Hierarchical generalized additive models in ecology: an introduction with mgcv
- Academic Editor
- Andrew Gray
- Subject Areas
- Ecology, Statistics, Data Science, Spatial and Geographic Information Science
- Generalized additive models, Hierarchical models, Time series, Functional regression, Smoothing, Regression, Community ecology, Tutorial, Nonlinear estimation
- © 2019 Pedersen et al.
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. Hierarchical generalized additive models in ecology: an introduction with mgcv. PeerJ 7:e6876 https://doi.org/10.7717/peerj.6876
In this paper, we discuss an extension to two popular approaches to modeling complex structures in ecological data: the generalized additive model (GAM) and the hierarchical model (HGLM). The hierarchical GAM (HGAM), allows modeling of nonlinear functional relationships between covariates and outcomes where the shape of the function itself varies between different grouping levels. We describe the theoretical connection between HGAMs, HGLMs, and GAMs, explain how to model different assumptions about the degree of intergroup variability in functional response, and show how HGAMs can be readily fitted using existing GAM software, the mgcv package in R. We also discuss computational and statistical issues with fitting these models, and demonstrate how to fit HGAMs on example data. All code and data used to generate this paper are available at: github.com/eric-pedersen/mixed-effect-gams.
Two of the most popular and powerful modeling techniques currently in use by ecologists are generalized additive models (GAMs; Wood, 2017a) for modeling flexible regression functions, and generalized linear mixed models (“hierarchical generalized linear models” (HGLMs) or simply “hierarchical models”; Bolker et al., 2009; Gelman et al., 2013) for modeling between-group variability in regression relationships.
At first glance, GAMs and HGLMs are very different tools used to solve different problems. GAMs are used to estimate smooth functional relationships between predictor variables and the response. HGLMs, on the other hand, are used to estimate linear relationships between predictor variables and response (although nonlinear relationships can also be modeled through quadratic terms or other transformations of the predictor variables), but impose a structure where predictors are organized into groups (often referred to as “blocks”) and the relationships between predictor and response may vary across groups. Either the slope or intercept, or both, may be subject to grouping. A typical example of HGLM use might be to include site-specific effects in a model of population counts, or to model individual level heterogeneity in a study with repeated observations of multiple individuals.
However, the connection between HGLMs and GAMs is quite deep, both conceptually and mathematically (Verbyla et al., 1999). HGLMs and GAMs fit highly variable models by “pooling” parameter estimates toward one another, by penalizing squared deviations from some simpler model. In an HGLM, this occurs as group-level effects are pulled toward global effects (penalizing the squared differences between each group-level parameter estimate and the global effect). In a GAM, this occurs via the enforcement of a smoothness criterion on the variability of a functional relationship, pulling parameters toward some function that is assumed to be totally smooth (such as a straight line) by penalizing squared deviations from that totally smooth function.
Given this connection, a natural extension to the standard GAM framework is to allow smooth functional relationships between predictor and response to vary between groups, but in such a way that the different functions are in some sense pooled toward a common shape. We often want to know both how functional relationships vary between groups, and if a relationship holds across groups. We will refer to this type of model as a hierarchical GAM (HGAM).
There are many potential uses for HGAMs. For example, we can use them to estimate how the maximum size of different fish species varies along a common temperature gradient (Fig. 1). Each species will typically have its own response function, but since the species overlap in range, they should have similar responses over at least some of the temperature gradient; Fig. 1 shows all three species reach their largest maximum sizes in the center of the temperature gradient. Estimating a separate function for each species throws away a lot of shared information and could result in highly noisy function estimates if there were only a few data points for each species. Estimating a single average relationship could result in a function that did not predict any specific group well. In our example, using a single global temperature-size relationship (Fig. 1, solid line) would miss that the three species have distinct temperature optima, and that the orange species is significantly smaller at all temperatures than the other two (Fig. 1). We prefer a hierarchical model that includes a global temperature-size curve plus species-specific curves that were penalized to be close to the mean function.
This paper discusses several approaches to group-level smoothing, and corresponding trade-offs. We focus on fitting HGAMs with the popular mgcv package (Wood, 2011) for the R statistical programming language (R Development Core Team, 2018), which allows for a variety of HGAM model structures and fitting strategies. We discuss options available to the modeller and practical and theoretical reasons for choosing them. We demonstrate the different approaches across a range of case studies.
This paper is divided into five sections. Part II is a brief review of how GAMs work and their relation to hierarchical models. In part III, we discuss different HGAM formulations, what assumptions each model makes about how information is shared between groups, and the different ways of specifying these models in mgcv. In part IV, we work through example analyses using this approach, to demonstrate the modeling process and how HGAMs can be incorporated into the ecologist’s quantitative toolbox. Finally, in part V, we discuss some of the computational and statistical issues involved in fitting HGAMs in mgcv. We have also included all the code needed to reproduce the results in this manuscript in Supplemental Code (online), and on the GitHub repository associated with this paper: github.com/eric-pedersen/mixed-effect-gams.
A Review of Generalized Additive Models
The generalized linear model (GLM; McCullagh & Nelder, 1989) relates the mean of a response (y) to a linear combination of explanatory variables. The response is assumed to be conditionally distributed according to some exponential family distribution (e.g., binomial, Poisson or Gamma distributions for trial, count or strictly positive real responses, respectively). The GAM (Hastie & Tibshirani, 1990; Ruppert, Wand & Carroll, 2003; Wood, 2017a) allows the relationships between the explanatory variables (henceforth covariates) and the response to be described by smooth curves (usually splines (De Boor, 1978), but potentially other structures). In general, we have models of the form: where is the expected value of the response Y (with an appropriate distribution and link function g), fj is a smooth function of the covariate xj, β0 is an intercept term, and g−1 is the inverse link function. Hereafter, we will refer to these smooth functions as smoothers. In the example equation above, there are j smoothers and each is a function of only one covariate, though it is possible to construct smoothers of multiple variables.
Each smoother fj is represented by a sum of K simpler, fixed basis functions (bj,k) multiplied by corresponding coefficients (βj,k), which need to be estimated:
K, referred to as “basis size,” “basis complexity,” or “basis richness,” determines the maximum complexity of each smoother.
It would seem that large basis size could lead to overfitting, but this is counteracted by a smoothing penalty that influences basis function coefficients so as to prevent excess wiggliness and ensure appropriate complexity of each smoother. For each smoother, one (or more) penalty matrices (S), specific to the form of the basis functions, is pre- and post-multiplied by the parameter vector β to calculate the penalty (βTSβ). A penalty term is then subtracted from the model log-likelihood L, controlling the trade-off via a smoothing parameter (λ). The penalized log-likelihood used to fit the model is thus:
Figure 2 shows an example of how different choices of the smoothing parameter (λ) affect the shape of the resulting smoother. Data (points) were generated from the blue function and noise added to them. In Fig. 2A, λ was selected using restricted maximum likelihood (REML) to give a good fit to the data. In Fig. 2B, λ was set to zero so the penalty has no effect and the function interpolates the data. Figure 2C shows when λ is set to a very large value, so the penalty removes all terms that have any wiggliness, giving a straight line.
To measure the complexity of a penalized smooth terms we use the effective degrees of freedom (EDF), which at a maximum is the number of coefficients to be estimated in the model, minus any constraints. The EDF can take noninteger values and larger values indicate more wiggly terms (see Wood (2017a, Section 6.1.2) for further details). The number of basis functions, K, sets a maximum for the EDF, as a smoother cannot have more than K EDF. When the EDF is well below K, increasing K generally has very little effect on the shape of the function. In general, K should be set large enough to allow for potential variation in the smoother while still staying low enough to keep computation time low (see section “Computational and Statistical Issues When Fitting HGAMs” for more on this). In mgcv, the function mgcv::gam.check can be used to determine if K has been set too low.
Random effects are also “smooths” in this framework. In this case, the penalty matrix is the inverse of the correlation matrix of the basis function coefficients (Kimeldorf & Wahba, 1970; Wood, 2017a). For a simple single-level random effect to account for variation in group means (intercepts) there will be one basis function for each level of the grouping variable. The basis function takes a value of 1 for any observation in that group and 0 for any observation not in the group. The penalty matrix for these terms is a g by g identity matrix, where g is the number of groups. This means that each group-level coefficient will be penalized in proportion to its squared deviation from zero. This is equivalent to how random effects are estimated in standard mixed effect models. The penalty term is proportional to the inverse of the variance of the fixed effect estimated by standard hierarchical model software (Verbyla et al., 1999).
