set. Manuel 2014-07-30 7:10 GMT-06:00 Bruce Miller : > Hi all, > > Sorry this is a bit long, but the explanation of what I want to do needs > to be clear to avoid issue

Re: [R-sig-eco] report out by t.test

ecology mailing list >> R-sig-ecology@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >> > > > -- > Botta-Dukát Zoltán > ------------ > Ökológiai és Botanikai Intézet > Magyar Tudományos Akadémia > Ökológiai Kutatóközpont > &g

[R-sig-eco] Error when installing packages in R.3.0.2 (Windows 7)

24aee/Rcmdr/doc/Commander-ru.pdf': Permission denied Any idea how to solve this issue? Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.co

Re: [R-sig-eco] How to remove space among columns

d", "d")) > ll=paste(l$col1, l$col2, l$col3, l$col4, sep="") > data.frame(ll, a=l$col5, b=l$col6) > > see ?paste > > bret > > > On 3/27/2013 8:15 AM, Manuel Spínola wrote: > >> Thank you very much to all that answered my question, some

Re: [R-sig-eco] How to remove space among columns

Thank you very much to all that answered my question, some one of you asked me to be more specific, here is my question again: I hava a data frame: col1 col2 col3 col4 col5 col6 01 1 0 ac 10 0 0 ad 01 1 1 bd I want to en

[R-sig-eco] How to remove space among columns

Dera list members, How to remove spaces among columns in a data frame. 1 2 3 4 to become 1234 Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol

[R-sig-eco] Error message in adehabitatHR

identicalCRS(x, y) is not TRUE Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfono: (506) 2277-3598 Fax: (506) 2237-7036 Personal we

Re: [R-sig-eco] Very large dispersion parameter in a negative binomial model

g glm instead of glm.nb > > cheers, > Mollie > > Mollie Brooks > Postdoctoral Researcher, Ponciano Lab > Biology Department, University of Florida > http://people.biology.ufl.edu/mbrooks > > > On 3 Feb 2013, at 10:16 AM, Manuel Spínola wrote: > > Dear list membe

[R-sig-eco] Very large dispersion parameter in a negative binomial model

rations: 1 Theta: 67553 Std. Err.: 1428117 Warning while fitting theta: iteration limit reached 2 x log-likelihood: -59.058 Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apart

[R-sig-eco] qAIC

=16) val [1] NA Thank you very much in advance, Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfono: (506) 2277-3598 Fax: (506) 2

Re: [R-sig-eco] Replacing values in a data frame

er >> >> -- >> Péter Sólymos, Dept Biol Sci, Univ Alberta, T6G 2E9, Canada AB >> soly...@ualberta.ca, Ph 780.492.8534, http://psolymos.github.com >> Alberta Biodiversity Monitoring Institute, http://www.abmi.ca >> Boreal Avian Modelling Project, http://www.borealbird

Re: [R-sig-eco] Replacing values in a data frame

Thank you very much Sarah. No, just to replace the values greater than 1 in X2. Best, Manuel 2012/10/25 Sarah Goslee > Hi, > > 2012/10/25 Manuel Spínola : > > Dear list members, > > > > I want to replace the values of a numerical variable in a data frame > ca

[R-sig-eco] Replacing values in a data frame

Dear list members, I want to replace the values of a numerical variable in a data frame called "A". A X1X2 2 1.5 31 41.2 How to replace any value greater than 1 by the value 1 in the variable X2. Thank you very much in advance. Best, Manuel -- *Manu

Re: [R-sig-eco] Comparing survival curves

Adrian, You can take a look at the R package wild1. Best, Manuel Spínola 2012/9/6 AdRiAnA HuMaNeS > Hi Rlisters: > > I'm doing survival analysis comparing 8 populations. I've used the > survdiff function for comparing survival curves and the result I obtained > s

Re: [R-sig-eco] Understanding cbind

[,c(3, 5)]) # Also does not. > > DET <- as.data.frame(finaldf[,3:6]) # Also attaches the column names > > DET <- as.data.framefinaldf[,3]) # Also does not. > > DET <- as.data.frame(finaldf[,c(3, 5)]) # Also does not. > > > Hope this helps, > Phil > > > >

