lme() is the function for estimating Linear Mixed Effects models in the nlme package for the R project for statistical computing. For general questions about mixed effects models, use the [mixed-effect] tag.

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What type of post hoc test does a LME use by default?

I need to know what type of post hoc test a LME model is using in R, by default? Is it Tukey? And is the alpha modified?
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22 views

How to build mixed-effect model for data pairs with daily-varying data and parameter invariant with time using lme R package [on hold]

I am now building linear mixed-effect model to link daily varying air pollutant concentration from monitoring sites with corresponding meteorological data and monitoring site elevation of 2012. Model ...
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1answer
43 views

Post Hoc test after lme [closed]

I am trying to run a Post Hoc test (glht) after a linear mixed model (lme) in R. I was ...
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28 views

Repeated measures linear mixed effects model

I am working with trees that were fertilized in a full factorial design (N x P x K) in plots that are replicated four times. I currently have a mixed effects model with this structure: ...
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18 views

Partial derivative from lme or lm object

I'm looking for an R package, or another approachable way in R to obtain the first partial derivative of choice from an lm or lme object. I'm aware of http://stats.stackexchange.com/a/8253/13758 but ...
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25 views

Assumptions for nlme

I want to analyze a repeated measure design with two independent variables (var1, var2) where the subjects had to solve three ...
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29 views

Hierarchical weighted linear regression through the origin and varying slopes within groups

I am trying to fit a hierarchical linear regression model. My data includes samples with 10 different classes, and samples have varying numbers of data points (from 1 to ~1000). I want to fit a ...
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13 views

Standard errors of estimates in multi factorial LMEM

This question may already be well-answered as it seems relatively straight forward, but my search of existing posts has failed... apologies if it is redundant. I am building a linear mixed effects ...
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1answer
83 views

What statistical test is performed by summary(glht(model, linfct=mcp(factor=“Tukey”)), test=adjusted(type=“none”))?

I have data that I have fit using lme with the following structure (Subject is implemented as a random effect in order to account for multiple paired comparisons): ...
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94 views

Accounting for heteroskedasticity in lme linear mixed model?

I have a data set where I measured the number of molecules (M) present in cells as a function of drug (with or without) and days of treatment (5 timepoints). I repeated the experiment 3 times, with ...
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1answer
73 views

Mixed and random effect model with multiple crossed random effects in lme4 vs nlme

I am trying to fit a few models as follows for my data of observations recorded from $p$ genotypes planted in $n$ locations for $m$ years. The aim is to estimate BLUPs finally. $$Y_{ijk} = \mu + G_i ...
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32 views

How to interpret 3 main effects when an interaction exists for only two of the variables?

I've been searching for interpretation guidance regarding the below problem, but all the resources I've seen have been fully crossed (i.e., all variables included in the interaction term). Below is a ...
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1answer
124 views

lme() with several within and between (categorical and continuous) subject factors

I am currently trying to analyse data from an experiment of mine and I have done some searching for instructions on the usage of the lme() function for R, since I am looking to analyse my data with a ...
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32 views

Estimated random effects correlation of 1 when fitting a random intercept model using lme

I am trying to fit the linear random effects model: $y_{ijk}=\theta_{ij}+\epsilon_{ijk},$ where $\theta_{ij}$ is a random effect. I assume the random effects and error distributions are normal. ...
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15 views

How to calculate confidence intervals using gamm?

I have a problem calculating confidence intervals from a gamm model. My data looks like this: As you can see, these are longitudinal data of subjects in groups (Each subject appears only in one ...
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43 views

Random effect model result of R and JMP

I have two groups of people, namely A and B. We have the hourly mean heart rate for 45-80 hrs, length differed by individual. We are interested in the group*time effect on the heart rate. Since I have ...
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89 views

including interactions in a mixed linear model in R (lme)

I'm trying to test for the effect of soil moisture on transpiration rates. I have plot-level data for 18 plots in 6 different stands of trees (3 plots x 6 stands). I want to treat "stand" as a random ...
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45 views

Intuitive feel in mixed effect models

This is something I have been thinking about for sometime. Consider the random effects model $y= Zu + e$ where $u \sim N(0, \sigma^{2}I)$ and $ e \sim N(0, \epsilon^{2}I)$ I now want to compare 2 ...
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1answer
159 views

Multivariate model in lme() with independent random effect, similar to MCMCglmm

I would like to specify a multivariate model with lme with a random effect for group which is independent across variables. I found this post, which explains that ...
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57 views

allowing for different variances between groups versus allowing for random slopes in lme

I have a data set that looks like this: Genotype Condition Trait A 1 0.0007 B 1 0.005 A 2 0.0003 B 2 ...
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27 views

differences between different notations in mixed effects model

I have never been so confused in my life. Could anyone please tell me what is the difference between the following mixed effects models: ...
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52 views

Choose random structure in LME. Should I rely on AIC?

I want to choose the best random structure for my mixed-effects model. I have compared four models: without a random part, random intercept, random intercept and slope, and random effects: ...
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45 views

What is the equivalent of a repeated ANOVA using a mixed effect model with lme?

