search for: seedling

Displaying 20 results from an estimated 31 matches for "seedling".

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2006 Apr 23
1
Comparing GLMMs and GLMs with quasi-binomial errors?
Dear All, I am analysing a dataset on levels of herbivory in seedlings in an experimental setup in a rainforest. I have seven classes/categories of seedling damage/herbivory that I want to analyse, modelling each separately. There are twenty maternal trees, with eight groups of seedlings around each. Each tree has a TreeID, which I use as the random effect (block...
2006 Sep 12
1
Using XY location data to calculate ecological parameters
Dear R gurus, I have XY data giving the locations of tree seedlings that were surveyed during a 210 meter belt transect. This belt transect was taken by stretching a line across the field, then measuring all seedlings within 1 meter on either side of the line. The end result was XY coordinates and height for ~1,300 seedlings. I would like to use that...
2009 Oct 28
2
x11(title=' ')
Dear all I was trying to put a title for my plot, but i got this result, > x11(width=10,height=5,title="seedling");par(mfrow=c(1,2))Error in x11(width = 10, height = 5, title = "seedling") : unused argument(s) (title = "seedling")> The title is not taking How can i give a title for the plot (where in need to make 2 plots within a window of x11() ) thanking you in anticipation...
2008 May 15
2
mixed effects models with nested factors
Hi everybody, I am trying to fit a model with the lmer function for mixed effects. I have an experimental design consisting of 5 field plots. Each plot is divided in 12 subplots where the influence of three factors on the growing of tree seedlings is tested: (1) seed (1 = presence; 0 = absence); (2) seedling species (oak holm vs. pine); (3) treatment (three different treatments). In each of these subplots we planted 13 seedlings. Therefore I would have a model with three fixed factors and one random factor (a block?). If I´m not wrong the m...
2011 Jun 28
2
coxph() - unexpected result using Crawley's seedlings data (The R Book)
...ok: http://books.google.com/books?id=8D4HVx0apZQC&lpg=PA799&ots=rQgd_8ofeS&dq=r%20coxph%20crawley&pg=PA799#v=onepage&q&f=false --------------------------------- My result: > summary(model1) Call: coxph(formula = Surv(death, status) ~ strata(cohort) * gapsize, data = seedlings) n= 60, number of events= 60 coef exp(coef) se(coef) z Pr(>|z|) gapsize -0.001893 0.998109 0.593372 -0.003 0.997 gapsize:strata(cohort)cohort=September 0.717407 2.049112 0.860807 0.833 0.405...
2003 Nov 04
1
glm offset and interaction bugs (PR#4941)
...ersion: 1.8.0 OS: i686-pc-linux-gnu (Suse 8.2) Submission from: (NULL) (134.84.86.22) Two bugs (perhaps related, perhaps independent) revealed by the same Poisson regression with offset mydata <- read.table(url("http://www.stat.umn.edu/geyer/5931/mle/seeds.txt")) out.fubar <- glm(seedlings ~ burn01 + vegtype * burn02 + offset(log(totalseeds)), data = mydata, family = poisson) summary(out.fubar) out.barfu <- glm(seedlings ~ burn01 + vegtype * burn02, offset = log(totalseeds), data = mydata, family = poisson) summary(out.barfu) out.ok <- glm(seedlings ~ vegtype * burn02...
2009 Feb 11
0
how to derive 5 level nested anova results table
Hello. I am new to R. And, I want to perform a multiple nested anova on a large datasets (with 9448 observations). Under the helps from R-Sig-ecology mailing list, I have gained many progresses. But I still have some confusions. I want to ask for some helps here. my dataset("SeedL.txt") was not attached. Data are not sorted by factors. In this dataset, "SpecN"
2009 Aug 28
1
Help with glmer {lme4) function: how to return F or t statistics instead of z statistics.
Hi, I'm new to R and GLMMs, and I've been unable to find the answers to my questions by trawling through the R help archives. I'm hoping someone here can help me. I'm running an analysis on Seedling survival (count data=Poisson distribution) on restoration sites, and my main interest is in determining whether the Nutrients (N) and water absorbing polymer Gel (G) additions to the soil substrate contribute positively to the survival of the seedlings, over a 3 year time period (for simplicity I...
2008 Feb 22
3
projection.matrix() {popbio} for more than one matrix
Hello, I am trying to use the projection.matrix( ) function and am following the example given. I have my data formatted very similar to the test.census example. > str(AsMi05mat) `data.frame': 1854 obs. of 6 variables: $ Tag : num 501 502 503 504 505 506 507 508 509 510 ... $ Year : int 1995 1995 1995 1995 1995 1995 1995 1995 1995 1995 ... $ Length : num 34
2005 Jul 19
2
Regression lines for differently-sized groups on the same plot
...iption and code are below: I have an unbalanced dataset consisting of three different species (hem, yb, and sm), with unequal numbers of wood pieces in each species group. I am trying to generate a plot that will show the size of the wood piece on the X axis, the probability of it having tree seedlings growing on it on the Y (a binomial yes or no variable), and three fitted curves showing how the probability of having tree seedlings changes with increasing wood piece size for each species. I have no problem generating fits using GLM, and no problem creating the plot. However, if I try to...
