Re: [R-sig-eco] Using multiple species data for gam (Rajendra Mohan panda)

the birders out there). Chris Howden B.Sc. (Hons) GStat. Founding Partner Data Analysis, Modelling and Training Evidence Based Strategy/Policy Development, IP Commercialisation and Innovation (mobile) +61 (0) 410 689 945 (skype) chris.howden ch...@trickysolutions.com.au Disclaimer: The informatio

Re: [R-sig-eco] Can I weight LS means estimates by elevation in lme4/lmerTest packages?

with those other predictors. That said you may need to convert elevation into a categorical predictor first. This would basically give you different predictor parameters for different elevations, you could then look to see if they differ. Chris Howden Founding Partner Tricky Solutions Tricky S

Re: [R-sig-eco] Regression with few observations per factor level

invoke the magic of the CLT and since there is no way to test whether the parameters are normal we take quite a risk assuming we have accurate p values at small sample sample sizes Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Devel

Re: [R-sig-eco] Standardising and transformation of explanatory/independent/predictor variables for multiple regression analysis

hould get the same\similar model irrelevant to how we define the ratio. E.g. log(1/2) = 0.3 and log(2) = -0.3. (although the parameters might have reversed signs). Chris Howden B.Sc. (Hons) GStat. Founding Partner Data Analysis, Modelling and Training Evidence Based Strategy/Policy Developmen

Re: [R-sig-eco] How to accommodate data with negative values for Canonical Correspondence Analysis in R using "vegan" Package

I mislead anyone! (and if someone can think of the correct scale property I'm trying to convey that hasn't changed I'd appreciate being told) Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Mode

Re: [R-sig-eco] How to accommodate data with negative values for Canonical Correspondence Analysis in R using "vegan" Package

nd be difficult to interpret) This will work if the scale is a human construct where negative and positive numbers convey the same info, however if they mean different things it may not work. For example some indices have different meanings if negative. Chris Howden Founding Partner Tricky Solutions T

Re: [R-sig-eco] Logistic regression with repeated measures ?

Hi Peter, Does it have the ability to fit random effects? Or some other way to address the pseudoreplication expected in RSF studies using GPS fix data with little time between fixes ? (Just had a quick look at the rspf package and I couldn't see any) Chris Howden B.Sc. (Hons) GStat. Fou

Re: [R-sig-eco] Logistic regression with repeated measures ?

duals from logistic regressions can be hard to interpret so some type of lagged correlation plot would likely be better. Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 68

Re: [R-sig-eco] Unbalanced data and random effects

Thanks Krzysztof, Your explanation makes a lot of sense. Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (skype) chris.howden ch...@trickysolutions.com.au

Re: [R-sig-eco] Unbalanced data and random effects

Hi Krysztof, Did you have a specific section of Zuur et als book in mind? I've pulled it off my shelf and tried looking up shrinkage, unbalanced design, design, etc in the index but couldn't find anything relevant. I'm sure it's in there, but it’s a rather large book to r

Re: [R-sig-eco] How to replace NA values

Bats.cast [is.na(Bats.cast)] <- 0 Or Bats.cast [Bats.cast == NA] <- 0 Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (skype) chris.how

Re: [R-sig-eco] Discriminant Analysis Crisis

The lda function has a corresponding predict function which u can use to classify new data. Try having a look at that and it's help contents. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innov

Re: [R-sig-eco] Should one remove highly correlated variables before doing PCA??

With reference to jims point 2. One can use Partial Least Squares, which finds orthogonal PC's that best explain a set of responses. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation,

Re: [R-sig-eco] Should one remove highly correlated variables before doing PCA??

correlated variables. So which do U remove??? If U must use them it's IMPERATIVE that U only remove 1 at a time and then rerun to get new VIF's, remove 1, get new VIF's, remove 1, etc this prevents U removing too many variables. Chris Howden B.Sc. (Hons) GStat. Founding Partner

Re: [R-sig-eco] anova

ation in your ANOVA table. I suggest u convert station to a factor like so: stationf <- factor(station) and then fit the model aov(zoo~stationf) Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Model

Re: [R-sig-eco] removing singleton taxa

ctor which is FALSE if a species occurs in 0 or 1 site, TRUE otherwise df2 <- df1[,check2]~ subset those columns that are TRUE i.e. have a species in more than 1 site. Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation a

Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu

ies u incorporate your study design via blocking or mixed modelling. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax / offic

Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu

Which factors are causing these changes? How these changes matter from the environment and us? 2012/4/25 Chris Howden > Why not try some type of ANOVA style glm? > > Chris Howden > Founding Partner > Tricky Solutions > Tricky Solutions 4 Tricky Problems > Evidence Based

Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu

Why not try some type of ANOVA style glm? Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax / office) ch

Re: [R-sig-eco] how-to identify redundant predictors

a 'black box' method I'd be interested to hear about it. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fa

Re: [R-sig-eco] Mantel

Thanks peter, So that means removing the /2 from my code Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax) +612 4782 9023 ch...@trickysolutions.com.au

