Questions tagged [gamm4]
R package to fit generalized additive mixed models (GAMM) using mgcv and lme4 packages.
68 questions
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INterpretting residuals from a GAMM model
I am trying to run GAMs using binomial data (link=logit) in r with the mgcv package. This is to attempt to describe which variables describe species presence using presence (1) and absence (0) data as ...
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Gaussian Markov Random Field fitting in GAMLSS with coordinates (UTMs)
I am building a model in gamlss with presence/absence ecological data (binary) that are spatially correlated. It appears my primary option in ...
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Determine distribution for GAMMS
I've collected eye-tracking data in a visual world experiment, i.e. subjects fixated a screen with four objects while listening to a sentence, and I analyse from when on they look more at the target ...
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Visualization and interpretation GAM three-way interaction (2 continuous, 1 categorical variable)
I'm relatively new with gams, yet handling a complex dataset.I've gone over some of the previous questions on related topics and have made some progress in understanding the interaction with GAM, but ...
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GAMs and random effects: Significant differences between GAMM and GAMM4 outputs
When introducing a random effect in gamm and gamm4, I receive different p-values for the $gam...
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"Fixed" effects when using mgcv and 'bs=fs' in GAMM?
I am curious what the most appropriate way to estimate both the overall/population level smooth effect of x while also estimating random smooths for different ...
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gamm and gamm4 give very different smooth term results for mixed models with factor-smooth interaction
I am analyzing an longitudinal dataset which has two groups (patient vs controls; ordered factor) with brain volume data over time. Participants entered the study at different ages and have varied ...
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Interpretation help of summary from basic GAM models with random smooths
I have run two GAM models to see if there is a non-linear relationship between my response variable (blood metabolites) and time.
I'm currently accounting for individuals (ID_new) with a random smooth ...
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Nonparametric version of lme- gamm function in R
Is there a non-parametric version of a linear mixed model? I've seen some people cite gamm in R as one but unsure of how I would go about using it.
In R, the code I ...
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Structuring new data when predicting via predict.merMod
I am trying to obtain predictions, given new data, from within a loop using the gamm4() function in the mgcv package of R. However, I run into an error message ...
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Obtaining, and manipulating, the prediction equation from a gamm model with smooth terms
I have read similar questions submitted here, and have looked in Wood's 2017 book (Generalized additive models: An introduction with R, 2nd edition) but cannot find an answer to my problem.
To set up ...
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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 ...
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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. ...
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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 ...
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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) ...
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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 ...
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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 ...
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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 ...
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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 ...
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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%]...
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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/...
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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=...
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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 ...
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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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What to do when GAMM is linear?
I have the following gamm4 output:
This is longitudinal data modeled as:
...
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How to interpret non-signicant intercept but significant smooth terms with GAM in R?
I have the following gam model:
...
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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