[R-sig-eco] Understanding cbind

0 0 0 0 0 0 [2,] 0 1 0 0 1 0 [3,] 0 0 0 0 0 0 [4,] 0 1 1 1 1 1 [5,] 1 1 1 0 1 0 [6,] 1 0 0 0 0 1 Best, Manuel -- *Manuel Spínola, Ph.D.* Instit

Re: [R-sig-eco] Example on trend analysis for biological monitoring

On 07/14/2012 10:05 AM, Manuel Spínola wrote: > > Dear list members, > > Is there any simple example for teaching purposes on how to use R to > analyze a time series in a biological monitoring context? > > Best, > > Manuel > > > > > _

[R-sig-eco] Example on trend analysis for biological monitoring

Dear list members, Is there any simple example for teaching purposes on how to use R to analyze a time series in a biological monitoring context? Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000

Re: [R-sig-eco] Recode several variables with conditions in a data frame

ta.frame(x=xx[,1], yy) > > bret > > > > > On 7/3/2012 9:18 PM, Manuel Spínola wrote: > >> Thank you Bret. >> >> What if I need to leave out some variables from my data frame. I have 22 >> variables and I need to leave the 2 first variables out o

Re: [R-sig-eco] Recode several variables with conditions in a data frame

=c(2, 10), y=c(2, 0)) > xx[xx!=0]=1 > xx > x y > 1 1 1 > 2 1 0 > > Bret > > > On 7/3/2012 8:12 PM, Manuel Spínola wrote: > >> Dear list members, >> >> I want to recode a data frame but do it for several variables at the same >> time. I

[R-sig-eco] Recode several variables with conditions in a data frame

o '.data' no encontrado I guess I am not setting the condition in a proper way. Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfon

[R-sig-eco] Re-arrange data frame

item2 5 4 item3 3 5 item3 4 3 Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfono: (506) 2277-3598 Fax

Re: [R-sig-eco] Carrying capacity in R

; Alberta Biodiversity Monitoring Institute, http://www.abmi.ca > Boreal Avian Modelling Project, http://www.borealbirds.ca > > > 2012/6/28 Manuel Spínola : > > Dear list members, > > > > Is there any package (and function) to assess carrying capacity for > > biological po

[R-sig-eco] Carrying capacity in R

Dear list members, Is there any package (and function) to assess carrying capacity for biological population? Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin

Re: [R-sig-eco] NMDS with metaMDS from vegan following an example from Numerical Ecology with R

Thank you very much Jari, Using weakties = FALSE it works very well. The results are similar to the book. Best, Manuel > e.mds = metaMDS(especies, distance = "bray", weakties = FALSE) Run 0 stress 0.1088505 Run 1 stress 0.113103 Run 2 stress 0.1356066 Run 3 stress 0.1088552 ... procrustes: rms

[R-sig-eco] NMDS with metaMDS from vegan following an example from Numerical Ecology with R

you have empty rows: their dissimilarities may be meaningless in method “bray” > My results are "strange" (stress is too low and different to the one on the book) and the plot is very different to the one that appears in the book. Any clue what is the problem? Best, Manuel -- *Manuel

[R-sig-eco] R and WinBUGS

? Is R not capable of doing the same type of analysis? Any input will be appreciated. Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com

Re: [R-sig-eco] Using partykit::ctree with observations that are spatially autocorrelated

> another point is that the practitioner that will be presented the results > won't be very happy with > regression-cofficients, model-comparisons, AIC and friends. contrary, > ctree would yield an intuitive and simple result which i would fancy for > this purpose! > > yours

Re: [R-sig-eco] Using partykit::ctree with observations that are spatially autocorrelated

browse_thread/thread/f45bd5ab12aa127d/26446409f3e2a140?lnk=gst&q=spatial%23#26446409f3e2a140 > > best, > kay > > > 2012/3/20 Manuel Spínola > >> You need to look in the "unmarked" package. >> >> Best, >> >> Manuel Spínola >> >> 2012/