Re: [R-sig-eco] Mantel

ix to ## # store all the data, max is 2*10^9: Its bigger ## (nrow(segment.input)^2)/2 - 2*10^9 ## ## interstingly nrow(segment.input)*nrow(segment.input) won't work for large numbers we get ## ## > nrows*nrows ## ## [1] NA ## ## Warning message: ## ## In nrows * nrows : NAs produced by integer ove

Re: [R-sig-eco] Weighting coefficient of variation (CV) in meta-analysis

to the mean for very different responses on different scales. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 9

Re: [R-sig-eco] aov vs. glm

If you want to comparee the 2 anova tables and want an anova table for the glm try anova(glm(...)). Not sure if is or should be the same ANOVA table as summary(aov(...)). If not the issue could well be what Scott has suggested. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4

Re: [R-sig-eco] aov vs. glm

It would help if u posted the results so we know how different. But have a look at the defaults for a call to glm. Are they the same as for lm? There are some differences in the output for glm and lm objects when using summary. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4

Re: [R-sig-eco] Weighting coefficient of variation (CV) in meta-analysis

tions that require sample size. What ever weighting Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax / offic

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

Expand.grid() is also an easy way to get all the different combination for input factors. Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax) +612 4782 9023

Re: [R-sig-eco] Calculate Prediction Interval for Regression by hand...

often use expand.grid to quickly get a matrix for all combinations. So something like this (predict.ci <- data.frame(expand.grid(model$xlevels), predict(model, expand.grid(model$xlevels), interval="conf"))) There's also confint() which is for single parameters. Chris Howden B.Sc.

Re: [R-sig-eco] Confidence intervals in lmer

U could try the predict function with se.fit=true. I believe this should give u the predicted score and se and u can calculate CI from there. U'll have to create an input matrix with the score u want to predict for. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 T

Re: [R-sig-eco] GLS - Plotting Graphs with 95% conf interval

Hi sam, I'm not familiar with the function with gls so can't help u with that.. But if u get no joy on this list there is a mixed effects list called r-sig-me. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Devel

Re: [R-sig-eco] Partially non-independent ANOVA?

Thanks for the explanation Michael, And there I was thinking I'd found a silver bullet, should have know if it's too good to be true it likely isn't. I've been meaning to buy Pinhero and Bates, and I think this is just the incentive I needed. Chris Howden Founding Part

Re: [R-sig-eco] Partially non-independent ANOVA?

;s. Can I just confirm your comments though? If I was testing some factor that I knew each group had unequal variances could I test it using something like the following? lmer(response~factor + (1|factor), data=data)? Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Pr

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

Try pa2$influencia<-factor(pa2$influencia) Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax / office) (+618) 8952 7

Re: [R-sig-eco] Converting species counts into species list

e a very large species list then creating the c(1,1,1,2,2,2,3,3,4,4,5) vector becomes quite tedious to do manually. Not sure how u would 'automate' it, but u should be able to do it somehow. Maybe using the rep() function. Chris Howden Founding Partner Tricky Solutions Tricky Solut

Re: [R-sig-eco] keeping a variable as qualitative even if it is coded with numbers

What do u mean it includes the 0's in your analysis? Are u sure as.factor is converting them to factors (have a look using str(data)) And if as.factor isn't working maybe try creating them as factors using factor() Chris Howden Founding Partner Tricky Solutions Tricky Solution

Re: [R-sig-eco] multiple regression analysis

knows, someone may have thought up a 3-d equivalent so u can also incorporate depth as well. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP development, Data Analysis, Modelling, and Training (mobile) 0410 689 945 (fax / o

Re: [R-sig-eco] memory size limits

ocesses. This should free up RAM for R. You'll likely need to restart R after you've done this so it can find the new memory. The other thing worth trying is buying some more RAM!!! Also, try looking at memory.size(max=TRUE) to see how much memory your OS is saying U have. Good luck

Re: [R-sig-eco] AIC / BIC vs P-Values / MAM

see if there are areas where the model is performing poorly. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP development, Data Analysis, Modelling, and Training (mobile) 0410 689 945 (fax / office) (+618) 8952 7878

Re: [R-sig-eco] AIC / BIC in lmer and glmer

Better to be safe than sorry. And I for one am glad u mentioned it. It's they type of knowledge one might not pick up when using R to fit a mixed model for the first time. It's certainly something I'll be keeping in mind should I ever use R for mixed models!!! Chris Howden F

Re: [R-sig-eco] AIC / BIC vs P-Values / MAM

Null model and other applicable models, and some common sense. 2. Then I evaluate the predictive ability of the best few models on a “test data set” which wasn’t used to create them. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based

Re: [R-sig-eco] AIC / BIC vs P-Values / MAM

might fit them also so I can test the hypothesis predictors effect in conjunction with the covariates. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP development, Data Analysis, Modelling, and Training (mobile) 0410 689 94

[R-sig-eco] is 1 hour long enough to assume independance?

it be further apart, like 1 day. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP development, Data Analysis, Modelling, and Training (mobile) 0410 689 945 (fax / office) (+618) 8952 7878 ch...@trickysolutions.com.au -

[R-sig-eco] do the standard R analysis functions handle spatial "grid" data?

27;grid' format and require data to be entered as a 2-d data.frame or matrix? Are there other special functions out there that can handle this type of data, and I should be using these instead? Thanks for your help Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problem