This connection between random effects and splines extends beyond the varying-intercept case. Any single-penalty basis-function representation of a smooth can be transformed so that it can be represented as a combination of a random effect with an associated variance, and possibly one or more fixed effects. See Verbyla et al. (1999) or Wood, Scheipl & Faraway (2013) for a more detailed discussion on the connections between these approaches.
Basis types and penalty matrices
The range of smoothers are useful for contrasting needs and have different associated penalty matrices for their basis function coefficients. In the examples in this paper, we will use three types of smoothers: thin plate regression splines (TPRS), cyclic cubic regression splines (CRS), and random effects.
Thin plate regression splines (Wood, 2003) are a general purpose spline basis which can be used for problems in any number of dimensions, provided one can assume that the amount of smoothing in any of the covariates is the same (so called isotropy or rotational invariance). TPRS, like many splines, use a penalty matrix made up of terms based on the integral of the squared derivatives of basis functions across their range (see Wood (2017a) page 216 for details on this penalty). Models that overfit the data will tend to have large derivatives, so this penalization reduces wiggliness. We will refer to the order of penalized derivatives by m. Typically, TPRS are second-order (m = 2), meaning that the penalty is proportionate to the integral of the squared second derivative. However, TPRS may be of lower order (m = 1, penalizing squared first derivatives), or higher order (m > 2, penalizing squared higher order derivatives). We will see in section “What are Hierarchical GAMs?” how lower-order TPRS smoothers are useful in fitting HGAMs. Example basis functions and penalty matrix S for a m = 2 TPRS with six basis functions for evenly spaced data are shown in Fig. 3.
Cyclic cubic regression splines are another smoother that penalizes the squared second derivative of the smooth across the function. In cyclic CRS the start and end of the smoother are constrained to match in value and first derivative. These are useful for fitting models with cyclic components such as seasonal effects. We will use these smoothers to demonstrate how to fit HGAMs to cyclic data.
Smoothing penalties vs. shrinkage penalties
Penalties can have two effects on how well a model fits: they can penalize how wiggly a given term is (smoothing) and they can penalize the absolute size of the function (shrinkage). The penalty can only affect the components of the smoother that have derivatives (the range space), not the other parts (the null space). For one-dimensional TPRS (when m = 2), this means that there is a linear term (F5) left in the model, even when the penalty is in full force (as λ → ∞), as shown in Fig. 3. (This is also why Fig. 2C shows a linear, rather than flat, fit to the data). The random effects smoother we discussed earlier is an example of a pure shrinkage penalty; it penalizes all deviations away from zero, no matter the pattern of those deviations. This will be useful later in “What are Hierarchical GAMs?,” where we use random effect smoothers as one of the components of a HGAM.
Interactions between smooth terms
It is also possible to create interactions between covariates with different smoothers (or degrees of smoothness) assumed for each covariate, using tensor products. For instance, if one wanted to estimate the interacting effects of temperature and time (in seconds) on some outcome, it would not make sense to use a two-dimensional TPRS smoother, as that would assume that a one degree change in temperature would equate to a 1 s change in time. Instead, a tensor product allows us to create a new set of basis functions that allow for each marginal function (here temperature and time) to have its own marginal smoothness penalty. A different basis can be used in each marginal smooth, as required for the data at hand.
There are two approaches used in mgcv for generating tensor products. The first approach (Wood, 2006a) essentially creates an interaction of each pair of basis functions for each marginal term, and a penalty for each marginal term that penalizes the average wiggliness in that term; in mgcv, these are created using the te() function. The second approach (Wood, Scheipl & Faraway, 2013) separates each penalty into penalized (range space) and unpenalized components (null space; components that don’t have derivatives, such as intercept and linear terms in a one-dimensional cubic spline). This approach creates new basis functions and penalties for all pair-wise combinations of penalized and unpenalized components between all pairs of marginal bases; in mgcv, these are created using the t2() function. The advantage of the first method is that it requires fewer smoothing parameters, so is faster to estimate in most cases. The advantage of the second method is that the tensor products created this way only have a single penalty associated with each marginal basis (unlike the te() approach, where each penalty applies to all basis functions), so it can be fitted using standard mixed effect software such as lme4 (Bates et al., 2015).
Comparison to hierarchical linear models
Hierarchical generalized linear models (Gelman, 2006; HGLMs; also referred to as generalized linear mixed effect models, multilevel models, etc.; e.g., Bolker et al., 2009) are an extension of regression modeling that allows the inclusion of terms in the model that account for structure in the data—the structure is usually of the form of a nesting of the observations. For example, in an empirical study, individuals may be nested within sample sites, sites are nested within forests, and forests within provinces. The depth of the nesting is limited by the fitting procedure and number of parameters to estimate.
Hierarchical generalized linear models are a highly flexible way to think about grouping in ecological data; the groupings used in models often refer to the spatial or temporal scale of the data (McMahon & Diez, 2007) though can be based on any useful grouping.
We would like to be able to think about the groupings in our data in a similar way, even when the covariates in our model are related to the response in a smooth way. The next section investigates the extension of the smoothers we showed above to the case where observations are grouped and we model group-level smoothers.
What are Hierarchical Gams?
What do we mean by hierarchical smoothers?
In this section, we will describe how to model intergroup variability using smooth curves and how to fit these models using mgcv. All models were fitted using mgcv version 1.8–26 (Wood, 2011). Model structure is key in this framework, so we start with three model choices:
Should each group have its own smoother, or will a common smoother suffice?
Do all of the group-specific smoothers have the same wiggliness, or should each group have its own smoothing parameter?
Will the smoothers for each group have a similar shape to one another—a shared global smoother?
These three choices result in five possible models (Fig. 4):
A single common smoother for all observations; We will refer to this as model G, as it only has a Global smoother.
A global smoother plus group-level smoothers that have the same wiggliness. We will refer to this as model GS (for Global smoother with individual effects that have a Shared penalty).
A global smoother plus group-level smoothers with differing wiggliness. We will refer to this as model GI (for Global smoother with individual effects that have Individual penalties).
Group-specific smoothers without a global smoother, but with all smoothers having the same wiggliness. We will refer to this as model S.
Group-specific smoothers with different wiggliness. We will refer to this as model I.
It is important to note that “similar wiggliness” and “similar shape” are two distinct concepts; functions can have very similar wiggliness but very different shapes. Wiggliness measures how quickly a function changes across its range, and it is easy to construct two functions that differ in shape but have the same wiggliness. For this paper, we consider two functions to have similar shape if the average squared distance between the functions is small (assuming the functions have been scaled to have a mean value of zero across their ranges). This definition is somewhat restricted; for instance, a cyclic function would not be considered to have the same shape as a phase-shifted version of the same function, nor would two normal distributions with the same mean but different standard deviations. The benefit of this definition of shape, however, is that it is straightforward to translate into penalties akin to those described in the section “A Review of Generalized Additive Models.” Figure 4, model S illustrates the case where models have different shapes. Similarly, two curves could have very similar overall shape, but differ in their wiggliness. For instance, one function could be equal to another plus a high-frequency oscillation term. Figure 4, model GI illustrates this.
We will discuss the trade-offs between different models and guidelines about when each of these models is appropriate in the section “Computational and statistical issues when fitting HGAMs”. The remainder of this section will focus on how to specify each of these five models using mgcv.
Coding hierarchical GAMs in R
Each of the models in Fig. 4 can be coded straightforwardly in mgcv. We will use two example datasets to demonstrate how to code these models (see the Supplemental Code to reproduce these examples):
The CO2 dataset, available in R via the datasets package. This data is from an experimental study by Potvin, Lechowicz & Tardif (1990) of CO2 uptake in grasses under varying concentrations of CO2, measuring how concentration-uptake functions varied between plants from two locations (Mississippi and Quebec) and two temperature treatments (chilled and warm). A total of 12 plants were used and CO2 uptake measured at seven CO2 concentrations for each plant (Fig. 5A). Here, we will focus on how to use HGAMs to estimate interplant variation in functional responses. This data set has been modified from the default version available with R, to recode the Plant variable as an unordered factor Plant_uo1.