Re: [R-sig-eco] R-sig-ecology Digest, Vol 48, Issue 16

You need to look in the "unmarked" package. Best, Manuel Spínola 2012/3/20 Isidore AMAHOWE > This may be possible with an R packages but i don't know. What i've been > told is that a kind of analysis can be done with accupancy analysis and > this will

Re: [R-sig-eco] Landscape ecology in R

Sefick > Third hit in a google search for: landscape ecology R > > http://nricaribou.cc.umanitoba.ca/R/ > > > On 03/09/2012 04:53 PM, Manuel Spínola wrote: > > Dear list members, > > I am looking for any reference or material on landscape ecology analysis in > R. &

[R-sig-eco] Fwd: Landscape ecology in R

-- Forwarded message -- From: Manuel Spínola Date: 2012/3/11 Subject: Re: [R-sig-eco] Landscape ecology in R To: Sarah Goslee Thank you Sarah and Stephen, I am in contact with Paul Galpern who developed some tutorials on landscape ecology in R (the ones that Stephen pointed

[R-sig-eco] Landscape ecology in R

Dear list members, I am looking for any reference or material on landscape ecology analysis in R. Thank you very much in advance. Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA

[R-sig-eco] Predict with 2 factors in an additive model

uot;a", "b")), f2 = factor(c("b", "a"))) > predict(mod1, newdata = newData, appendData = TRUE) 1 2 1.0460148 0.9468983 Thank you very much in advance. Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación

Re: [R-sig-eco] Change the text in the strips of a Lattice plot

enfriado", "enfriado") > > xyplot(uptake ~ conc | Type * Treatment, > groups = Plant, type = "b", lty = rep(1:3, 4), strip = strip.custom( > var.name = c("Type", > "Treatment "), strip.names = c(T,T), style = 3), data = CO2) > >

[R-sig-eco] Change the text in the strips of a Lattice plot

instead of "Quebec" and "Mississippi" for Type. Thank you very much in advance. Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac

Re: [R-sig-eco] subsetting data in R

factor by default (which is what gdata::drop.levels [insanely in my > opinion] does). > > On 11-04-24 11:21 AM, Manuel Spínola wrote: >> Thank you for all the responses. >> >> Is there a way to do a complete data set from an object in R? >> I have a data set with

Re: [R-sig-eco] subsetting data in R

Thank you for all the responses. Is there a way to do a complete data set from an object in R? I have a data set with more than 3000 columns. The subsetting is ok but it could be dangerous if you are using other factors to do some analysis as you need to specify the levels for all your factors

Re: [R-sig-eco] subsetting data in R

Thank you very much Gustavo. That works. Manuel On 24/04/2011 08:30 a.m., Gustavo Carvalho wrote: > pa2<- subset(pa, influencia=="AP") > pa2$influencia<- factor(pa2$influencia) > levels(pa2$influencia) > > On Sun, Apr 24, 2011 at 11:24 AM, Manuel Spínola > wrote: >> Thank you very much for yo

Re: [R-sig-eco] subsetting data in R

Thank you Christian. Following your suggestion I got the following result, > pa2 = subset(pa, influencia=="AP") > pa2$influencia<-as.factor(pa2$influencia) > levels(pa$influencia) [1] "AID" "AII" "AP" On 24/04/2011 07:42 a.m., Christian Parker wrote: > You are creating a new object, but the

Re: [R-sig-eco] subsetting data in R

; $ value: int 1 2 3 4 5 6 >> subset(testdata, group=="A") > group value > 1 A 1 > 4 A 4 >> subset(testdata, group=="A")$group > [1] A A > Levels: A B C >> ?subset >> factor(subset(testdata, group=="A")$group) &g

[R-sig-eco] subsetting data in R

uot; "AII" "AP" Why is that? I was thinking that I was creating a new data frame with only AID as a level for influencia. How can I make a complete new object with only the observations for "AID" and that the only level for influencia is indeed "AID"? B

