Stack Overflow
Stack Overflow

Questions tagged [nlme]

An R package for fitting Non-Linear Mixed Effects statistical models.

An package for fitting Non-Linear Mixed Effects statistical models ().

Repositories

Books

Other resources

Related tags

494 questions
0
votes
0 answers

Error "Downdated VtV is not positive definite" when using nlmer from lme4

I am attempting to implement a NLME model using lme4 (lme4_1.1-31) in R. vW_start = 0.045/0.042 vK_start = exp(0.9)*vW_start vW_start = log(vW_start-1) vK_start = log(vK_start-1) b2_start = 1.718 b3_start = 0.968 b4_start = -0.131 m_start =…
asingh
  • 1
  • 1
0
votes
1 answer

How do I solve MEEM error from linear mixed-effect model in R? lme() function from nlme package

I am trying to build a linear mixed-effect model (lmm) using the lme() function. To give some context, the research project looked at changes in reaction time of athletes as a function of number of digits they were asked to remember during their…
domwill
  • 11
  • 3
0
votes
0 answers

Why is giving me this convergence problem

I'm running mixed models with the database pasted below It`s a simple linear mixed model in which the particular situation is when I want to include the quadratic effect of time. For time being linear I don't have any convergence problem but…
Javier Hernando
  • 181
  • 7
0
votes
1 answer

How do you incorporate presence/absence of 5 species into a Linear Mixed Effect Model?

I have a dataset of the Visitation Rate(VR) of 5 bird species on 3 species of flower, and the measured Pollen Deposition(PD) of each flower. Each flower species is represented by 20 individuals. Not all bird species visited every individual flower.…
Rasmusdj97
  • 1
0
votes
0 answers

plotting 95% intervals in gls in r

I have built a model using the gls function of the nlme and I have plot the the model with ggplot. Here an example of the data and the code: df t count 4 4051 5 2028 6 4.58 7 7.87 8 11.2 9 8950 20 2938 29 4.89 31 23292 44 10.18 46 …
Franc
  • 15
  • 6
0
votes
0 answers

mixed-models in "nlme" package using lme() - nested data structure - error in model fitting - system is computationally singular

I am working with a dataset having the following structure (download data here). The variable resp is a physiological response measured once for every subject during the study. In the study, each subject was observed for 5 days at 10 time points.…
Suhas Bharadwaj
  • 21
  • 3
0
votes
0 answers

Philips & Horton models for water infiltration

I'm trying to run soil-water infiltration data in Rstudio for an experiment set up as an RCBD with treatments and a blocking effect. My variables include the depth and time measured in the field (i.e. multiple values for each variable per…
Segeana
  • 1
  • 3
0
votes
0 answers

No covariate specified, species will be taken as ordered in the data frame: An error message from running PGLS in nlme library

I am new to PGLS analysis and trying to run it on tree root trait data in the nlme library. I have imported the phylogenetic tree into R and used the drop.tip function to match the tree data to the species data by running this code tree <-…
confidence
  • 1
0
votes
0 answers

Repeated measures in lme R vs. SPSS

I'd like to present you with a problem. I cannot replicate in R's lme (nlme package) a repeated measures model I built in SPSS. I hope someone is able to solve this conundrum. See below for the steps I took. Thanks! My SPSS model is the…
Hans van der Horn
  • 1
0
votes
0 answers

glm function in split experiment in r

I am carrying out an split experiment with microbiology. Totally 3 blocks I set: A,B,C; each block contains 2 replicates; each replicate contains 2 species. I want to test if the density ratio of these 2 species change with time. I write this…
Scrooge Mike
  • 17
  • 3
0
votes
1 answer

time variable in split experiment in lme function

I am carrying out an split experiment with microbiology. Totally 3 blocks I set: A,B,C; each block contains 2 incobators, with setting temperature at 19 and 31 °c, respectively. In each incubator, 2 replicated microganism sample are cultured…
Scrooge Mike
  • 17
  • 3
0
votes
0 answers

lme correlation structure for three-level model - follow up question

From the example in lme specifying correlation structure for three-level model. For each Family, I was hoping to see 2 (# of subject per family) diagonal blocks of 10 x 10 (# time pts x # time pts) as specified by Phi in the AR1 model as well some…
Tony
  • 1
  • 1
0
votes
0 answers

How can I use a custom covariance matrix in nlme for random effect modelling

I have created a custom covariance matrix (converted to correlation matrix) that I wish to you in nlme. How do use I fit my model as random effect model where gen, rep:row and rep:col are all considered random effects. See below my gls…
Fola
  • 9
  • 1
0
votes
0 answers

Syntax of how to code a nonlinear mixed effects model in R with nlme package

I am having difficulty with programming a nonlinear mixed effects model in R using the nlme package. I am not concerned with fitting to data at this point, rather I just want to make sure I have the model coded correctly. The model I am trying to…
tsss
  • 1
0
votes
1 answer

My interaction term doesn't cover all groups

I am trying to execute linear-mixed models with 3 factors as groups. However running the syntax, I just get 2 terms: time:grup_int2 or time:grup_int3 as you can see in the picture. There should be another term for time:grup_int1. My reference…
Javier Hernando
  • 181
  • 7
1 2 3
…
32 33