search for: veg

Hi, I would like to construct a transition matrix from a data frame with annual transitions of marked plants. plant<-c(1:6) class<-c("seed","seed", "seed", "veg", "rep", "rep") fate<-c("dead", "veg","veg","rep", "rep", "veg") trans<-data.frame(plant, class, fate) plant class fate 1 1 seed dead 2 2 seed veg 3 3 seed veg 4 4 veg rep 5 5...

...t when I only ran the part of the code with the for loop with no if statement I still had the above problem (works outside function, fails when wrapped into a function). Below is the code and example output. Please help! Thanks, Aaron concov.test<-function(vegetation,specieslist) { test.veg<-vegetation names(test.veg)<-specieslist$LifeForm tmp<-matrix(nrow=nrow(test.veg),ncol=length(unique(names(test.veg)))) for (i in unique(names(test.veg))) {test.out<-apply(test.veg[,names(test.veg)==i],1,sum) tmp.match<-unique(names(test.veg))[uni...

...to search which are flagged as 0. please help me with the R script. *Menu Name* 9\ bobbie" 9\ chz steak" 9\ tuna" provolone 20\ bobbie" bottled soda 20oz cran-slam ww american small chips medium drink 9\ meatball" capriotti's water 20'' chicken cheese steak 9\ veg turkey" medium chips 9\ capastrami" 12\ bobbie" 12'' chicken cheese steak cookie 12\ chz steak" 9\ cole turkey" kid grilled cheese white 12\ italian" 12\ meatball" 12\ capastrami" turkey sand w 20\ slaw be jo" swiss 12\ cole turkey" large dr...

...rious suggestions, but I am too new to get any of them to work. I am trying to generate an xyplot (or bwplot) for a presentation on Tuesday. As part of my dissertation I have 3 treatments divided into 2 time periods (before and after treatment). Code that works (stripped of labels) is: xyplot(veg$litter_depth ~ veg$status | veg$treatment, layout=c(3,1), type=c("p","r")) Status is "before" and "after" In essence I am plotting a change in litter depth (and about 50 other variables) over time for each of the treatments. This generates a graph with 3...

Hello, I'm trying to calculate non-parametric probabilities using the np package and having some difficulties. OS is Windows, R version 2.11.1 Here is what I've done so far. library(np) veg <- data.frame(factor(Physiogomy), meanAnnualDepthAve, TP) attach(veg) : for clarification dim(veg) returns 1292 3 fy.x <- npcdens(veg$factor.Physiogomy ~ veg$meanAnnualDepthAve, nmulti=1) # this works, but I haven't found any information explaining what the nmulti=1 term is doing? Doe...

...I tried to post this earlier, but it seems that it did not appear on the list. If you've rec'd 2 m I'm trying to calculate non-parametric probabilities using the np package and having some difficulties. OS is Windows, R version 2.11.1 Here is what I've done so far. library(np) veg <- data.frame(factor(Physiogomy), meanAnnualDepthAve, TP) attach(veg) : for clarification dim(veg) returns 1292 3 fy.x <- npcdens(veg$factor.Physiogomy ~ veg$meanAnnualDepthAve, nmulti=1) # this works, but I haven't found any information explaining what the nmulti=1 term is doing? Doe...

Hi R listers, I am trying to group distances of nests to the vegetation into classes that are define by (0-5m, 6-10m, 11-15m, 16-20m, 21-25m, 26-30m, 31-35m, 36-40m, 41-45m, 46-50m, 51-55m, 56-60m). Each row is a nest and all the distances to the vegetation is in a column. In plyr, I have tried - below script but I think I am going about this the wrong way an...

Hi all, How can I overlay these two histograms? ggplot(gg, aes(gg$Alz, fill = gg$veg)) + geom_histogram(alpha = 0.2) ggplot(tt, aes(tt$Cont, fill = tt$veg)) + geom_histogram(alpha = 0.2) thanks for any help! Elahe

Hi R-listers, I am trying to do an ANOVA for the following scatterplot and received the following error: library(car) scatterplot(HSuccess ~ Veg, data = data.to.analyze, xlab = "Vegetation border (m)", ylab = "Hatching success (%)") anova(HSuccess ~ Veg, data=data.to.analyze) Error in UseMethod("anova") : no applicable method for 'anova' applied to an object of...

Hello all, I am going slightly mad trying to create a table for running co-correspondence analysis. What I have is seed bank and vegetation data, and my aim is to see if the vegetation found in a site (containing several seed bank samples) can predict the composition of a seed bank sample within that site. So for this I need two tables with matching rows. I have created an empty matrix, where the rows correspond to the seed...