Data generated from a hypothetical study of bird movement along a migration corridor, sampled throughout the year (see Supplemental Code). This dataset consists of simulated sample records of numbers of observed locations of 100 tagged individuals each from six species of bird, at 10 locations along a latitudinal gradient, with one observation taken every 4 weeks. Counts were simulated randomly for each species in each location and week by creating a species-specific migration curve that gave the probability of finding an individual of a given species in a given location, then simulated the distribution of individuals across sites using a multinomial distribution, and subsampling that using a binomial distribution to simulate observation error (i.e., not every bird present at a location would be detected). The data set (bird_move) consists of the variables count, latitude, week, and species (Fig. 5B). This example allows us to demonstrate how to fit these models with interactions and with non-normal (count) data. The true model used to generate this data was model GS: a single global function plus species-specific deviations around that global function.
Throughout the examples we use REML to estimate model coefficients and smoothing parameters. We strongly recommend using either REML or marginal likelihood (ML) rather than the default generalized cross-validation criteria when fitting GAMs, for the reasons outlined in Wood (2011). In each case some data processing and manipulation has been done to obtain the graphics and results below. See Supplemental Code for details on data processing steps. To illustrate plots, we will be using the draw() function from the gratia package. This package was developed by one of the authors (Simpson, 2018) as a set of tools to extend plotting and analysis of mgcv models. While mgcv has plotting capabilities (through plot() methods), gratia expands these by creating ggplot2 objects (Wickham, 2016) that can be more easily extended and modified.
A single common (global) smoother for all observations (Model G)
We start with the simplest model from the framework and include many details here to ensure that readers are comfortable with the terminology and R functions.
For our CO2 data set, we will model loge(uptake) as a function of two smoothers: a TPRS of loge-concentration, and a random effect for Plant_uo to model plant-specific intercepts. Mathematically: where is the random effect for plant and εi is a Gaussian error term. Here, we assume that loge(uptakei) is normally distributed.
In R we can write our model as:
CO2_modG <- gam(log(uptake) ∼ s(log(conc), k=5, bs="tp") + s(Plant_uo, k=12, bs="re"), data=CO2, method="REML", family="gaussian")
This is a common GAM structure, with a single smooth term for each variable. Specifying the model is similar to specifying a GLM in R via glm(), with the addition of s() terms to include one-dimensional or isotropic multidimensional smoothers. The first argument to s() are the terms to be smoothed, the type of smoother to be used for the term is specified by the bs argument, and the maximum number of basis functions is specified by k. There are different defaults in mgcv for K, depending on the type of smoother chosen; here we use a TPRS smoother (bs="tp") for the concentration smoother, and set k=5 as there are only seven separate values of concentration measured, so the default k=10 (for TPRS) would be too high; further, setting k=5 saves on computational time (see section “Computational and Statistical Issues When Fitting HGAMs”). The random effect smoother (bs="re") that we used for the Plant_uo factor always has a k value equal to the number of levels in the grouping variable (here, 12). We specified k=12 just to make this connection apparent.
Figure 6 Illustrates the output of gratia's draw() function for CO2_modG: the panel labelled s(log(conc)) shows the estimated smoother for concentration, and the panel labelled Plant_uo shows a quantile–quantile plot of the estimated random effects vs. Gaussian quantiles, which can be used to check our model.
Looking at the effects by term is useful, but we are often interested in fitted values or predictions from our models. Using the built in prediction functions with mgcv, we can estimate what the fitted function (and uncertainty around it) should look like for each level, as shown in Fig. 7 (see Supplemental Code for more details on how to generate these predictions).
Examining these plots, we see that while functional responses among plants are similar, some patterns are not captured by this model. For instance, for plant Qc2 the model clearly underestimates CO2 uptake. A model including individual differences in functional responses may better explain variation.
For our bird example, we model the count of birds as a function of location and time, including their interaction. For this we structure the model as: where we assume that Counti ∼ Poisson. For the smooth term, f, we employ a tensor product of latitude and week, using a TPRS for the marginal latitude effect, and a cyclic CRS for the marginal week effect to account for the cyclic nature of weekly effects (we expect week 1 and week 52 to have very similar values)2, both splines had basis complexity (k) of 10.
bird_modG <- gam(count ∼ te(week, latitude, bs=c("cc", "tp"), k=c(10, 10)), data=bird_move, method="REML", family="poisson", knots=list(week=c(0, 52)))
Figure 8 shows the default draw(bird_modG) plot for the week-by-latitude smoother. It shows birds starting at low latitudes in the winter then migrating to high latitudes from the 10th to 20th week, staying there for 15–20 weeks, then migrating back. However, the plot also indicates a large amount of variability in the timing of migration. The source of this variability is apparent when we look at the timing of migration of each species (cf. Fig. 5B).
All six species in Fig. 5B show relatively precise migration patterns, but they differ in the timing of when they leave their winter grounds and the amount of time they spend at their summer grounds. Averaging over all of this variation results in a relatively imprecise (diffuse) estimate of migration timing (Fig. 8), and viewing species-specific plots of observed vs. predicted values (Fig. 9), it is apparent that the model fits some of the species better than others. This model could potentially be improved by adding intergroup variation in migration timing. The rest of this section will focus on how to model this type of variation.
A single common smoother plus group-level smoothers that have the same wiggliness (model GS)
Model GS is a close analogue to a GLMM with varying slopes: all groups have similar functional responses, but intergroup variation in responses is allowed. This approach works by allowing each grouping level to have its own functional response, but penalizing functions that are too far from the average.
This can be coded in mgcv by explicitly specifying one term for the global smoother (as in model G above) then adding a second smooth term specifying the group-level smooth terms, using a penalty term that tends to draw these group-level smoothers toward zero. mgcv provides an explicit basis type to do this, the factor-smoother interaction or "fs" basis (see ?mgcv::factor.smooth.interaction for details). This smoother creates a copy of each set of basis functions for each level of the grouping variable, but only estimates one smoothing parameter for all groups. To ensure that all parts of the smoother can be shrunk toward zero effect, each component of the penalty null space is given its own penalty3.
We modify the previous CO2 model to incorporate group-level smoothers as follows: where fPlant_uoi(loge(conci)) is the smoother for concentration for the given plant. In R we then have:
CO2_modGS <- gam(log(uptake) ∼ s(log(conc), k=5, m=2) + s(log(conc), Plant_uo, k=5, bs="fs", m=2), data=CO2, method="REML")
Figure 10 shows the fitted smoothers for CO2_modGS. The plots of group-specific smoothers indicate that plants differ not only in average log-uptake (which would correspond to each plant having a straight line at different levels for the group-level smoother), but differ slightly in the shape of their functional responses. Figure 11 shows how the global and group-specific smoothers combine to predict uptake rates for individual plants. We see that, unlike in the single global smoother case above, none of the curves deviate from the data systematically.
The factor-smoother interaction-based approach mentioned above does not work for higher-dimensional tensor product smoothers (fs() does still work for higher dimensional isotropic smoothers). Instead, the group-specific term can be specified with a tensor product of the continuous smoothers and a random effect for the grouping parameter4. e.g.:
y ∼ te(x1, x2, bs="tp", m=2) + t2(x1, x2, fac, bs=c("tp","tp","re"), m=2, full=TRUE)
We illustrate this approach below on the bird migration data.
bird_modGS <- gam(count ∼ te(week, latitude, bs=c("cc", "tp"), k=c(10, 10), m=2) + t2(week, latitude, species, bs=c("cc", "tp", "re"), k=c(10, 10, 6), m=2, full=TRUE), data=bird_move, method="REML", family="poisson", knots=list(week=c(0, 52)))
Model GS is able to effectively capture the observed patterns of interspecific variation in migration behavior (Fig. 12A). It shows a much tighter fit between observed and predicted values, as well as less evidence of over-dispersion in some species compared to model G (Fig. 12B).
