Questions tagged [gamm4]
R package to fit generalized additive mixed models (GAMM) using mgcv and lme4 packages.
58
questions
3
votes
0
answers
101
views
GAMs falsely suggest non-linear function (edf>2) for about 15-25% of simulated data?
I've been learning about GAMs and was curious about how sensitive they are to noise within a given sample. I know people generally say that GAMs are more prone to overfitting than GLMs and need to be ...
1
vote
0
answers
15
views
Properly set random effect of nested design in gam?
I have a set of insect traps, where I have counts of beetles per year. I have several records per each trap and year. I would like to estimate the number of beetles per trap, given several predictors. ...
2
votes
1
answer
52
views
High autocorrelation in GAMM
I am fitting a GAMM model to understand the evolution of fire elevation in time. I am using the mgcv package from R. My dataset contains 820 fires events with its corresponding elevation, time of ...
0
votes
1
answer
27
views
How to analyse a response variable with a right-skewed QQplot and categorical predictors
I am trying to apply a model to my dataset. The way my response variable has been generated is a bit convoluted but it's been checked by my supervisor - I have strings of numbers (e.g 112222333322111) ...
0
votes
0
answers
123
views
Problem fitting GAMM4 with interaction term: "fixed-effect model matrix is rank deficient so dropping 1 column / coefficient"
I am trying to use a gamm4() (mgcv package) equation to model 1) how brain regional volumes change over time and 2) how brain regional volume development differs between males and females. My data is ...
1
vote
0
answers
72
views
How to deal with collinearity or concurvity between fixed effect variables and random effect variables?
My current work involves asking subjects from different groups to pronounce multiple words, and I am interested in understanding the relationship between word duration and groups.
In R syntax, this ...
0
votes
0
answers
23
views
Interpretation of significant parametric coefficients group difference without difference in smooths gamm4
I am running longitudinal models using gamm4 with interest in looking at main effects of group and group by age interactions (age range 8-25 years). I am using the following syntax.
model1 <- gamm4(...
1
vote
1
answer
46
views
Unable to extract AR(p) values from the GAMM function in mgcv
I am using generalized additive models in R with an correlated structure on the residuals, however I am unable to extract the actual coefficients of the AR(p) structure even though they are provide in ...
0
votes
1
answer
93
views
GAMM4 models in R with either a continuous OR categorial variable in the smooth, and model comparison
To note: I am fairly new to GAMMs. I have read many StackExchange questions/answers and general documentation on GAMMs, and consistently question the proper way to set up my models to answer my ...
0
votes
0
answers
119
views
Calculate annual rates from the gam model over time?
I am trying to express the difference in the 'speed of increase' between two categories in gam modelling. My data represents the cumulative values over time [0-100%]...
4
votes
1
answer
628
views
Calculation of degrees of freedom for B-splines
I am confused about how the degrees of freedom in a B-spline are calculated in the package splines. The documentation for the B-spline function can be found here:
https://www.rdocumentation.org/...
1
vote
0
answers
78
views
Calculating confidence intervals for gamm4 models [closed]
I am working with gamm4 models in my research and am having trouble understanding how to go about calculating confidence intervals for my models.
EX model: m<-gamm4(turbidity~ year+discharge,data=...
0
votes
1
answer
134
views
CIs for random intercepts from gam and stan_gamm4 are similar, but those from gamm4 are not. why?
Question: how can one obtain a good confidence interval for the estimated random effects from gamm4?
Motivation: The example below, using binomial data with a random intercept, shows that estimated ...
2
votes
1
answer
464
views
Is my GAM modeling longitudinal change appropriately?
My data includes the following:
Y which is a physiological measure
Age continuous
Gender ...
2
votes
1
answer
151
views
What to do when GAMM is linear?
I have the following gamm4 output:
This is longitudinal data modeled as:
...
5
votes
1
answer
405
views
How to interpret non-signicant intercept but significant smooth terms with GAM in R?
I have the following gam model:
...
2
votes
1
answer
405
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 ...
1
vote
0
answers
141
views
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?...
1
vote
0
answers
181
views
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 ...
0
votes
2
answers
389
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 ...
4
votes
2
answers
449
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 ...
1
vote
0
answers
142
views
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 &...
7
votes
1
answer
2k
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 ...
1
vote
0
answers
75
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 ...
2
votes
0
answers
121
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 ...
2
votes
1
answer
253
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 ...
1
vote
0
answers
62
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(...
4
votes
1
answer
1k
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:
...
1
vote
1
answer
489
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 ...
2
votes
1
answer
826
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:
...
1
vote
0
answers
287
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 ...
0
votes
0
answers
587
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'...
1
vote
0
answers
669
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 ...
1
vote
1
answer
297
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 ...
2
votes
1
answer
1k
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 ...
2
votes
0
answers
103
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 ...
2
votes
0
answers
793
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 ...
6
votes
1
answer
2k
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 ...
7
votes
1
answer
3k
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 ...
1
vote
0
answers
62
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 ...
1
vote
1
answer
365
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'...
2
votes
0
answers
1k
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 ...
1
vote
1
answer
1k
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. ...
1
vote
2
answers
657
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 ...
2
votes
1
answer
386
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 ...
4
votes
0
answers
2k
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 ...
1
vote
1
answer
128
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 ...
5
votes
1
answer
349
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/...
2
votes
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 ...
6
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 ...