search for: germin

Dear all! I tried to fit Gompertz growth models to describe cummulative germination rates using nls. I used the following code: germ.model<-nls(percent.germ~a*exp(-b*exp(-k*day)),data=tab,start=list(a=100,b=10,k=0.5)) My problem is that I want that the fitted model goes through the origin, since germination cannot start before the experiment was started, and y-max should...

...11, 12, 13, 14, 16, 17, 18, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 16, 17, 18), germinated = c(0L, 0L, 0L, 0L, 0L, 4L, 6L, 8L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 11L, 7L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 12L, 3L, 0L, 3L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 8L, 0L, 8L, 3L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 5L, 11L, 1L, 1L, 0L, 0L, 0L, 0L, 1L,...

Hi all, I am trying to use nonlinear regression (nls) to analyze some seed germination data, but am having problems with error codes. The data that I have closely matches the germination dataset included in the drc package. Here is the head of the data temp species start end germinated TotSeeds TotGerminated Prop 1 10 wheat 0 1 0 20 0 0...

Does someone out there have an example of R-code for a split-split plot ANOVA using aov or another function? The design is not balanced. I never set up one in R before and it would be nice to see an example before I tackle a very complex design I have to model. Thanks, Mike Mike Saunders Research Assistant Forest Ecosystem Research Program Department of Forest Ecosystem Sciences University of

Hi, I am rather new to R, but both myself and another much more experience user cannot figure this out. I have a collegue who has a 800+ nonlinear regressions to run for seed germination (different species, treatments, etc.) over time. I created a looping structure to extract the parameters from each regression; I will then use the parameters themselves for further analysis. I would like to fit a 4-parameter, sigmoidal shape Weibull because it it paramatized to have a maximu...

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...

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Hi R-people, I performed controlled experiments to evaluated the seeds germination of two palms under four levels of water treatments. I conducted a generalized linear model (GLM) with a Poisson distribution to verify whether there were significant differences in the number of seed germination (NS-count variable) between treatments and species (explanatory variables). Thus,...

Hello everybody I want to compare the proportions of germinated seeds (seed batches of size 10) of three plant types (1,2,3) with a glm with binomial data (following the method in Crawley: Statistics,an introduction using R, p.247). The problem seems to be that in two plant types (2,3) all plants have proportions = 0. I give you my data and the mode...

...or bar analogous to each value of "cut" in the data example. ? When I calculate the SEs appropriately ggplot2 won't stack.? This is first time posting and I've scoured the various forums and websites for a worked example. ?? In case it is relevant, my response variable is fitted germination of an lmer model ("germination"), x is a categorical variable (treatment, with 3 levels), and I am using a categorical variable ("species") to stack.? Kind regards,? Olivia MSc student

...a continuous variable, normally distributed. *Water*: Categorical Levels- wet and dry. *Density*: Categorical Levels- high, medium and solo *Plot*: Counts from 1 to 20 The *response variable *(Y) was the number of seeds produced at the end of the season. The experiment started 15 days after plants germinated in the field. 20 plots were chosen where there was high enough density so I could manipulate it. In an area where artificial irrigation was possible for the wet treatment, dry treatment was natural precip. Water was blocked so 10 plots were wet and the other 10 were dry. Randomly assigned. With...

Hello, I'm trying to adjust a non linear model in which the biological response variable (ratio of germinated fungus spores) is dependent on 2 covariates (temperature and time). The response to temperature is modeled by a kind of beta function with 2 parameters (optimal and maximum temperatures) and the time function is a 2-parameter Weibull. Adjustments with nls or gnls work, but I need to do mixed-ef...

...ene (row) from a dataframe of 37 columns > d1 <- as.matrix(dat.g100[,1:18]) # subset 1 > d2 <- as.matrix(dat.g100[,19:37]) # subset 2 # boxplots > par(mfrow=c(2,1)) > boxplot(d1, cex=0.3, col="red", las=2,cex.axis=0.6,ylab="intensity",main="B cells: germinal center – gene 100") > boxplot(d2, cex=0.3, col="blue", las=2,cex.axis=0.6,ylab="intensity",main="B cells: activated – gene 100") [[alternative HTML version deleted]]

Hi, I have a data set on germination and plant growth with the following variables: dataset=fm mass (response) sub (fixed effect) moist (fixed effect) pop (fixed effect) mum (random effect nested within population) iheight (covariate) plot (random effect- whole plot factor for split-plot design). I want to see if moist or sub i...

I have a set of data with 2 columns: time, size. There are 20 sets of data. The data is looking at whether the size of a seed affects the time it takes to germinate. How do I then create a numerical variable called 'order' with values 1 to 20 in order to plot a graph or order against time? -- View this message in context: http://r.789695.n4.nabble.com/Order-function-tp4651022.html Sent from the R help mailing list archive at Nabble.com.

...ry(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :" [170] "170: there is no package called ?hglm?" Checking installed.packages() shows that hglm is indeed installed in the appropriate directory. agridat "Suggests:" hglm. The "crowder.germination" example in agridat tries require(hglm) and fails; it therefore doesn't fit the relevant HGLM model -- when the example tries to reference this model a few lines later, the example fails. Admittedly this could be seen as a bug in the example (it shouldn't try to access a model it...

...this: Factors: Hormone - Levels: SH, CH (S = without; C=with; H=Hormone) Time - Levels: 19/08/09, 04/09/09, 18/09/09, 08/10/09, 20/10/09 (DD/MM/YY) Nutrition - Levels: Completa, Sem (without) Macronutrition - Levels: Ca, K, Mg, P, Sem (without) Time is the measures day. It reflect the days after germination. Blocks : 4 plants per sub-plots: 16 Each plot was divided in two parts equals. In each part, there was 6 sub-plots with 16 plants (2x8 plants). In the first part of the plot, it was treated with CH and other-one was treated with SH. No randomization here. Factors Nutrition and Macronutrit...

...to analyze it as a mixed-effects model. For the diameter and height measurements, you can probably get away with using normal errors, but for the counts, you may well have to use a generalized linear mixed model." So, I am trying to analyze my data with car package. I have: time (days after germination) -> 4 levels (38, 53, 73, 85) Hormone -> 2 levels (SH, CH) on sub-plots Block -> 4 blocks Treatment -> 6 levels (1, 2, 3, 4, 5, and 6) on sub-sub-plots Plant -> subjects I measured Diameter (mm), Height (cm), HD (height/diameter), and Number of Leaves (count) at each time point...

Hey, Maybe you guys remember us, I'm from the Neuros forums. I've got to say, having a player that supports Ogg Vorbis has really turned things around for everybody. We're still struggling with higher bitrate Vorbis streams, but that is only because of our terribly underpowered DSP. Anyway, to the point of my email. Recently the discussion of bitrate peeling has been floating

Estimada comunidad, tengo unas dudas que son muy básicas creo, pero es mi primera incursión en GLM. Estoy ajustando un modelo binomial a unos datos de germinación. El modelo es muy sencillo, tengo un factor "Condicion" con dos niveles: "a" y "b" (nivel de humedad en suelo). Por otro lado, tengo una variable explicativa "HF" (horas frío=estratificación) que va de 0 a 2160 (en el modelo esta variable es HFe por esta...