Questions tagged [gamm4]

R package to fit generalized additive mixed models (GAMM) using mgcv and lme4 packages.

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Is my GAM modeling longitudinal change appropriately?

My data includes the following: Y which is a physiological measure Age continuous Gender ...
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2 votes
1 answer
102 views

What to do when GAMM is linear?

I have the following gamm4 output: This is longitudinal data modeled as: ...
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3 votes
1 answer
141 views

How to interpret non-signicant intercept but significant smooth terms with GAM in R?

I have the following gam model: ...
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2 votes
1 answer
97 views

AIC comparison of GAMM and LMM: Is it valid?

I have 2 models, using exactly the same variables, one fitted as a linear mixed model (LMM) and another fitted as a generalised additive mixed model (GAMM). I am interested in the fixed effect X and ...
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GAMM with BETAR(Link = "Logit") [closed]

I'm trying to use betar in gamm4 models but keep hitting an error. As far as I can tell, betar is one of the families that should be available - can anyone identify why I would keep hitting this error?...
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Interpreting a GAM model output

I have been working on a GAM regressing model with interaction and the summary output have several parameter coefficient and also a some approximate significant of smooth terms. Do u need to interpret ...
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0 votes
2 answers
129 views

use GAMM models for full circular wind direction data

using a GAM modeling approach enables to include circular data as fixed effects. I wish to analyze the effect of wind on the flight behaviour of birds. In order to do so I want to add wind speed and ...
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4 votes
2 answers
104 views

GAM with many binary factors

I am trying to model the blood glucose response at 15-minute intervals after a meal. The meal event has many continuous variables (like time of day, body weight, etc) and many binary variables (like ...
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Decomposition of r square into fixed and random effect in a GAMM (mgcv)

for a paper I estimated a generalized additive model using R's mgcv. One reviewer now asks whether it would be possible to report a marginal and conditional r square instead of a global r square to &...
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60 views

GAMM4 and interaction between two continuous variables

We want to run a general additive model with fixed and random effects. We have a brain measure (Diff) done at four different ages (Age) on the same subject and a behavioural measure (Beh) done only ...
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3 votes
1 answer
582 views

Basis dimension (k) too low for the smooth term in a GAMM

I am running a generalized additive model (GAM), but when I check the model diagnostics (using gam.check()) I run into problems. I have tried adjusting the value ...
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1 vote
0 answers
61 views

Times series forecasting , why predictions are the same over time

This is my first time posting here , I am doing an energy consumption forecast , my data contains the energy every hours I have two seasonality ,every 24 hours and every 7 days (daily and weekly). I ...
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2 votes
0 answers
46 views

Adding interaction term with multiple variables in gamm4?

I am using gamm4 model from R package gamm4 (random slope=age_m, random intercept=FLEHS_ID and groupdescription): m1 I only look ...
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2 votes
1 answer
179 views

Is GAM appropriate for these data

I am strangling to find the right modeling method for my data. Short explain of the dataset : I have a variable called alpha diversity ( Alpha diversity refers to the average species diversity in a ...
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1 vote
0 answers
38 views

Error in X %*% diag(diagU[indi]) : non-conformable arguments with GAMM4 [closed]

I've started working with gams recently and I am having a bit of trouble with gamm. I built my model with the gam function and everything runs smoothly with the following code. gamtot <- gam(...
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3 votes
1 answer
613 views

Specifying random effects using GAMM4

I am missing something when trying to specifiy random effects on Gamm4. Reproducible example: Consider the following simulated data: ...
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1 vote
1 answer
377 views

INTERPRETATION OF GRAPHIC RESULTS OF GAM IN R

Hello I am trying to adjust a GAM in R. I am new to GAM and I am trying to see the relationship that can exist through time in 57 river stations that are divided into Impacted and not previously ...
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1 vote
1 answer
552 views

How to interpret the plotted difference of in-factor smooths

I used the gamm4 R package to analyze the location effect on heart rate over time (Inc_age), including some linear co-variates and a random effect. My model looks like this: ...
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1 vote
0 answers
175 views

Using and interpreting GAMMs

I have been struggling to fit a model using gamm4. context of my study I'm trying to fit a 'gamm binomial' to model the probability of having a new component in a group. In my data, components are ...
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0 answers
397 views

how to interpret the smoothed effect of time in GAMM models

I have recently taken a plunge into the world of Generalized Additive Mixed Models (GAMMs) after learning that including the quadratic and cubic fixed and random effects of time to understand students'...
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0 answers
433 views

Negative binomial random effects models (glmmTMB/gamm/gamm4)

Can anyone help please. Am I missing something fundamental here? I would like to test for a Cave and a Category effect in the same model, and I'd like to know if I've specified the random effects ...
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1 vote
1 answer
225 views

Irregular time series with multiple sampling sites

I have a dataset of marine debris items (number of items standardized per effort: Items/(number of volunteers * Hours * Length)) taken from 2 main locations (WA and Queensland) in Australia (8 Sub ...
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1 vote
1 answer
909 views

Using gamm4 on zero-inflated count data with Tweedie or zero-inflated Poisson distributions

I'm working with a dataset with a large number of zero-counts on the response variable. This dataset consists of qualitatively coded interviews in a number of important categories, but many of the ...
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2 votes
0 answers
87 views

gam/gamm when response variable is complex

I would like to fit a generalized additive mixed model using mgcv or gamm4, but have a response variable consisting of complex numbers where y=a+1i*b. Is this possible, and if so are there any special ...
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2 votes
0 answers
580 views