Hi R-users: [R 2.2 on OSX 10.4.3] I have a (sparse) vegetation data frame with 500 rows (sampling units) and 177 columns (plant species) where the data represent % cover. I need to summarize the cover data by returning the names of the most dominant and the second most dominant species per plot. I reduced the data frame to omit cover below 5%; t...

Hi All, I am wondering if anyone can tell me what the warning message below the model means? J add1(DTA.glm,~ Aeventexhumed + Veg + Berm + HTL + Estuary + Rayos) Single term additions Model: cbind(MaxHatch, TotalEggs - MaxHatch) ~ Aeventexhumed + Veg + Berm + HTL Df Deviance AIC <none> 488.86 4232.9 Estuary 1 454.96 4201.0 Rayos 3 258.80 4008.9 Warning messages: 1: In model.matrix.default(...

...ing the points. However, I've been really struggling to change the color of the points based on a factor (see 'group' below). Is such a thing possible? My data look like this: food group x y z apple fruit 0.216 -0.112 -0.893 orange fruit 0.814 0.097 0.460 broccoli veg -0.239 0.240 -0.425 banana fruit 0.222 0.968 -0.050 parsnip veg 0.139 0.897 0.378 garlic veg -0.104 0.510 -0.400 pca <- read.table(... p3d<- plot3d(pca$x, pca$y, pca$z, xlab="Component 1", ylab="Component 2", zlab="Component 3", col="blue&quot...

Hello I'm trying to create a barplot with a couple of stacked positive values and with one negative value for each group. example: trees<-c(20,30,10) shrubs<-c(12,23,9) veg<-c(2,3,4) soil<-c(-100,-123,-89) example1<-t(cbind(trees,shrubs,veg)) barplot(example1) #this works so far #but now: example2<-t(cbind(trees,shrubs,veg,soil)) barplot(example2) This shows no more stacked bars. But I want to keep the bars like example1 and just add the negative val...

...les? 2) I am trying to develop the most simplest model ideally. Even though adding another variable would lower the AIC, how do I interpret it is worth it to include another variable in the model? How do I know when to stop? Definitions of Variables: HTL - distance to high tide line (continuous) Veg - distance to vegetation Aeventexhumed - Event of exhumation Sector - number measurements along the beach Rayos - major sections of beach (grouped sectors) TotalEggs - nest egg density Example of how all models were created: Model2.glm <- glm(cbind(Shells, TotalEggs-Shells) ~ Aeventexhumed, d...

Hi all, Given a data frame as... > head(veg) genus species trophia type geo zone importance 1 Sphagnum subsecundum M A En 100 2 Sphagnum denticulatum M A En 200 3 Molinia caerulea M A En 300 4 Sphagnum flexuosum M A En 400 5 Juncus...

Dear R community, Below you may find the details of my model (lm11). I receive the error message "Error: cannot allocate vector of size 220979 Kb" after applying the autocorrelation function update(lm11, corr=corAR1()). lm11<-lme(Soil.temp ~ Veg*M+Veg*year, data=a, random = list(Site=pdDiag(~Veg), Plot=pdDiag(~Veg)) Dataset: a-data frame of daily measurements of soil temperature (Soil.temp) over six years Site (6 sites), Plot(2 plots per site), Veg(2 vegetation types: 2 sites...

...coxon rank sum test with continuity correction", data.name = ".column by site"), .Names = c("statistic", "parameter", "p.value", "null.value", "alternative", "method", "data.name" ), class = "htest"), veg = structure(list(statistic = structure(399.5, .Names = "W"), parameter = NULL, p.value = 0.0091447786580201, null.value = structure(0, .Names = "location shift"), alternative = "two.sided", method = "Wilcoxon rank sum test with continuity correction",...

Hi R-listers, Q1) What is the difference between the scatterplot and plot function? Q2) I am able to make a graph with the scatterplot function: scatterplot(DevelopIndex ~ Veg, + data = Turtle, + xlab = "Vegetation border (m)", + ylab = "Embryonic development index") And have been successful. But I do not know if the lines are for: linear, non-linear, mean, upper and lower limits or percentile? This shows side boxp...

...uot;Mean Number Foxtail Seeds Remaining", xlab="Station Type",ylim=c(10,20),xlim=c(-.25,1.25)) axis(1,at=c(0,1),labels=c("Invertebrate Only","Open Access")) # Poster figure 3 meantime=22.1 meancumrainfall=.4837 meanavelowt=35.4920071 meanavehight=55.3242738 meanvegcover=81.1729167 pred.veg = 33.3160 + -.2439*meantime - .8409*(.5) + 8.6833*(.5) + .5427*(meancumrainfall)-.3087*(meanavehight) + .01087*(seq(0,164.5,by=5)) pred.veg plot(seq(0,164.5,by=5),pred.veg,type='l',col='blue',lwd=2, main='Foxtail Seeds Remaining vs. Vegetative Cov...