Questions tagged [gamm4]
R package to fit generalized additive mixed models (GAMM) using mgcv and lme4 packages.
2
votes
0answers
20 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 ...
1
vote
1answer
120 views
GAMM with Zero-Inflated Negative Binomial - Looking for a package on R
I am looking for an R package to fit Generalized Additive Mixed Models with ZINB distribution, as ZINB is not available in the mgcv package nor in the gamm4 package. I read here that it might be ...
1
vote
0answers
34 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
1answer
54 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
1answer
153 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 ...
0
votes
0answers
48 views
Checking for overdispersion in gamm4
I would like to check for overdispersion in a gamm4 model and I'm having trouble finding a method (I only find them for glm, glmer and glmm). Is there a simple way to do this? I am relatively new to R....
0
votes
2answers
135 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. ...
0
votes
1answer
150 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 ...
1
vote
1answer
159 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 ...
2
votes
0answers
827 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
0answers
84 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 ...
3
votes
1answer
182 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/...
1
vote
1answer
2k 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 ...
3
votes
0answers
2k 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 ...
2
votes
0answers
1k 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 ...
1
vote
0answers
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 ...
7
votes
0answers
2k 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 ...
4
votes
1answer
1k views
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 ...
0
votes
1answer
482 views
1
vote
0answers
145 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 ...
6
votes
1answer
1k 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
...
5
votes
1answer
4k 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 ...