A single common smoother plus group-level smoothers with differing wiggliness (Model GI)
This model class is very similar to model GS, but we now allow each group-specific smoother to have its own smoothing parameter and hence its own level of wiggliness. This increases the computational cost of the model (as there are more smoothing parameters to estimate), and means that the only information shared between groups is through the global smoother, the common error term, and through the random effect for group-level intercepts (if used). This is useful if different groups differ substantially in how wiggly they are.
Fitting a separate smoother (with its own penalties) can be done in mgcv by using the by argument in the s() and te() (and related) functions. Therefore, we can code the formula for this model as:
y ∼ s(x, bs="tp") + s(x, by=fac, m=1, bs="tp") + s(fac, bs="re")
Note two major differences here from how model GS was specified:
We explicitly include a random effect for the intercept (the bs="re" term), as group-specific intercepts are not incorporated into factor by variable smoothers (as would be the case with a factor smoother or a tensor product random effect).
We specify m=1 instead of m=2 for the group-level smoothers, which means the marginal TPRS basis for this term will penalize the squared first derivative of the function, rather than the second derivative. This, also, reduces colinearity between the global smoother and the group-specific terms which occasionally leads to high uncertainty around the global smoother (see section “Computational and Statistical Issues When Fitting HGAMs” for more details). TPRS with m=1 have a more restricted null space than m=2 smoothers, so should not be as collinear with the global smoother (Wieling et al., 2016; Baayen et al., 2018). We have observed that this is much more of an issue when fitting model GI compared to model GS.
We modify the CO2 model to follow this approach like so:
CO2_modGI <- gam(log(uptake) ∼ s(log(conc), k=5, m=2, bs="tp") + s(log(conc), by=Plant_uo, k=5, m=1, bs="tp") + s(Plant_uo, bs="re", k=12), data=CO2, method="REML")
Figure 13 shows a subsample of the group-specific smoothers from this model. It is apparent from this that some groups (e.g., Qc1) have very similar shapes to the global smoother (differing only in intercept), others do differ from the global trend, with higher uptake at low concentrations and lower uptake at higher concentrations (e.g., Mc1, Qn1), or the reverse pattern (e.g., Mn1).
Using model GI with higher-dimensional data is also straightforward; by terms work just as well in tensor-product smoothers as they do with isotropic smoothers. We can see this with our bird model:
bird_modGI <- gam(count ∼ species + te(week, latitude, bs=c("cc", "tp"), k=c(10, 10), m=2) + te(week, latitude, by=species, bs= c("cc", "tp"), k=c(10, 10), m=1), data=bird_move, method="REML", family="poisson", knots=list(week=c(0, 52)))
As above, we have set (m=1) for the latitude marginal effect to avoid issues of collinearity between the global and group-level smoother. Note that switching m=1 to m=2 does not have any effect on the marginal basis for week, where we are using a cyclic smoother instead of a TPRS.
The fitted model for bird_modGI is visually indistinguishable from bird_modGS (Fig. 12) so we do not illustrate it here.
Models without global smoothers (models S and I)
We can modify the above models to exclude the global term (which is generally faster; see section “Computational and Statistical Issues When Fitting HGAMs”). When we do not model the global term, we are allowing each group to be differently shaped without restriction. Though there may be some similarities in the shape of the functions, these models’ underlying assumption is that group-level smooth terms do not share or deviate from a common form.
Model S (shared smoothers) is model GS without the global smoother term; this type of model takes the form: y∼s(x, fac, bs="fs") or y∼t2(x1, x2, fac, bs=c("tp", "tp", "re") in mgcv. This model assumes all groups have the same smoothness, but that the individual shapes of the smooth terms are not related. Here, we do not plot these models; the model plots are very similar to the plots for model GS. This will not always be the case. If in a study there are very few data points in each grouping level (relative to the strength of the functional relationship of interest), estimates from model S will typically be much more variable than from model GS; there is no way for the model to share information on function shape between grouping levels without the global smoother. See section “Computational and Statistical Issues When Fitting HGAMs” on computational issues for more on how to choose between different models.
CO2_modS <- gam(log(uptake) ∼ s(log(conc), Plant_uo, k=5, bs="fs", m=2), data=CO2, method="REML") bird_modS <- gam(count ∼ t2(week, latitude, species, bs=c("cc", "tp", "re"), k=c(10, 10, 6), m=2, full=TRUE), data=bird_move, method="REML", family="poisson", knots=list(week=c(0, 52)))
Model I is model GI without the first term: y∼fac+s(x, by=fac) or y∼fac+te(x1,x2, by=fac) (as above, plots are very similar to model GI).
CO2_modI <- gam(log(uptake) ∼ s(log(conc), by=Plant_uo, k=5, bs="tp", m=2) + s(Plant_uo, bs="re", k=12), data=CO2, method="REML") bird_modI <- gam(count ∼ species + te(week, latitude, by=species, bs=c("cc", "tp"), k=c(10, 10), m=2), data=bird_move, method="REML", family="poisson", knots=list(week=c(0, 52)))
Comparing different HGAM specifications
These models can be compared using standard model comparison tools. Model GS and model GI will generally be nested in model G (depending on how each model is specified) so comparisons using generalized likelihood ratio tests (GLRTs) may be used to test if group-level smoothers are necessary (if fit using method="ML"). However, we do not currently recommend this method. There is not sufficient theory on how accurate parametric p-values are for comparing these models; there is uncertainty about what degrees of freedom to assign to models with varying smoothness, and slightly different model specifications may not result in nested models (See Wood (2017a) Section 6.12.4 and ?mgcv::anova.gam for more discussion on using GLRTs to compare GAMs).
Comparing models based on AIC is a more robust approach to comparing the different model structures. There is well-developed theory of how to include effects of penalization and smoothing parameter uncertainty when estimating the model complexity penalty for AIC (Wood, Pya & Säfken, 2016). We demonstrate this approach in Table 1. Using AIC, there is strong support for including among-group functional variability for both the CO2 dataset and the bird_move dataset (compare models G vs. all other models). For the CO2 dataset (Table 1A), there is relatively strong evidence that there is more intergroup variability in smoothness than model GS allows, and weaker evidence that model S or I (separate smoothers for all plants) show the best fit.
|A. CO2 models|
|B. bird_move models|
For the bird_move dataset (Table 1B), model GS (global smoother plus group-level smoothers with a shared penalty) gives the best fit for all models including a global smooth (which is good as we simulated the data from a model with this structure!). However, model S (without a global term) still fits this data better than model GS based on AIC. This highlights an issue with AIC for selecting between models with and without a global smooth: as it is possible to fully recreate the global term by just allowing each group-level smoother to have a similar shape to one another (i.e., the global term is totally concurve with the group-level smoothers; see section “Computational and Statistical Issues When Fitting HGAMs”) model selection criteria such as AIC may indicate that the extra parameters required to fit the global smoother are unnecessary5.
Given this issue with selecting global terms, we strongly recommend not selecting models based purely on AIC. Instead, model selection should be based on expert subject knowledge about the system, computational time, and most importantly, the inferential goals of the study. Table 1A indicates that models S and I (which do not have a global function) fit the CO2 data better than models with a global function, and that model S fits the bird_move data better than model GS. However, it is the shape of the global function that we are actually interested in here, as models S and I cannot be used to predict the concentration-uptake relationship for plants that are not part of the training set, or the average migration path for birds. The same consideration holds when choosing between model GS and GI: while model GI fits the CO2 data better than model GS (as measured by AIC), model GS can be used to simulate functional variation for unobserved group levels, whereas this is not possible within the framework of model GI. The next section works through two examples to show how to choose between different models, and section “Computational and Statistical Issues When Fitting HGAMs” discusses these and other model fitting issues in more depth.
It also is important to recognize that AIC, like any function of the data, is a random variable and should be expected to have some sampling error (Forster & Sober, 2011). In cases when the goal is to select the model that has the best predictive ability, we recommend holding some fraction of the data out prior to the analysis and comparing how well different models fit that data, or using k-fold cross validation as a more accurate guide to how well a given model may predict out of sample. Predictive accuracy may also be substantially improved by averaging over multiple models (Dormann et al., 2018).
We now demonstrate two worked examples on one data set to highlight how to use HGAMs in practice, and to illustrate how to fit, test, and visualize each model. We will demonstrate how to use these models to fit community data, to show when using a global trend may or may not be justified, and to illustrate how to use these models to fit seasonal time series.