Re: [R-sig-eco] Sites names with spaces in ordiplot

Thank you very much Gavin. I understand now. Best, Manuel On 01/04/2011 05:29 a.m., Gavin Simpson wrote: > On Fri, 2011-04-01 at 05:14 -0600, Manuel Spínola wrote: >> Gavin and Jari, thank you very much. >> >> Actually, I am interested in both, sites and species. I have 3000 >> species (tropi

Re: [R-sig-eco] Sites names with spaces in ordiplot

Gavin and Jari, thank you very much. Actually, I am interested in both, sites and species. I have 3000 species (tropical forest trees) and I am trying to read the txt file with read.table. I tried also read.delim, but I don't know how to bring the sites names in the plot. I guess now I have

[R-sig-eco] Sites names with spaces in ordiplot

Dear list members, I would like to include sites names with blank spaces in an ordiplot for an nmds (in vegan). How I do that? Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA

Re: [R-sig-eco] Error with "raup" distance, in metaMDS

e current version of vegdist() has been updated to reflect > discussion in Chase et al 2011 in Ecosphere > (http://www.esajournals.org/doi/abs/10.1890/ES10-00117.1). > > -Brian > > On 3/28/2011 12:00 PM,"Manuel Spínola" wrote: >> Is the Raup--Crick dissimilari

Re: [R-sig-eco] [POSIBLE SPAM] Re: Error with "raup" distance in metaMDS

Thank you very much Jari. Is the Raup--Crick dissimilarity metric the only option for a presence/absence data in "vegdist" or using binary = T could I use any other dissimilarity metric? Best, Manuel On 27/03/2011 09:07 a.m., Jari Oksanen wrote: > On 26/03/11 17:35 PM, &q

[R-sig-eco] Error with "raup" distance in metaMDS

cts 1 and 2 In addition: Warning message: In distfun(comm, method = distance, ...) : data have empty species which influence the results im method raup Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 H

[R-sig-eco] Species richness in R

each site (i.e., the number of visits to the sites varies)? I am trying to get also an estimate of the detection probability, but it seems that this parameter is not included in those functions. Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida

[R-sig-eco] se and confidence limits for predictors from a model output not obtained in R

se (and the confidence limits) for different predictors in the model to obtain a plot for each predictor like the effect package does. Thank you very much in advance. Best, Manuel -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad

[R-sig-eco] CI for mixed models with lme

87600 -0.08655534 0.06944999 2.05895746 Number of Observations: 196 Number of Groups: tempo localidad %in% tempo 4 196 -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 135

[R-sig-eco] Logistic regression plot

e for each variable in the model. Thank you very much in advance. Best, Manuel -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfono: (506) 2277-359

[R-sig-eco] Transforming logits to probabilities

des: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 433.04 on 319 degrees of freedom Residual deviance: 424.30 on 314 degrees of freedom (25 observations deleted due

[R-sig-eco] Function predict

27; were specified with different types from the fit I don't understand what is wrong. Any help will be appreciated. Best, Manuel -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@un

[R-sig-eco] Effect size for factors in lm and glm

Thank you very much in advance. Best, Manuel -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfono: (506) 2277-3598 Fax: (506)

[R-sig-eco] Modeling when all variables are categoricalb

with a saturated model? How is the way to model this type of data (1 categorical response variable and 6 explanatory factors)? I also used classification trees for the data but the error is bigger after the first split. Best, Manuel -- Manuel Spínola, Ph.D. Instituto Internacional en Conserva

[R-sig-eco] Multiple proportions analysis in R

independent. I want to assess the effect of zone, humidity and temp on the proportion of different stages at each nest. Is this a case for a multinomial model? How is a simple way to analyze this data set? Best, Manuel Spínola -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de

[R-sig-eco] Changing the reference level of a factor

standard error: 1.474 on 9 degrees of freedom Multiple R-squared: 0.552, Adjusted R-squared: 0.4525 F-statistic: 5.545 on 2 and 9 DF, p-value: 0.02696 Any idea why? Best, Manuel Spínola -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Unive

[R-sig-eco] Zero-truncated Poisson model in R

Dear list members, Is there any function to do zero-truncated poisson or zero-truncated negative binomail in R? Thank you very much in advance. Best, Manuel Spínola -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350

