fit: Fit the GAM part of a sspm model

In pedersen-fisheries-lab/spaspm: Spatial Surplus Production Model Framework for Northern Shrimp Populations

Fit the GAM part of a sspm model

Description

Once formulas have been mapped onto a sspm discrete object, the GAMs can be fitted with this function. Arguments can be passed onto bam.

Usage

fit_smooths(
  sspm_object,
  boundaries,
  keep_fit = TRUE,
  predict = TRUE,
  family = mgcv::tw,
  drop.unused.levels = F,
  method = "fREML",
  ...
)

fit_spm(
  sspm_object,
  sspm_formula,
  keep_fit = TRUE,
  family = mgcv::scat,
  drop.unused.levels = F,
  select = TRUE,
  method = "REML",
  ...
)

## S4 method for signature 'sspm_dataset,sspm_discrete_boundary'
fit_smooths(
  sspm_object,
  boundaries,
  keep_fit = TRUE,
  predict = TRUE,
  family = mgcv::tw,
  drop.unused.levels = F,
  method = "fREML",
  ...
)

## S4 method for signature 'sspm,sspm_formula'
fit_spm(
  sspm_object,
  sspm_formula,
  keep_fit = TRUE,
  family = mgcv::scat,
  drop.unused.levels = F,
  select = TRUE,
  method = "REML",
  ...
)