For these examples, data are from a long-term study in seasonal dynamics of zooplankton, collected by the Richard Lathrop. The data were collected from a chain of lakes in Wisconsin (Mendota, Monona, Kegnonsa, and Waubesa) approximately bi-weekly from 1976 to 1994. They consist of samples of the zooplankton communities, taken from the deepest point of each lake via vertical tow. The data are provided by the Wisconsin Department of Natural Resources and their collection and processing are fully described in Lathrop (2000).
Zooplankton in temperate lakes often undergo seasonal cycles, where the abundance of each species fluctuates up and down across the course of the year, with each species typically showing a distinct pattern of seasonal cycles. The inferential aims of these examples are to (i) estimate variability in seasonality among species in the community in a single lake (Mendota), and (ii) estimate among-lake variability for the most abundant taxon in the sample (Daphnia mendotae) across the four lakes. To enable evaluation of out-of-sample performance, we split the data into testing and training sets. As there are multiple years of data, we used data from the even years to fit (train) models, and the odd years to test the fit.
Each record consists of counts of a given zooplankton taxon taken from a subsample from a single vertical net tow, which was then scaled to account for the relative volume of subsample vs. the whole net sample and the area of the net tow, giving population density per m2. Values are rounded to the nearest 1,000. Observed densities span four orders of magnitude. We modelled density using a Gamma distribution with a log-link. For any net tow sample where a given taxon was not observed, we set that taxon’s density to 1,000 (the minimum possible sample size)6. To evaluate how well each model fits new data (not used to fit the model), we calculated the total deviance of the out-of-sample data that we had previously held out. The deviance is equal to two times the sum of the difference between the log-likelihood of the out-of-sample data (as predicted by each model) and a saturated model that has one predictor for each data point, all multiplied by the scale parameter for the family of interest. It can be interpreted similarly to the residual sum of squares for a simple linear regression (Wood, 2017a, p. 109).
First, we demonstrate how to model community-level variability in seasonality, by regressing scaled density on day of year with species-specific curves. As we are not interested in average seasonal dynamics, we focus on models S and I (if we wanted to estimate the seasonal dynamics for rarer species, adding a global smooth term might be useful, so we could borrow information from the more common species). As the data are seasonal, we use cyclic smoothers as the basis for seasonal dynamics. Therefore, we need to specify start and end points for our cycles using the knots argument to gam(), as well as specify this smoother type as a factor-smooth interaction term using the xt argument (the xt argument is how any extra information that a smoother might need is supplied; see ?mgcv::s for more information). Note that we also include a random effect smoother for both taxon and taxon:year_f, where year_f is year transformed into a factor variable. This deals with the fact that average zooplankton densities can show large year-to-year variation. The argument drop.unused.levels=FALSE is also included so the gam function does not drop the year factor levels corresponding to those in the held-out test data set.
zoo_comm_modS <- gam(density_adj ∼ s(taxon, year_f, bs="re") + s(day, taxon, bs="fs", k=10, xt=list(bs="cc")), data=zoo_train, knots=list(day=c(0, 365)), family=Gamma(link="log"), method="REML", drop.unused.levels=FALSE)
# Note that s(taxon, bs="re") has to be explicitly included here, as the # day by taxon smoother does not include an intercept zoo_comm_modI <- gam(density_adj ∼ s(day, by=taxon, k=10, bs="cc") + s(taxon, bs="re") + s(taxon, year_f, bs="re"), data=zoo_train, knots=list(day=c(0, 365)), family=Gamma(link="log"), method="REML", drop.unused.levels=FALSE)
At this stage of the analysis (prior to model comparisons), it is useful to determine if any of the fitted models adequately describe patterns in the data (i.e., goodness of fit testing). mgcv’s gam.check() facilitates this model-checking. This function creates a set of standard diagnostic plots: a QQ plot of the deviance residuals (see Wood (2017a)) compared to their theoretical expectation for the chosen family, a plot of response vs. fitted values, a histogram of residuals, and a plot of residuals vs. fitted values. It also conducts a test for each smooth term to determine if the number of degrees of freedom (k) for each smooth is adequate (see ?mgcv::gam.check for details on how that test works). The code for checking model S and I for the community zooplankton model is:
We have plotted QQ plots and fitted-vs. residual plots for model I (fitted vs. response plots are generally less useful for non-normally distributed data as it can be difficult to visually assess if the observed data shows more heteroskedasticity than expected). The results for model S are virtually indistinguishable to the naked eye. We have also used alternate QQ-plotting code from the gratia package (Simpson, 2018), using the qq_plot() function, as this function creates a ggplot2 object that are easier to customize than the base plots from gam.check(). The code for generating these plots is in the Supplemental Material. These plots (Fig. 14) indicate that the Gamma distribution seems to fit the observed data well except at low values, where the deviance residuals are larger than predicted by the theoretical quantiles (Fig. 14A). There also does not seem to be a pattern in the residual vs. fitted values (Fig. 14B), except for a line of residuals at the lowest values, which correspond to all of those observations where a given taxon was absent from the sample.
The k.check() test (Table 2) shows that the default maximum degrees of freedom for the smoothers used in model I are sufficient for all species, as the EDF for all estimated smoothers are well below their maximum possible value (k′), and the p-value for the observed k-index (which measures pattern in the residuals) is not significant.
Each row corresponds to a single model term. The notation for term names uses mgcv syntax. For instance, “s(day):taxonC. sphaericus” refers to the smoother for day for the taxon C. sphaericus.
In this table, each row corresponds to a single smooth term, k′ corresponds to the number of basis functions used for that smoother in the fitted model (smaller than the specified k in the model itself, as some basis functions are automatically dropped to ensure the model is identifiable). The column EDF is the estimated EDF for that smoother, the k-index is a measure of the remaining pattern in the residuals, and the p-value is calculated based on the distribution of the k-index after randomizing the order of the residuals. Note that there is no p-value for the random effects smoothers s(taxon) and s(taxon,year_f) as the p-value is calculated from simulation-based tests for autocorrelation of the residuals. As taxon and year_f are treated as simple random effects with no natural ordering, there is no meaningful way of checking for autocorrelation.
Differences between models S (shared smoothness between taxa) and I (different smoothness for each taxa) seem to be driven by the low seasonality of Leptodiaptomus siciloides relative to the other species, and how this is captured by the more flexible model I (Fig. 15). Still, both models show very similar fits to the training data. This implies that the added complexity of different penalties for each species (model I) is unnecessary here, which is consistent with the fact that model S has a lower AIC (4667) than model I (4677), and that model S is somewhat better at predicting out-of-sample fits for all taxa than model I (Table 3). Both models show significant predictive improvement compared to the intercept-only model for all species except Keratella cochlearis (Table 3). This may be driven by changing timing of the spring bloom for this species between training and out-of-sample years (Fig. 15).
|Taxon||Total deviance of out-of-sample data|
|Intercept only||Model S||Model I|
Deviance values represent the total deviance of model predictions from observations for out-of-sample data. “Intercept only” results are for a null model with only taxon-level random effect intercepts included.
Next, we look at how to fit interlake variability in dynamics for just Daphnia mendotae. Here, we will compare models G, GS, and GI to determine if a single global function is appropriate for all four lakes, or if we can more effectively model variation between lakes with a shared smoother and lake-specific smoothers.
zoo_daph_modG <- gam(density_adj ∼ s(day, bs="cc", k=10) + s(lake, bs="re") + s(lake, year_f, bs="re"), data=daphnia_train, knots=list(day=c(0, 365)), family=Gamma(link="log"), method="REML", drop.unused.levels=FALSE)
zoo_daph_modGS <- gam(density_adj ∼ s(day, bs="cc", k=10) + s(day, lake, k=10, bs="fs", xt=list(bs="cc")) + s(lake, year_f, bs="re"), data=daphnia_train, knots=list(day=c(0, 365)), family=Gamma(link="log"), method="REML", drop.unused.levels=FALSE)
zoo_daph_modGI <- gam(density_adj∼s(day, bs="cc", k=10) +s(lake, bs="re") + s(day, by=lake, k=10, bs="cc") + s(lake, year_f, bs="re"), data=daphnia_train, knots=list(day=c(0, 365)), family=Gamma(link ="log"), method="REML", drop.unused.levels=FALSE)
Diagnostic plots from gam.check() indicate that there are no substantial patterns comparing residuals to fitted values (not shown), and QQ-plots are similar to those from the zooplankton community models; the residuals for all three models closely correspond to the expected (Gamma) distribution, except at small values, where the observed residuals are generally larger than expected (Fig. 16). As with the community data, this is likely an artifact of the assumption we made of assigning zero observations a value of 1,000 (the lowest possible value), imposing an artificial lower bound on the observed counts. There was also some evidence that the largest observed values were smaller than expected given the theoretical distribution, but these fell within the 95% CI for expected deviations from the 1–1 line (Fig. 16).