[R-sig-eco] repeated measures design in R

oblems? Also, is this the way to analyze a repeated measure design in R? The counties (localidad) are all the county that I am interested, is that still random? Thank you very much in advance. Best, Manuel Spínola -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo d

Re: [R-sig-eco] multiple regression

/software.html Best, Manuel Spínola -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfono: (506) 2277-3598 Fax: (506) 2237-7036 Peter Solymos wrote: Dear

[R-sig-eco] Repeated measures model in R

subject) Year: from 2002 to 2007 My data set is unbalanced (the counties do not have information for all the years). Thank you very much in advance. Best, Manuel Spínola -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000

Re: [R-sig-eco] Statistics applied to Geography using R

--Original Message----- From: Manuel Spínola Sent: 02.07.2009, 23:17 To: r-sig-ecology@r-project.org Subject: [R-sig-eco] Statistics applied to Geography using R Dear list members, Do you know any references for statistics applied to geography that are in some way related to R? I think it will

[R-sig-eco] Statistics applied to Geography using R

Dear list members, Do you know any references for statistics applied to geography that are in some way related to R? I think it will be ok also for references that do not use R but it will be easy to use through R. Thank you very much in advance. Best, Manuel Spínola -- Manuel Spínola, Ph.D

[R-sig-eco] Confidence intervals for predicted probabilities in logistic regression

intercept that is the reference level, "no"). I was expecting to get the same lower and upper limit for the intercept. Do you know why the results are different? Do I need the covariance to calculate the se? Thank you very much in advance. Best, Manuel -- Manuel Spínola, Ph.D. In

[R-sig-eco] Analyzing frequencies in R

sis on a P value when analyzing frequencies in R? Is it possible to obtain standardized Pearson residuals in this situation? Thank you very much in advance. Best, Manuel Spínola -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apa

Re: [R-sig-eco] testing for distribution

Dear Jacob, May be you can use cluster sampling or adaptive cluster sampling (Design-based estimation) to get a density estimate. Best, Manuel Spínola Capelle, Jacob wrote: Dear all, I have a kind of a theoretical question from which I hope it might interest you and hopefully can help me

[R-sig-eco] Constrained quadratic ordination in VGAM

Dear list members, I am running a constrained quadratic ordination (cqo) from package VGAM. I contacted the author package, Thomas Yee, regarding to inertia in cqo but he is not aware of inertia. Has anybody worked trhough cqo and know how to obtain constrained variance in the cqo context? Thank

[R-sig-eco] 2 questions about NMDS in vegan

variables? 2) In a plot for a nmds with fitted environmental variables (function envfit) how can I change the name of the labels of the vectors (arrows)? Thank you very much in advance. Best, Manuel Spínola -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Sil

[R-sig-eco] Possion model for paired data

Dear list memebers, Is there a way to do a paired t test but using a poisson model (for counts). Thank you very much in advance. Best, Manuel Spínola [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r

[R-sig-eco] Problems with correspondence analysis in vegan

and I got the same message: cca(varespec) Error in data.frame(sitenv) : argument "sitenv" is missing, with no default I ran a PCA with rda function on the same data set (roeesp) and no problem. I am working with R 2.8.0, Windows plataform. Thank you very much in advance. Best, Manuel

[R-sig-eco] Multivariate regression tree (mvpart)

trees? Thank you very much in advance. Best, Manuel -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gamil.com Teléfono: (506) 2277-3598 Fax: (506) 2237-7036

[R-sig-eco] Intepreting a plot from a "constrained" NMDS

n in the vegan package. Is it possible to interpret the resulting plot in the same way that a constrained ordination, for example CCA? Thank you very much in advance. Best, Manuel -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartad

[R-sig-eco] Problems with vegdist in Vegan

their dissimilarities may be meaningless in method bray 2: In vegdist(avesp.esp, dist = "jaccard") : missing values in results I have sites (point counts) without species, is it a problem? Thank you very much in advance. Best, Manuel Spínola -- Manuel Spínola, Ph.D. Instituto Inter

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