Arguments

sspm_object	[sspm_dataset] An object of class sspm_dataset.
boundaries	[sspm_boundary] An object of class sspm_discrete_boundary.
keep_fit	[logical] Whether or not to keep the fitted values and model (default to TRUE, set to FALSE to reduce memory footprint).
predict	[logical] Whether or not to generate the smoothed predictions (necessary to fit the final SPM model, default to TRUE).
family	This is a family object specifying the distribution and link to use in fitting etc. See glm and family for more details. The extended families listed in family.mgcv can also be used.
drop.unused.levels	by default unused levels are dropped from factors before fitting. For some smooths involving factor variables you might want to turn this off. Only do so if you know what you are doing.
method	The smoothing parameter estimation method. "GCV.Cp" to use GCV for unknown scale parameter and Mallows' Cp/UBRE/AIC for known scale. "GACV.Cp" is equivalent, but using GACV in place of GCV. "REML" for REML estimation, including of unknown scale, "P-REML" for REML estimation, but using a Pearson estimate of the scale. "ML" and "P-ML" are similar, but using maximum likelihood in place of REML. Default "fREML" uses fast REML computation.
...	Arguments passed on to mgcv::bam formula A GAM formula (see formula.gam and also gam.models). This is exactly like the formula for a GLM except that smooth terms, s and te can be added to the right hand side to specify that the linear predictor depends on smooth functions of predictors (or linear functionals of these). data A data frame or list containing the model response variable and covariates required by the formula. By default the variables are taken from environment(formula): typically the environment from which gam is called. weights prior weights on the contribution of the data to the log likelihood. Note that a weight of 2, for example, is equivalent to having made exactly the same observation twice. If you want to reweight the contributions of each datum without changing the overall magnitude of the log likelihood, then you should normalize the weights (e.g. weights <- weights/mean(weights)). subset an optional vector specifying a subset of observations to be used in the fitting process. na.action a function which indicates what should happen when the data contain ‘NA’s. The default is set by the ‘na.action’ setting of ‘options’, and is ‘na.fail’ if that is unset. The “factory-fresh” default is ‘na.omit’. offset Can be used to supply a model offset for use in fitting. Note that this offset will always be completely ignored when predicting, unlike an offset included in formula (this used to conform to the behaviour of lm and glm). control A list of fit control parameters to replace defaults returned by gam.control. Any control parameters not supplied stay at their default values. scale If this is positive then it is taken as the known scale parameter. Negative signals that the scale paraemter is unknown. 0 signals that the scale parameter is 1 for Poisson and binomial and unknown otherwise. Note that (RE)ML methods can only work with scale parameter 1 for the Poisson and binomial cases. gamma Increase above 1 to force smoother fits. gamma is used to multiply the effective degrees of freedom in the GCV/UBRE/AIC score (so log(n)/2 is BIC like). n/gamma can be viewed as an effective sample size, which allows it to play a similar role for RE/ML smoothing parameter estimation. knots this is an optional list containing user specified knot values to be used for basis construction. For most bases the user simply supplies the knots to be used, which must match up with the k value supplied (note that the number of knots is not always just k). See tprs for what happens in the "tp"/"ts" case. Different terms can use different numbers of knots, unless they share a covariate. sp A vector of smoothing parameters can be provided here. Smoothing parameters must be supplied in the order that the smooth terms appear in the model formula. Negative elements indicate that the parameter should be estimated, and hence a mixture of fixed and estimated parameters is possible. If smooths share smoothing parameters then length(sp) must correspond to the number of underlying smoothing parameters. Note that discrete=TRUEmay result in re-ordering of variables in tensor product smooths for improved efficiency, and sp must be supplied in re-ordered order. min.sp Lower bounds can be supplied for the smoothing parameters. Note that if this option is used then the smoothing parameters full.sp, in the returned object, will need to be added to what is supplied here to get the smoothing parameters actually multiplying the penalties. length(min.sp) should always be the same as the total number of penalties (so it may be longer than sp, if smooths share smoothing parameters). paraPen optional list specifying any penalties to be applied to parametric model terms. gam.models explains more. chunk.size The model matrix is created in chunks of this size, rather than ever being formed whole. Reset to 4*p if chunk.size < 4*p where p is the number of coefficients. rho An AR1 error model can be used for the residuals (based on dataframe order), of Gaussian-identity link models. This is the AR1 correlation parameter. Standardized residuals (approximately uncorrelated under correct model) returned in std.rsd if non zero. Also usable with other models when discrete=TRUE, in which case the AR model is applied to the working residuals and corresponds to a GEE approximation. AR.start logical variable of same length as data, TRUE at first observation of an independent section of AR1 correlation. Very first observation in data frame does not need this. If NULL then there are no breaks in AR1 correlaion. discrete with method="fREML" it is possible to discretize covariates for storage and efficiency reasons. If discrete is TRUE, a number or a vector of numbers for each smoother term, then discretization happens. If numbers are supplied they give the number of discretization bins. Parametric terms use the maximum number specified. cluster bam can compute the computationally dominant QR decomposition in parallel using parLapply from the parallel package, if it is supplied with a cluster on which to do this (a cluster here can be some cores of a single machine). See details and example code. nthreads Number of threads to use for non-cluster computation (e.g. combining results from cluster nodes). If NA set to max(1,length(cluster)). See details. gc.level to keep the memory footprint down, it can help to call the garbage collector often, but this takes a substatial amount of time. Setting this to zero means that garbage collection only happens when R decides it should. Setting to 2 gives frequent garbage collection. 1 is in between. Not as much of a problem as it used to be, but can really matter for very large datasets. use.chol By default bam uses a very stable QR update approach to obtaining the QR decomposition of the model matrix. For well conditioned models an alternative accumulates the crossproduct of the model matrix and then finds its Choleski decomposition, at the end. This is somewhat more efficient, computationally. samfrac For very large sample size Generalized additive models the number of iterations needed for the model fit can be reduced by first fitting a model to a random sample of the data, and using the results to supply starting values. This initial fit is run with sloppy convergence tolerances, so is typically very low cost. samfrac is the sampling fraction to use. 0.1 is often reasonable. coef initial values for model coefficients G if not NULL then this should be the object returned by a previous call to bam with fit=FALSE. Causes all other arguments to be ignored except sp, chunk.size, gamma,nthreads, cluster, rho, gc.level, samfrac, use.chol, method and scale (if >0). fit if FALSE then the model is set up for fitting but not estimated, and an object is returned, suitable for passing as the G argument to bam. drop.intercept Set to TRUE to force the model to really not have the a constant in the parametric model part, even with factor variables present. in.out If supplied then this is a two item list of intial values. sp is initial smoothing parameter estiamtes and scale the initial scale parameter estimate (set to 1 if famiy does not have one).
sspm_formula	[sspm_formula] The formula specifying the the smoothing model.
select	Should selection penalties be added to the smooth effects, so that they can in principle be penalized out of the model? See gamma to increase penalization. Has the side effect that smooths no longer have a fixed effect component (improper prior from a Bayesian perspective) allowing REML comparison of models with the same fixed effect structure.

Value

A object of the class sspm_fit.

Examples

## Not run: 
fit_smooths(boundaries = boundaries, keep_fit = TRUE, ...)
fit_spm(sspm_object = sspm_object, sspm_formula = sspm_formula, ...)

## End(Not run)

pedersen-fisheries-lab/spaspm documentation built on Feb. 16, 2025, 7:39 p.m.