AIC values indicate that both model GS (1,093.71) and GI (1,085.7) are better fits than model G (1,097.62), with model GI fitting somewhat better than model GS.7 There does not seem to be a large amount of interlake variability (the EDF per lake are low in models GS & GI). Plots for all three models (Fig. 17) show that Mendota, Monona, and Kegonsa lakes are very close to the average and to one another for both models, but Waubesa shows evidence of a more pronounced spring bloom and lower winter abundances.
Model GI is able to predict as well or better than model G or GS for all lakes (Table 4), indicating that allowing for interlake variation in seasonal dynamics improved model prediction. All three models predicted dynamics in Lake Mendota and Lake Menona significantly better than the intercept-only model (Table 4). None of the models did well in terms of predicting Lake Waubesa dynamics out-of-sample compared to a simple model with only a lake-specific intercept and no intra-annual variability, but this was due to the influence of a single large outlier in the out-of-sample data that occurred after the spring bloom, at day 243 (Fig. 17; note that the y-axis is log-scaled). However, baring a more detailed investigation into the cause of this large value, we cannot arbitrarily exclude this outlier from the goodness-of-fit analysis; it may be due either to measurement error or a true high late-season Daphnia density that our model was not able to predict.
|Lake||Total deviance of out-of-sample data|
|Intercept only||Model G||Model GS||Model GI|
Deviance values represent the total deviance of model predictions from observations for out-of-sample data. “Intercept only” results are for a null model with only lake-level random effect intercepts included.
Computational and Statistical Issues when Fitting Hgams
Which of the five model formulations (Fig. 4) should you choose for a given data set? There are two major trade-offs to consider. The first is the bias-variance trade-off: more complex models can account for more fluctuations in the data, but also tend to give more variable predictions, and can overfit. The second trade-off is model complexity vs. computational cost: more complex models can include more potential sources of variation and give more information about a given data set, but will generally take more time and computational resources to fit and debug. We discuss both of these trade-offs in this section. We also discuss how to extend the HGAM framework to fit more complex models.
The bias-variance trade-off is a fundamental concept in statistics. When trying to estimate any relationship (in the case of GAMs, a smooth relationship between predictors and data) bias measures how far, on average, an estimate is from the true value. The variance of an estimator corresponds to how much that estimator would fluctuate if applied to multiple different samples of the same size taken from the same population. These two properties tend to be traded off when fitting models. For instance, rather than estimating a population mean from data, we could simply use a predetermined fixed value regardless of the observed data8. This estimate would have no variance (as it is always the same regardless of what the data look like) but would have high bias unless the true population mean happened to equal the fixed value we chose. Penalization is useful because using a penalty term slightly increases model bias, but can substantially decrease variance (Efron & Morris, 1977).
In GAMs, the bias-variance trade-off is managed by the terms of the penalty matrix, and equivalently random effect variances in HGLMs. Larger penalties correspond to lower variance, as the estimated function is unable to wiggle a great deal, but also correspond to higher bias unless the true function is close to the null space for a given smoother (e.g., a straight line for TPRS with second derivative penalties, or zero for a random effect). The computational machinery used by mgcv to fit smooth terms is designed to find penalty terms that best trade-off bias for variance to find a smoother that can effectively predict new data.
The bias-variance trade-off comes into play with HGAMs when choosing whether to fit separate penalties for each group level or assign a common penalty for all group levels (i.e., deciding between models GS & GI or models S & I). If the functional relationships we are trying to estimate for different group levels actually vary in how wiggly they are, setting the penalty for all group-level smoothers equal (models GS & S) will either lead to overly variable estimates for the least variable group levels, over-smoothed (biased) estimates for the most wiggly terms, or a mixture of these two, depending on the fitting criteria.
We developed a simple numerical experiment to determine whether mgcv’s fitting criteria tend to set estimated smoothness penalties high or low in the presence of among-group variability in smoothness when fitting model GS or S HGAMs. We simulated data from four different groups, with all groups having the same levels of the covariate x, equally spaced across the range from 0 to 2π. For each group, the true function relating x to the response, y, was a cosine wave, but the frequency varied from 0.5 (equal to half a cycle across the range of x) to 4 (corresponding to 4 full cycles across the range). As all four sine waves spanned the whole range from −1 to +1 across the range of x, and as they were all integer or half-integer frequencies, the signal for all groups had the same variance across the range of x, approximately equal to 0.5. Therefore, the true function for all groups had the same strength of signal; all that varied between groups was how rapidly the signal fluctuated. We added normally distributed error to all y-values, with three different noise levels, given by standard deviations of 0.5, 1, and 2. These correspond to signal-to-noise ratios (i.e., variance of the cosine curve divided by variance of the noise) of 2, 0.5, and 0.125. For each noise level we created 25 replicate data sets to illustrate the amount of simulation-to-simulation variation in model fit. We then fit both model S (where all curves were assumed to be equally smooth) and model I (with varying smoothness) to each replicate for each noise level, using REML criteria to estimate penalties.
A sample of the fits for each group for three of the replicates for each model are shown in Fig. 18A, with model S in red and model I in blue. Figure 18B illustrates how well each model fared across the range of replicates at accurately estimating the true smoothness of the highest frequency terms as measured by the squared second derivative of the smooth fit vs. that of the true function, with the distance to the black one-to-one line indicating the degree to which the estimated function for each group over- or under-estimated the smoothness of the true signal. In general, under low noise conditions (Fig. 18, signal-to-noise ratio of 2), model S tended to overfit the smoothest, lowest-frequency, groups, while accurately fitting the highest frequency groups. Under moderate signal-to-noise ratios, model S tended to over-penalize high-frequency groups and under-penalize low frequency groups, and in the lowest signal-to-noise ratio tested (0.125), model S tended to penalize all groups toward very smooth functions (Fig. 18B). Curves estimated by model I, on the other hand, tended to accurately capture the true wiggliness of the function across the whole range of frequencies and noises, except for the lowest-frequency groups, and the highest frequency groups it the presence of high noise; in both cases, model I tended to over-smooth (Fig. 18B).
This implies that assuming equal smoothness will result in underestimating the true smoothness of low-variability terms in cases of high signal-to-noise, and overestimating the true smoothness of high-frequency terms in low signal-to-noise data sets. If this is a potential issue, we recommend fitting both models S and I and using standard model evaluation criteria (e.g., AIC) or out-of-sample predictive accuracy (as in the section “Examples”) to determine if there is evidence for among-group variability in smoothness. However, it may be the case that there are too few data points per group to estimate separate smoothness levels, in which case model GS or model S may still be the better option even in the face of varying smoothness.
The ideal case would be to assume that among-group penalties follow their own distribution (estimated from the data), to allow variation in smoothness while still getting the benefit of pooling information on smoothness between groups. This is currently not implemented in mgcv. It is possible to set up this type of varying penalty model in flexible Bayesian modeling software such as Stan (see below for a discussion of how to fit HGAMs using these tools), where intergroup variation in smoothing penalties could be modelled with a hierarchical prior. However, to the best of our knowledge, how to fit this type of model has not been well studied in either the Bayesian or frequentist literature.
It may seem there is also a bias-variance trade-off between choosing to use a single global smoother (model G) or a global smoother plus group-level terms (models GS and GI). In model G, all the data is used to estimate a single smooth term, and thus should have lower variance than models GS and GI, but higher bias for any given group in the presence of intergroup functional variability. However, in practice, this trade-off will be handled via penalization; if there are no average differences between functional responses, mgcv will penalize the group-specific functions toward zero, and thus toward the global model. The choice between using model G vs. models GS and GI should generally be driven by computational costs. Model G is typically much faster to fit than models GS and GI, even in the absence of among-group differences. If there is no need to estimate intergroup variability, model G will typically be more efficient.
