search for: aphid

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, fi...

...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) >...

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, fi...

...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 com...

...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". How...

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 rec...

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 = list(c("d0","d1","d2","d3","d4","d5","d6","d7","d8&quo...

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, 277,291.4,392,461.2,470,418,410.8,39...

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 <- read.csv("http://depot.northwestern.edu/class/2012WI_PBC_435-0_AND_BIOL_S...

.... $ Dimen : int 10 13 52 2 1 19 18 0 2 116 ... $ Farm : int 6 2 3 0 0 2 0 1 2 1 ... $ Sums : int 30 26 164 8 2 65 88 24 8 217 ... $ Family: chr NA NA NA NA ... ># This is where I will grab the info to put into the above. > head(fam,2) Family Sp 1 Scelionidae 1 2 Aphid 2 ># This shows the id of my object I want to copy > fam$Family[1] [1] Scelionidae 180 Levels: ? ? = 97 ? immature ? sp sample ?? ???? 1 2 3 ... wolf? > ># This shows me copying Scelionidae into dataframe least > least$Family[1] <- fam$Family[1] > ># Here is where I do...

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 type test as the data samples are of...

...2 116 ... > $ Farm : int 6 2 3 0 0 2 0 1 2 1 ... > $ Sums : int 30 26 164 8 2 65 88 24 8 217 ... > $ Family: chr NA NA NA NA ... >># This is where I will grab the info to put into the above. >> head(fam,2) > Family Sp > 1 Scelionidae 1 > 2 Aphid 2 >># This shows the id of my object I want to copy >> fam$Family[1] > [1] Scelionidae > 180 Levels: ? ? = 97 ? immature ? sp sample ?? ???? 1 2 3 ... wolf? >> >># This shows me copying Scelionidae into dataframe least >> least$Family[1] <- fam$Family[1] &g...

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

...3 0 0 2 0 1 2 1 ... > > $ Sums : int 30 26 164 8 2 65 88 24 8 217 ... > > $ Family: chr NA NA NA NA ... > >># This is where I will grab the info to put into the above. > >> head(fam,2) > > Family Sp > > 1 Scelionidae 1 > > 2 Aphid 2 > >># This shows the id of my object I want to copy fam$Family[1] > > [1] Scelionidae > > 180 Levels: ? ? = 97 ? immature ? sp sample ?? ???? 1 2 3 ... wolf? > >> > >># This shows me copying Scelionidae into dataframe least > >>least$Family[1] &...

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

...01-14 19:53:22] DBUG yp/send_to_yp YP touch at http://dir.xiph.org/cgi-bin/yp-cgi succeeded [2018-01-14 19:53:23] DBUG yp/send_to_yp YP touch at http://dir.xiph.org/cgi-bin/yp-cgi succeeded [2018-01-14 19:53:43] DBUG stats/modify_node_event update "/feting" yp_currently_playing (Beck - Aphid Manure Heist (Intro)) [2018-01-14 19:53:43] DBUG yp/send_to_yp YP touch at http://dir.xiph.org/cgi-bin/yp-cgi succeeded [2018-01-14 19:53:43] DBUG yp/handle_returned_header server touch interval is 360 [2018-01-14 19:53:43] DBUG yp/send_to_yp YP touch at http://yp.shoutcast.com succeeded [2018-0...