2009 Aug 31
2
interactions and stall or memory shortage
...le pair of interactions, when I try to evaluate two pairs of interactions( flowers*gopher, flowers*rockiness) my computer runs out of memory, and the larger desktop I use just doesn't go anywhere after about 20 minutes. Is it really that big a calculation? to start: mle2(minuslogl = Lily_sum$seedlings ~ dnbinom(mu = a, size = k), start = list(a = 10, k = 1)) then: i2<-interaction(Lily_sum$flowers, Lily_sum$gopher) i3<-interaction(Lily_sum$flowers, Lily_sum$rockiness) mle2(Lily_sum$seedlings ~ dnbinom(mu = a, size = k), start=list(a=10,k=1) ,parameters=list(a~i3+i2+Lily_sum$flowers)) (...
2001 Aug 08
1
NLME augPred error
...1,2,3 not allowed for block > predict.nlme(area3.pen.nlme) does not produce an error. area3.pen.nlme was created with: > area3.pen.nlme <- nlme(area ~ SSlogis(day, Asym, xmid, scal), + data=area.pen.data, + fixed = Asym + xmid + scal ~ dose + block, + random = Asym + xmid + scal ~ 1|seedling, + weights = varPower(), + start = c(2887,0,0,0,10.7,0,0,0,2.29,0,0,0)) > area, day and dose are numeric block and seedling are factors area is the area in mm2 of one growing leaf for each seedling. with fixed = Asym + xmid + scal ~ dose or fixed = Asym + xmid + scal ~ block it works....
2005 Sep 22
3
anova on binomial LMER objects
..., as can be seen by running the example I have given below. First an explanation of what I'm trying to do. I am trying to fit a glmm with binomial errors to some data. The experiment involves 10 shadehouses, divided between 2 light treatments (high, low). Within each shadehouse there are 12 seedlings of each of 2 species (hn & sl). 3 damage treatments (0, 0.1, 0.25 leaf area removal) were applied to the seedlings (at random) so that there are 4 seedlings of each species*damage treatment in each shadehouse. There maybe a shadehouse effect, so I need to include it as a random effect. Li...
2009 Aug 28
0
Help with glmer {lme4} function: how to return F or t statistics instead of z statistics?
Hi, I'm new to R and GLMMs, and I've been unable to find the answers to my questions by trawling through the R help archives. I'm hoping someone here can help me. I'm running an analysis on Seedling survival (count data=Poisson distribution) on restoration sites, and my main interest is in determining whether the Nutrients (N) and water absorbing polymer Gel (G) additions to the soil substrate contribute positively to the survival of the seedlings, over a 3 year time period (for simplicity I...
2011 Apr 10
1
survival object
Hi All, I am trying to do a survivorship analysis with library(survival)from a data set that looks like this: I followed a bunch of naturally germinated seedlings of an annual plant from germination to death (none made it to reproduce, and died in a period of ~60 days after germination.) I also know the size of the seed of every individual censused. So I am trying to analyze seedling survival as a function of seed size. I performed 5 censuses in unequal in...
2010 Apr 20
1
multiple plots problem
...quot;Abundance (%)",ylim=c(0,100),xlim=c(0.7,4.3),pch=22,bg="white",cex=0.75,las=1) par(new=T) plot(c(1:4),mw[5:8],type="o",xaxt="n",xlab="",yaxt="n", ylab="",ylim=c(0,100),xlim=c(0.7,4.3),pch=15,cex=0.75) text(0.7,90,adj=0,"Seedlings",font=2) legend("topright",c("Surr.","Gaps"),bty="n",pch=c(15,0)) ################################################################### par(ps=8,mgp=c(2.25,1,0),mar=c(0,4,0,2)) attach(ad) plot(c(1:4),mw[1:4],type="o",xaxt="n",xlab=&q...
2009 Oct 05
1
interpreting glmer results
Hi all, I am trying to run a glm with mixed effects. My response variable is number of seedlings emerging; my fixed effects are the tree species and distance from the tree (in two classes - near and far).; my random effect is the individual tree itself (here called Plot). The command I've used is: mod <- glmer(number ~ Species + distance + offset(area) + (1|Plot), family = poisson)...
2009 Nov 13
0
z-test with NAs
...ine=='below'],alternative = "two.sided", + mu = 0, sigma.x =(sd(growth[type=='SD'& from_treeline=='above'],na.rm = T)), + sigma.y =(sd(growth[type=='SD'& from_treeline=='below'],na.rm = T)), conf.level = 0.95)> sdgr.ztest # Z-test for Seedling Growth above and below treeline Two-sample z-Test data: growth[type == "SD" & from_treeline == "above"] and growth[type == "SD" & from_treeline == "below"] z = NA, p-value = NAalternative hypothesis: true difference in means is not equal to 0...
2009 Oct 15
2
converting to data.frame
dear allI have a data set with three types (Tree, Sapling, Seedling). I have estimated the correlation values. now i need to bring all the correlation values in a table like the one i have shown in attached file with R codes.could you please give me idea on this problem thanking you MSNepal ______________________________________________________________...
2009 Sep 26
1
Multiple comparisons for coxph survival analysis model
...16 1 Group3 57 16 1 ========================== And I need to compare surviving among the particular groups. Fitting works normally: ================================================================ > cph.1 <- coxph(Surv(death, censor) ~ group + cluster(block), data = seedlings) > summary(cph.1) Call: coxph(formula = Surv(death, censor) ~ group+ cluster(block), data = seedlings) n= 27000 coef exp(coef) se(coef) robust se z p groupGroup2 0.436 1.55 0.0539 0.296 1.47 0.14 groupGroup3 3.048 21.06 0.0439 0.283 10.77...