Correct way to account for repeated measures and spatial autocorrelation in GAMM (R)

I am using the gamm function in the mgcv package in R to specify a model that predicts abundance with respect to elevation and year based on repeated measures from several sites. My overarching ...
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6 votes
1 answer
1k views

GAMM with multiple and crossed random effects

I am new to Generalized additive mixed models (GAMM) and I'm trying to model a behavioral response variable (time spent shading eggs by a nesting bird in minutes ...
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4 votes
1 answer
2k views

GAMM with Zero-Inflated Negative Binomial - Looking for a package in R

I am looking for an R package to fit Generalized Additive Mixed Models (GAMMs) with ZINB distribution. ZINB is not available in the mgcv package nor in the ...
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1 vote
0 answers
59 views

Determine maxima and minima of fitted GAMM smooth

I have been using gamm4 to model the daily activity pattern of a certain behavior as a binomial response (whether the behavior occurs or not for each hour of the day). I am comparing the daily ...
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1 vote
1 answer
262 views

Does family 'ocat' work with gamm4 in R? [closed]

I am trying to fit a GAMM to ordered categorical data using gamm4 in R. In the help file for gamm4, it says the argument 'family'...
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2 votes
0 answers
945 views

Model Comparison of GAMs using gamm4

I am using a GAM from package gamm4 in R to fit a varying coefficient model for longitudinal data. I have data consisting of ...
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0 votes
2 answers
814 views

Gamm residuals patterns: temporal and spatial

I'm trying to fit a GAMM model with this dataset, which can be downloaded here: https://ufile.io/8umh6 . The dataset consists of 60 pixels sampled in two different areas: BAR and MON, 30 for each one. ...
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1 vote
2 answers
484 views

Getting better p-values for a gam model with multiple explanatory terms using bootstrapping

I'm running a GAMM in R on count data with multiple explanatory variables, including both continuous variables with smoothers and factors, a random effect, and a Poisson distribution using the gamm4 ...
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2 votes
1 answer
313 views

GAMM with fragmented spatial data - presence/absence response

Quite stuck so hope someone could help me in the right direction. Some background for the data: For the last 15 years data have been collected on a specific species during the period from early ...
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3 votes
0 answers
1k views

Help interpreting plot.gam in R (gamm4)

I'm not sure this question is better suited for Cross Validated or Stack Overflow, please don't hesitate to tell me if I ask it on the wrong forum. I'd appreciate some help interpreting what shows the ...
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1 vote
1 answer
116 views

R^2 for mixed effect models (both generalized linear and additive)

I have seen from several discussion threads that there are a few ways of calculating R^2 for LMMs and GLMMs - albeit with a caveat for GLMM being that the existing methods work for only gaussian ...
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4 votes
1 answer
292 views

Presence/Absence GAMM with penalized smoother convergence/completion problem, data set too large

I am having issues running a GAMM to determine presence/absence with a very large data set (9,000,000 rows x 13 cols) using GAM4 in R. I think the data set may be too large and is causing convergence/...
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1 vote
1 answer
3k views

gam models with random effect R

I am modeling fishery CPUE as a function of a number of a number of covariates using a GAM approach that includes fixed and random effects. I understand that there are limitations with regards to ...
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5 votes
0 answers
3k views

How to calculate deviance explained for a general additive mixed model (GAMM)?

I am working with the package mgcv fitting some GAMs with several covariates, and the same models with GAMMs including annual correlation. Applying the ...
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2 votes
0 answers
2k views

Binomial Temporal GAMM does not converge (R::mgcv)

I am new to both mixed effect and Additive models so I'm sorry if the answer here is trivial. I have data collected on several metabolic chemicals (M1,M2...), covariates (time,Race,Gender...) and ...
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1 vote
0 answers
1k views

Generalized additive mixed model in R - specifying a fit function

The data in question comprise two response groups (no response vs. stress signal), different individuals, repeated measures ...
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12 votes
0 answers
3k views

Interpreting and reporting gamm4 result

I am new to gam, and most of my knowledge comes from this document http://www3.nd.edu/~mclark19/learn/GAMS.pdf. Now I am using generalized addictive model with random effects to model some data, where ...
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5 votes
1 answer
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Adding a variance structure when fitting a gamm with Gamma distribution

I am using the code below to fit a gamma GAMM introducing a variance structure that informs the model that variance of the response variable is much larger in one of the levels of the factor coast ...
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0 votes
1 answer
806 views

gamm4 what does s() do?

say we have the following: ...
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1 vote
0 answers
156 views

Can i use a mixture model for when I have an omitted variable?

I plan to fit a GAM or GAMM. There is one categorical variable which I think is important for explaining Y (or Y*), but it is not in my dataset - it is measurable but has not been measured. Can I use ...
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8 votes
1 answer
3k views

QR factorization and linear regression

I have been reading "Generalized Additive Models an Introduction with R" by Simon Wood and have come across a section I'm having trouble with. On page 13 it is stated that the model or design matrix ...
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5 votes
1 answer
7k views

Using a gamm4 model to predict estimates in new data

I have been experimenting with gamm4 to derive GAMMs of some repeated measures data. The models looks very nice and seem to give more flexibility than my LMMs. Ultimately I want to compare models ...
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