search for: larvae

Dear all I have made some lattice graphs (bwplot(dead ~ treat | group,...). 'group' is a factor with three levels (Artemia larvae, Abalone larvae and Abalone spat), and the result is a graph with three panels corresponding to the levels in 'group', ordered in alphabetical order from bottom to top, as expected. How does one re-order the order in which the levels of 'group' in the graph? I want Abalone spat...

Hello r-list members, I've been doing some linear modeling with a dataset structured as follows. Tubes containing 500 larvae of Trichinella each were treated with one of four different temperatures. Each day (or every 10 days depending on treatment group), 3 tubes were selected from each treatment and all the dead larvae were counted. The tubes were discarded. Final larvae counts were averaged. Then we have: y =...

Dear all, How do I make R show the R-squared (deviance explained by the model) in a logistic regression? Below is how I write my syntax. Basically I want to investigate density-dependence in parasitism of larvae. Note that in the end I perform a F-test because the dispersion factor (residual deviance / residual df) is significantly higher than 1. But how do I make R show the "R-squared"? Best wishes Johan > y<-cbind(para,unpara) > model<-glm(y~log(larvae),binomial) > summary(mode...

Background: OS: Linux Ubuntu Dapper R : Version 2.3.1 (2006-06-01) Emacs 21.4.1 ESS Colleagues This is neither a bug report, nor a complaint, so I think this is the appropriate list. I am getting an odd font problem with a pdf generated using pdf(file = "../figures/PCNM.models.larvae.fluor.zoo.stability.2001.and.2002.pdf", title="", family="serif", pointsize=10, width=6.75, height=8.625) The figure produced from my code is here: <http://www.members.iinet.net.au/~s.mcclatchie/aslo/PCNM.models.larvae.fluor.zoo.stability.2001.and.2002.pdf> (I...

> Background: > OS: Linux Ubuntu Dapper > release: R 2.3.0 > editor: GNU Emacs 21.4.1 > front-end: ESS 5.2.3 > ----------------------------- > Colleagues > I have two spatial datasets (latitude, longitude, fish eggs) and (latitude, longitude, fish larvae) at the same 280 stations (i.e. 280 cases). I want to determine if the 2 datasets are spatially correlated. In other words, do high numbers of larvae occur where there are high numbers of eggs? I would like to calculate the cross correlation for these bivariate data and calculate a Mantel statistic...

Hi everyone, I am beginner using R but I try to learn more. I need this graphic or similar but instead of tropical and temperate are three ontogenetic states Larva Met Juv CTMAX CTMIN SP SP SP This is my scrip: Ex = subset(Expr, Outlayer=="N") Ex2 = subset (Ex, S0 == 1) Ex3

Dear All, I'm confortable with xyplot(...) and panel.lmline(...) statements (at least I thought I did :). I've used the following code to plot the decline in log-abundance of fish larvae (no.larvae) with age (age.cls, 4 to 27 days-old) for specific dates of sampling (day, 9 dates). I further plotted data with different colors and regression lines for ages 5-14 d and 17-23 d in a 7-by-1 layout. xyplot(log(no.larvae)~age.cls|factor(day),data=mortal, layout=c(7,1),aspect=5/3, xl...

...> I have now recieved some helpful hints in this matter and will summarize them but first let me reiterate the problem: > > I had two treatments: 2 types of food fed to females. Each female were present only in one treatment and laid one clutch (female ID = clutch ID). From each clutch, 50 larvae were taken and divided on 5 cups; 10 larvae in each cup (the cups were not meant to differ in any way, it's just impossible to count 50 larvae in motion, but ok with 10). The day of death was recorded for each larva. Since there's only one data point per larva, I see no need of including la...

Background: OS: Linux Mandrake 10.1 release: R 2.0.0 editor: GNU Emacs 21.3.2 front-end: ESS 5.2.3 --------------------------------- Colleagues I have a set of lattice plots, and want to plot 4 of them on the page. I am having trouble with the layout. grid.newpage() pushViewport(viewport(layout = grid.layout(2,2))) pushviewport(viewport(layout.pos.col = 1, layout.pos.row = 1)) working trellis

Hi, I have some difficulty in figuring out whether I am doing correct or not. A brief introduction about the work: It is a light/dark choice test conducted in insect larvae.  The response is binary (0- present in dark area, 1-present in light area) and the experiment is run for 15 min, so there are 15 repeated measurements per individual larva at 1 min intervals.  The factors which affect this study are Strain (2 levels-G and S),  wavelength of light (4 levels-blu...