I have a data frame with this structure: ...
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29 views

Trial with two sites, two years - lme model building and simplification (Q2)

I have got two questions on an agricultural field trial that was conducted at two sites in two conscutive years. Virtually everything was the same in all trials (variety, spacing, planting ...
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36 views

Trial with two sites, two years - Different number blocks - Problem? (Q1)

I have got two questions on an agricultural field trial that was conducted at two sites in two conscutive years. Virtually everything was the same in all trials (crop variety, planting density...). ...
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356 views

lme / lmer - split-plot with Non orthogonal subdesign

I have an agricultural field experiment (testing a plant protection agent): Split plot design with: ...
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3answers
112 views

Which test for this data set of chemical concentrations

I have a very simple data set: a parameter (concentration of a chemical) was measured at day 0, day 1 and day 2 in three subjects (there is a control group as well, but here all the values are always ...
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1answer
69 views

Good way to plot a variable between conditions with multiple measurements

I've a frame containing Participant----Condition----Duration Participant1,One,2000 Participant1,One,2780 Participant1,One,200 Participant2,Two,2000 Participant2,Two,2340 ...
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152 views

Fixed, random effect and nested factor in lme

I have a dataset with the following variables: Treatment : (fixed,3 levels) Location : (fixed, 4 levels) Sample (random, 5 levels): 5 samples are taken in each location (randomly) Subsample ...
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1answer
150 views

Demonstrate difference in growth over time

Short version Is there a difference per treatment given time and this dataset? Or if the difference we're trying to demonstrate is important, what's the best method we have for teasing this out? ...
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1answer
219 views

Using lme with a fixed beta (slope), and estimating the intercept only

lme.1.combo <- lme(ComboRate ~ p_w, random = ~1 | Rat,data=x) The line above will return a fitted intercept term, and a fitted beta (slope) term given these ...
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1answer
632 views

Dropping term for correlation between random effects in lme and interpretting summary output

I want to fit a model without a correlation term between the random effects with lme. In lmer this is fairly straighforward.... ...
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1answer
143 views

Linear Mixed Model Interpretation

I'm working on analyzing some data that need to use lme model, but I'm not sure about interpreting the output. Data looks like this: ...
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65 views

Translating from aov to lmer or lme with three levels of nesting

I have data from a split-plot (or repeated measure) experiment with three factors: A is random, B is fixed and nested within A, and C is fixed and nested within B. I can test for the effect of B, C ...
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237 views

Non-converging heteroscedastic linear mixed-effects model (R lme)

I'm working on a project where I try to determine the influence of consulting expenditures companies made the year before on several economic figures. My dataset consists of roughly 2'000 different ...
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79 views

Mixed-model specification in R - exploring individual differences

My current experiment aims to explore the effect of viewing condition, difficulty and depth perception on object grasping. I'm mostly interested in the effect of individual differences in depth ...
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1answer
583 views

Specifying contrasts for lme in 3x3 repeated-measures design

I would like to test the effects of two categorical variables, each with 3 levels, on some continuous data. Three groups of participants completed the same task for 3 types of stimuli, so it's a 3x3 ...
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1answer
305 views

Checking assumptions LMM: residual plot with diamond shape

I am running a linear mixed model and want to check its assumptions. The model I run is comparing if males and females behave differently over time (timeclass=1,2,3,4): ...
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1answer
97 views

Determine individual consistency from mixed model?

To investigate the difference between three tasks I tested 30 individuals on each of the three tasks and ran the linear model as follows: ...
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3answers
4k views

Checking assumptions lmer/lme mixed models in R

I ran a repeated design whereby I tested 30 males and 30 females across three different tasks. I want to understand how the behaviour of males and females is different and how that depends on the ...
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1answer
452 views

How to specify partially crossed random effect in lme?

I am new to R and would like your help with lme formula for partially crossed random effect in a random-intercept, random-slope model. In the longitudinal data I have, each subject (barring some ...
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88 views

Linear model or component analysis on timecourse data

I have some timecourse data which plotted looks like the figure below. I want to better describe the difference between the two conditions. My adviser advised :D me to use a linear model and observe ...
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1answer
128 views

What's the value of ANOVA/LME?

I have some data I want to analyze, for which I was curious whether one or more conditions lead to measurements significantly different from the rest. I started out by making a table of t-test ...
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73 views

Using REML in mixed models if random factor is small

I'm trying to fit linear mixed models to 3 different DV (so three models). I understand that REML gives less biased variance estimates. As im more interested in the fixed effects, I use ML for the ...
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0answers
2k views

Nested random effects group size using lme (in nlme)

I'm wrestling with a question regarding random effects that I haven't been able to figure out with my regular resources. I am examining the effects of two treatments (heat and water) on plant biomass ...
4
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1answer
150 views

GLMM model specification help gender effects + an effect that is nested only within female

Main question: "What are the contributing variates to daily movement distances?" Specifically my question today relates to: "What is the contribution related to gender, and then within female what ...
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1answer
77 views

Translating R lme comand to mathematical equation

I would appreciate if someone could help me in translating the following R command into a mathematical equation: ...
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54 views

Using R - lme() with Log dataset

this is a question regarding using lme() in R to calculate between-group and within-group variation in a dataset containing log values. I have read that when using lme() to calculate sigma ...
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1answer
151 views

How to fit different ARMA models by group in R?

I have $Y$ measurements per several Subjects and I'm studying impact of factor on $Y$ measurements. I've fit a lognormal mixed model with a random interaction, but I'm finding autoregressive ...
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2answers
1k views

Interpretation of interaction effects in linear mixed models with numeric and factorial IVs

I hope my question is not too basic for this community. I can*t figure out how to interpret the output of my linear mixed model, especially the interaction effects. I do my analysis in R using lme ...