A similar issue exists when choosing between models GS and GI and models S and I. If all group levels have very different functional shapes, the global term will get penalized toward zero in models GS and GI, so they will reduce to models S and I. The choice to include a global term should be made based on scientific considerations (is the global term of interest?) and computational considerations.
The more flexible a model is, the larger an effective parameter space any fitting software has to search. It can be surprisingly easy to use massive computational resources trying to fit models to even small datasets. While we typically want to select models based on their fit and our inferential goals, computing resources can often act as an effective upper bound on model complexity. For a given data set, assuming a fixed family and link function, the time taken to estimate an HGAM will depend (roughly) on four factors: (i) the number of coefficients to be estimated (and thus the number of basis functions chosen), (ii) the number of smoothing parameters to be estimated, (iii) whether the model needs to estimate both a global smoother and group-level smoothers, and (iv) the algorithm and fitting criteria used to estimate parameters.
The most straightforward factor that will affect the amount of computational resources is the number of parameters in the model. Adding group-level smoothers (moving from model G to the other models) means that there will be more regression parameters to estimate. For a dataset with g different groups and n data points, fitting a model with just a global smoother, y∼s(x,k=k) will require k coefficients, and takes operations to evaluate. Fitting the same data using a group-level smoother (model S, y∼s(x,fac,bs="fs",k=k)) will require operations to evaluate. In effect, adding a group-level smoother will increase computational cost by an order of the number of groups squared. The effect of this is visible in the examples we fit in the section “What are Hierarchical GAMs?.” Table 5 compares the relative time it takes to compute model G vs. the other models.
|Model||Relative time||Number of terms|
|A. CO2 data|
|B. Bird movement data|
All times are scaled relative to the length of time model G takes to fit to that data set. The number of coefficients measures the total number of model parameters (including intercepts). The number of smoothers is the total number of unique penalty values estimated by the model.
One way to deal with this issue would be to reduce the number of basis functions used when fitting group-level smoothers when the number of groups is large, limiting the flexibility of the model. It can also make sense to use more computationally-efficient basis functions when fitting large data sets, such as P-splines (Wood, 2017b) or cubic splines. TPRSs entail greater computational costs (Wood, 2017a).
Including a global smoother (models GS and GI compared to models S and I) will not generally substantially affect the number of coefficients that need to be estimated (Table 5). Adding a global term will add at most k extra terms. It can be substantially less than that, as mgcv drops basis functions from co-linear smoothers to ensure that the model matrix is full rank.
Adding additional smoothing parameters (moving from model GS to GI, or moving from model S to I) is more costly than increasing the number of coefficients to estimate, as estimating smoothing parameters is computationally intensive (Wood, 2011). This means that models GS and S will generally be substantially faster than GI and I when the number of groups is large, as models GI and I fit a separate set of penalties for each group level. The effect of this is visible in comparing the time it takes to fit model GS to model GI (which has a smoother for each group) or models S and I for the CO2 example data (Table 5). Note that this will not hold in all cases. For instance, model GI and I take less time to fit the bird movement data than models GS or S do (Table 5B).
Alternative formulations: bam(), gamm(), and gamm4()
When fitting models with large numbers of groups, it is often possible to speed up computation substantially by using one of the alternative fitting routines available through mgcv.
The first option is the function bam(), which requires the fewest changes to existing code written using the gam() function. bam() is designed to improve performance when fitting large data sets via two mechanisms. First, it saves on memory needed to compute a given model by using a random subset of the data to calculate the basis functions. It then blocks the data and updates model fit within each block (Wood, Goude & Shaw, 2015). While this is primarily designed to reduce memory usage, it can also substantially reduce computation time. Second, when using bam()’s default method="fREML" (“Fast REML”) method, you can use the discrete=TRUE option: this first bins continuous covariates into a smaller number of discrete values before estimating the model, substantially reducing the amount of computation needed (Wood et al., 2017; see ?mgcv::bam for more details). Setting up the five model types (Fig. 4) in bam() uses the same code as we have previously covered; the only difference is that you use the bam() instead of gam() function, and have the additional option of discretizing your covariates.
bam() has a larger computational overhead than gam(); for small numbers of groups it can be slower than gam() (Fig. 19). As the number of groups increases, computational time for bam() increases more slowly than for gam(); in our simulation tests, when the number of groups is greater than 16, bam() can be upward of an order of magnitude faster (Fig. 19). Note that bam() can be somewhat less computationally stable when estimating these models (i.e., less likely to converge). While base bam() (not fit using discrete=TRUE) is slower than the other approaches shown in Fig. 19, that does not imply that bam() is a worse choice in general; it is designed to avoid memory limitations when working with big data rather than explicitly speeding up model fitting. The bam() functions would likely show much better relative performance when the number of individuals per group were large (in the hundreds to thousands, compared to the 20 individuals per group used in Fig. 19).
The second option is to fit models using one of two dedicated mixed effect model estimation packages, nlme and lme4. The mgcv package includes the function gamm(), which uses the nlme package to estimate the GAM, automatically handling the transformation of smooth terms into random effects (and back into basis function representations for plotting and other statistical analyses). The gamm4() function, in the separate gamm4 package, uses lme4 in a similar way. Using gamm() or gamm4() to fit models rather than gam() can substantially speed up computation when the number of groups is large, as both nlme and lme4 take advantage of the sparse structure of the random effects, where most basis functions will be zero for most groups (i.e., any group-specific basis function will only take a nonzero value for observations in that group level). As with bam(), gamm(), and gamm4() are generally slower than gam() for fitting HGAMs when the number of group levels is small (in our simulations, <8 group levels), however they do show substantial speed improvements even with a moderate number of groups, and were as fast as or faster to calculate than bam() for all numbers of grouping levels we tested (Fig. 19)9.
Both gamm() and gamm4() require a few changes to model code. First, there are a few limitations on how you are able to specify the different model types (Fig. 4) in both frameworks. Factor-smoother interaction (bs="fs") basis setup works in both gamm() and gamm4(). However, as the nlme package does not support crossed random effects, it is not possible to have two factor-smoother interaction terms for the same grouping variable in gamm() models (e.g., y∼s(x1, grp, bs="fs")+s(x2, grp, bs="fs"). These type of crossed random effects are allowed in gamm4. The use of te() terms are not possible in gamm4, due to issues with how random effects are specified in the lme4 package, making it impossible to code models where multiple penalties apply to a single basis function. Instead, for multidimensional group-level smoothers, the alternate function t2() needs to be used to generate these terms, as it creates tensor products with only a single penalty for each basis function (see ?mgcv::t2 for details on these smoothers, and Wood, Scheipl & Faraway (2013) for the theoretical basis behind this type of tensor product). For instance, model GS for the bird movement data we discussed in the section “What are Hierarchical GAMs?” would need to be coded as:
bird_modS <- gamm4(count ∼ t2(week, latitude, species, k=c(10, 10, 6), m=2, bs=c("cc", "tp", "re")), data=bird_move, family="poisson")
These packages also do not support the same range of families for the dependent variable; gamm() only supports non-Gaussian families by using a fitting method called penalized quasi-likelihood, that is, slower and not as numerically stable as the methods used in gam(), bam(), and gamm4(). Non-Gaussian families are well supported by lme4 (and thus gamm4), but can only fit them using ML rather than REML, so may tend to over-smooth relative to gam() using REML estimation. Further, neither gamm() nor gamm4() supports several of the extended families available through mgcv, such as zero-inflated, negative binomial, or ordered categorical and multinomial distributions.
Estimation issues when fitting both global and group-level smoothers
When fitting models with separate global and group-level smoothers (models GS and GI), one issue to be aware of is concurvity between the global smoother and group-level terms. Concurvity measures how well one smooth term can be approximated by some combination of the other smooth terms in the model (see ?mgcv::concurvity for details). For models GS and GI, the global term is either entirely or almost entirely10 concurved with the group-level smoothers. This is because, in the absence of the global smooth term, it would be possible to recreate that average effect by shifting all the group-level smoothers so they were centered around the global mean.