I'm using the image.plot() function (fields package), but I want to enlarge the characters of the legend (as they are too small to be read in a combined figure), but there is no way I can find a command to do this. I can enlarge the legend bar (with legend.witdh), axis character size (cex.axis) or the total legend size (legend.shrink), but not the character size of the legend characters

Dear All, Help is needed! I have a matrix with frequencies of fish larvae per length class (var. sl) and age-group (var. median.no) obtained with >k<-table(cut(sl,(5:22)),median.no) >k[2:5,1:5] #to ilustrate k 4 5 6 7 (6,7] 3 1 0 0 (7,8] 3 0 1 0 (8,9] 3 4 3 5 (9,10] 3 15 7 13 from this matrix I would like to obtain the mean age...

...soundly make my point w/ the referee (can I use your replies? If so I intend to properly cite its use?!?). Regards, Eduardo Esteves ps - Sorry for not explaining the "biological details" of my posting: RNA/DNA is the ratio of RNA content to DNA content obtained for individual fish larvae (plus for each one I noted if it had visible prey items in the gut or not, thus the levels Prey and Empty of factor Gut); and sl is the standard length (distance from the tip of snout to the posterior extremity of the hypurals, the expanded bones at the end of the backbone that support the...

Hi there, I'm using the lattice package to create an xy plot of abundance vs. depth for 5 stages of barnacle larvae from 5 species. Each panel of the plot represents a different stage, while different loess smoothers within each panel should represent different species. However, I would like depth to be on the y-axis and abundance to be on the x-axis, because this is more intuitive as an oceanographer. The smoo...

...unbalanced mixed model design with two fixed effects "site" (2 levels) and "timeOfDay" (4 levels) and two random effects "day" (3 consecutive days) and "trap" (6 unique traps, 3 per site). The dependent variable is the body length ("BL") of insect larvae from 7 to 29 individuals per trap (104 individuals in total). To account for pseudo replication I used nlme (or lme4 as suggested for crossed random factors). The results indicate, that the random effects are very small, so I followed the lme example and tried to fit a model with random=~1. U...

Dear R list, I have a sequence of weekly observations of number of adults and larvae in various size classes from a butterfly population living in a subtropical area with pronounced wet and dry seasons. Wet and dry seasons are each defined 26 weeks long with fixed start and end dates. The data span 103 weeks (two seasons each of wet and dry) with some missing weeks. What I would...

Hi, In the help files in the ?mgcv package for the gam.control() function, there is an option irls.reg. The help files describe this option as: For most models this should be 0. The iteratively re-weighted least squares method by which GAMs are fitted can fail to converge in some circumstances. For example, data with many zeroes can cause problems in a model with a log link, because a mean of

Hi, I have a dataset like this, > testdata Grouped Data: expr ~ visit | subject expr visit subject 1 6.502782 V1 A 2 6.354506 V1 B 3 6.349184 V1 C 4 6.386301 V2 A 5 6.376405 V2 B 6 6.758640 V2 C 7 6.414142 V3 A 8 6.354521 V3 B 9 6.396636 V3 C I tried the command >

Dear R users, x-values (EI) = Adw, EG1, LA1, Ad1, LA2, LA3...(14 levels, insect stages) y-valus = antpop within the boxplot function x-values are ordered alphabetically Idea: x-values ranked by list order (insect stage: Egg stage 1 is followed by Larvae 1 and not by Egg stage 2 as it would be in an alphabetically order) Problems with the order(tapply()) function: variable lengths differ thanks Sibylle R-code (as later insect stages have higher means, ordering was based on mean or median...) SOPRA<-read.table("SOPRA206_WG_WAE.txt&quo...

...uld be using the newer lme4 package, I just haven't had a chance to update my version of R yet, so the question below relates to nmle. I have data from a classical quantitative genetics experiment, with 33 sires mated each to 2 dams, with 15 progeny from each dam raised on 5 host plants (3 larvae per host). So the model I would like to run has the following factors: Host (fixed) Sire (random) Dam [nested within sire] (random) Host * Sire (random interaction) Host * Dam [nested within sire] (random interaction) This is the code I am using for that complete model: lme1=lme(gain~host,random...