search for: aphids

Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export,

...oup, I tried to run a Repeated Mesures Anova for Mixed effects model and I got a warnning after entering the model specification saying: "Reached total allocation of 254Mb: see help(memory.size)". here is part of the log: *********************************************************** > aphids<-read.table("aphid.txt",header=T) > attach(aphids) > names(aphids) [1] "site" "time" "shade" "treatp" "aphid" > library(nlme) > aphids<-groupedData(aphid~time|site/shade/treatp,data=aphids,outer=~shade*treatp) > m...

Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export,

...rums and it seems possible to do so but don't understand how to write the function and I couldn't find an example in Pinheiro and Bates. lme {nlme} has a contrasts argument but I can't understand how to code it. Here is a simple example of my working lme model: dependent variable: APHIDS: log (number of aphids) Fixed effects: DAY (time) and TREATMENT ( 6 different aphid treatments) Random effects: POPULATION (each population is counted through time) lme.fit<-lme(log(APHIDS)~ DAY*TREATMENT, random = ~ DAY| POPULATION,data= aphid.data) My hypothesis testing focuses on comp...

...forgive me if this question is irrelevant. If I try to find the significance of the fixed factor "spikes" in a generalized linear mixed model, with "site" nested within "zone" as a random factor, I compare following two models with the anova function: model1<-lmer(aphids~spikes+(1|zone:site), method="ML", family=quasipoisson) model2<-lmer(aphids~(1|zone:site), method="ML", family=quasipoisson) anova(model1,model2) This gives me a p< 2.2e-16 ***, concluding that "spikes" has a highly significant effect on "aphids". Howe...

Dear R-users, I'm new to R, so my apologies if this question doesn't make sense. I've tried the following model in lmer, and it works perfectly: model<-lmer(aphids~densroot+zone+(1|zone/site), family=quasipoisson) But if I try the exact same model with a different variable, totmas, the model looks as follows: model<-lmer(aphids~totmas+zone+(1|zone/site), family=quasipoisson) Totmas is also a continuous variable just like densroot, but in this case I rece...

Hi, I am performing a repeated measures 2-way ANOVA to assess the influence of plant and leaf on aphid fecundity. Fecundity is measured for each aphid on a single leaf. Here is what I typed. wingless <- reshape(Wingless, varying =

Hi theora-list, I'm involved in in a project to redistribute C-SPAN's floor footage from the US house and senate that we're capturing and converting*. This footage is in the public doman, however there's a C-SPAN overlay which is a registered trademark - we're having to overlay a "public domain" graphic on top of it. We're currently doing this with

Hello R-Community, we are running aprogram to fit Non-linear differential equations to Aphid population Data and to estimate the birth and death parameters, here is the code: dat<-data.frame(Time=c(0:60),Cur=c(5,6.2,59,39,38,44,20.4,19.4,34.2,35.4,38.2,48.2,55.4,113.2, 97,112,115,126,136.6,140.6,147.2,151.6,157.8,170,202,210.4,221.2,224.4,248.2,266,

Greetings. I'm a Master's student working on an analysis of herbivore damage on plants. I have a tried running a glm with one categorical predictor (aphid abundance) and a binomial response (presence/absence of herbivore damage). My predictor has four categories: high, medium, low, and none. I used the "ordered" function to sort my categories for a glm. ah <-

This is a simple problem, but a mystery to me. I'm trying to grab $Family "Scelionidae" from one dataframe and put it into another dataframe occupied with NA in $Family. The result is a "158" ends up there instead of Scelionidae. Simply put fam$Family[1] <- least$Family[1] If I have made a mistake here, can somebody point it out. I've included the simple

Post-hoc test for a zero inflated continuous data set with a tweedie distribution? I have a zero inflated continuous data set of aphid feeding duration on 10+ species of plant. I have fitted a glm model with a tweedie distribution and used anova() function to show that there is significance between the plant species. However, I would now like to perform of post-hoc test, ideally a Tukey-Kramer

Your data frame fam contains factors. Turn it into character strings using fam$Family = as.character(fam$Family) and try again. It may be helpful if you read up on R's factors, see ?factor. HTH, Peter On Tue, Nov 21, 2017 at 2:14 PM, Glen Forister <gforister at gmail.com> wrote: > This is a simple problem, but a mystery to me. > I'm trying to grab $Family

Hi, I'm working on updates to the WWW FAQ (okay, it's a little much to use the singular in 2006, but it was the first!). Embedded multimedia has been a sore spot for a while. I've been recommending that people embed old-school MPEG, because it works in all players. But it's awful. Terrible bitrates. I'm on the verge of recommending SWF instead, even though it's a hideous

Well, ?factor does not say anything about this behaviour (assigning numeric code instead of level of factor). And actually if you do assignment for whole vector the result is different (vector in data frame is changed to factor). > temp2$fff[1]<-vec[1] > head(temp2,2) pokus minuty fff 1 T42 240 3 2 T42 300 <NA> > temp2$fff<-vec > head(temp2,2) pokus

Oggz 0.9.8 Release ------------------ Oggz comprises liboggz and the command-line tools oggzinfo, oggzdump, oggzdiff, oggzmerge, oggzrip, oggz-chop, oggz-comment, oggz-scan, oggz-sort and oggz-validate. oggz-chop can be used to serve time ranges of Ogg media over HTTP by any web server that supports CGI. liboggz is a C library providing a simple programming interface for reading and writing Ogg

Oggz 0.9.8 Release ------------------ Oggz comprises liboggz and the command-line tools oggzinfo, oggzdump, oggzdiff, oggzmerge, oggzrip, oggz-chop, oggz-comment, oggz-scan, oggz-sort and oggz-validate. oggz-chop can be used to serve time ranges of Ogg media over HTTP by any web server that supports CGI. liboggz is a C library providing a simple programming interface for reading and writing Ogg

I am having problems YP listing my opus and webm streams. The mp3 streams get listed though. my ffmpeg for the webm stream: ffmpeg \ -f v4l2 -video_size 640x480 -framerate 30 -i /dev/video0 \ -i http://mustafejen.se:8000/feting \ -f oss -i /dev/dsp1 \ -f webm -cluster_size_limit 2M -cluster_time_limit 5100 -content_type video/webm \ -c:a libvorbis -b:a 96K \ -c:v libvpx-vp9 -b:v 1.5M