In practical terms, this has the consequence of increasing uncertainty around the global mean relative to a model with only a global smoother. In some cases, it can result in the estimated global smoother being close to flat, even in simulated examples with a known strong global effect. This concurvity issue may also increase the time it takes to fit these models (e.g., compare the time it takes to fit models GI and I in Table 5). These models can still be estimated because of penalty terms; all of the methods we have discussed for fitting model GS (factor-smoother terms or random effect tensor products) automatically create a penalty for the null space of the group-level terms, so that only the global term has its own unpenalized null space. Both the REML and ML criteria work to balance penalties between nested smooth terms (this is why nested random effects can be fitted). We have observed that mgcv still occasionally finds solutions with simulated data where the global term is over-smoothed.
To avoid this issue, we recommend both careful choice of basis and relative degrees of freedom of global and group-level terms. In the examples in section “What are Hierarchical GAMs?,” we used smoothers with an unpenalized null space for the global smoother and ones with no null space for the group-level terms. When using TPRS this can be achieved with splines with a lower order of derivative penalized in the group-level smoothers than the global smoothers, as lower-order TPRS have fewer basis functions in the null space. For example, we used m=2 (penalizing squared second derivatives) for the global smoother, and m=1 (penalizing squared first derivatives) for group-level smoothers in models GS and GI. Another option is to specify the maximum degrees of freedom (k) for the group-level smoother either substantially higher or lower than the global smoother; this is in effect an approximate way to specify a prior belief in the relative smoothness of the global vs. group-level functions. If the group-level term is set to have greater k compared to the global term, this encodes the assumption that the global function should not be very wiggly, but group-level deviations from that smooth might vary from that, and vice versa if k is set lower for group-level terms than for the global smoother.
As noted above, interpreting the shape of global terms and group-wise deviations separately for GS models fit using tensor-product group-level terms is complicated by the fact that mgcv will drop some basis-functions from the group-level terms to prevent perfect concurvity. For tensor-product smoothers, mgcv will generally drop ≤K terms from the group-level smoother, where K is the number of basis functions in the global smoother. The total number of terms dropped will depend on the smoothers used for the global and group-level terms. This means that some groups will have a different range of potential deviations from the global smoother than others. This has the effect of also somewhat altering the shape of the global smooth relative to what it would be based on model G (the average curve through all the data); this will be a larger issue when the number of basis functions in the global smooth and the number of group levels are small. We have tested the effect of this issue on our simulated bird_move data set and did not find that it lead to substantial bias in estimating the shape of the global smoother, relative to the amount of bias inherent in any smooth estimation method11 (Fig. 20). As noted in the section “What are hierarchical GAMs?”, we found that t2() tensor product smoothers with full penalties (full = TRUE in the t2() function) for group-level smoothers showed the best performance at recreating the true global function from our simulated bird_move data set, compared to other possible types of tensor product. Using te() tensor products for the group-level terms lead to the global smoother being heavily smoothed relative to the actual average function, used to simulate the data (Fig. 20). However, more work on when these models accurately reconstruct global effects is still needed.
There is currently no way to disable dropping side constraints for these terms in mgcv. In cases where accurately estimating the global smoother or group-level deviations is essential, we recommend either fitting model G, GS using factor-smooth group-level terms (bs="fs", which can also be used to model multi-dimensional isotropic group-level smoothers), or model GI. Alternatively, there is specialized functional regression software such as the pffr function in the refund package (Scheipl, Gertheiss & Greven, 2016), which does not impose these side constraints; instead the package uses a modified type of tensor-product to ensure that group-level terms sum to zero at each level of the predictor (Scheipl, Gertheiss & Greven, 2016). See below for more information on functional regression.
A brief foray into the land of Bayes
As mentioned in the section “A Review of Generalized Additive Models,” the penalty matrix can be interpreted as the prior precision (inverse prior covariance) matrix for the model parameters β. Intuitively, the basis functions and penalty are an informal prior on how we’d like our model term to behave. REML gives an empirical Bayes estimate of the smooth model (Laird & Ware, 1982), where terms in the null space of the smoother have improper, flat priors (i.e., any value for these terms are considered equally likely). Any terms in the range space are treated as having a multivariate normal prior, and the smoothing parameters are treated as having an improper flat prior (see Wood (2017a), Section 5.8 for more details on this connection). The posterior covariance matrix (Wood, 2006b) for model parameters can be extracted from any fitted gam() or bam() model with vcov(model) (this is conditional on the estimated smoothing parameters unless the option unconditional=TRUE is specified). Given the normal posterior for the estimates of β, we can sample from a multivariate normal with mean β̂ and posterior covariance matrix. Such samples can be used to estimate uncertainty in functions of the predictors. Viewing our GAM as Bayesian is a somewhat unavoidable consequence of the equivalence of random effects and splines—if we think that there is some true smoother that we wish to estimate, we must take a Bayesian view of our random effects (splines) as we do not think that the true smoother changes each time we collect data (Wood, 2017a, Section 5.8). The standard confidence intervals used in mgcv are in fact Bayesian posterior credible intervals, which happen to have good frequentist across-the-function properties (Wood, 2006b; Marra & Wood, 2012). The newest version of mgcv as of this writing (v. 1.8–28) also includes an experimental implementation of integrated nested Laplace approximation to calculate full posterior distributions for GAMs, via the ginla function (Wood, in press).
This also means that HGAMs can be included as components in a more complex fully Bayesian model. The mgcv package includes a function jagam() that can take a specified model formula and automatically convert it into code for the JAGS (or BUGS) Bayesian statistical packages, which can be adapted by the user to their own needs.
Similarly, the brms package (Bürkner, 2017), which can fit complex statistical models using the Bayesian software Stan (Carpenter et al., 2017) allows for the inclusion of mgcv-style smooth terms as part of the model specification. The brms package does not currently support te() tensor products, but does support factor-smooth interactions and t2()-style tensor products, which means all of the models fitted in this paper can be fitted by brms. Finally, the bamlss package (Umlauf, Klein & Zeileis, 2018) can fit complex GAMs using a number of computational backends, including JAGS and BayesX, using mgcv syntax for model specification.
Beyond HGAMs: functional regression
The HGAMs we have discussed are actually a type of functional regression, which is an extension of standard regression models to cases where the outcome variable yi and/or the predictor variables xi for a given outcome are functions, rather than single variables (Ramsay & Silverman, 2005). HGAMs as we have described them are a form of function-on-scalar regression (Ramsay & Silverman, 2005; Reiss, Huang & Mennes, 2010), where we are trying to estimate a smooth function that varies between grouping levels. Here the “scalar” refers to the grouping level, and the function is the smooth term that varies between levels; in contrast, a standard GAM is a type of scalar-on-scalar regression, as the goal is to use a set of single values (scalars) to estimate each (scalar) response.
We have deliberately focused our paper on these simpler classes of functional regression model, and chosen to use the term HGAM rather than functional regression, as we believe that this more clearly connects these models to modeling approaches already familiar to ecologists. Further, we consider the unit of analysis to still be individual observations, as compared to functional regression where the unit of analysis is whole functions. For instance, we are interested in applications such as species distribution modeling, where the presence of a given species may be predicted from a sum of several species-specific functions of different environmental variables.
However, there is an extensive literature dedicated to the estimation of more complex functional regression models for any interested reader (see Morris (2015) and Greven & Scheipl (2017) for a good introduction and overview of more recent work in this field). The refund package (Greven & Scheipl, 2017) uses the statistical machinery of mgcv to fit these models, and should be usable by anyone familiar with mgcv modeling syntax. Functional regression is also a major area of study in Bayesian statistics (Kaufman & Sain, 2010).
Hierarchical GAMs are a powerful tool to model intergroup variability, and we have attempted to illustrate some of the range and possibilities that these models are capable of, how to fit them, and some issues that may arise during model fitting and testing. Specifying these models and techniques for fitting them are active areas statistical research, so this paper should be viewed as a jumping-off point for these models, rather than an end-point; we refer the reader to the rich literature on GAMs (Wood, 2017a) and functional regression (Ramsay & Silverman, 2005; Kaufman & Sain, 2010; Scheipl, Staicu & Greven, 2014) for more on these ideas.