DLNMs: building and visualizing crossbasis functions

This is part of series about distributed lag non-linear models. Please read the first post for an introduction and a disclaimer.

The dlnm package

The dlnm package offers two ways of fitting crossbasis functions: an “internal” and an “external” method. The “external” method involves fitting the crossbasis function outside of a model, using some functions in the dlnm package, then including the results as a predictor in a model such as a generalized linear model (GLM). I’m going to focus entirely on the “internal” method that fits the crossbasis function in the context of a generalied additive model (GAM) to take advantage of the penalization and other stuff the mgcv package offers.

The data

Throughout this series, I’m going to use a subset of data from my postdoc project on Heliconia acuminata. In this subset, 100 plants were tracked over a decade. Every year in February their size was recorded as height and number of shoots, and it was recorded whether or not they flowered. Any dead plants were marked as such. The goal is to determine how drought impacted growth, survival, and flowering probability with a potentially delayed and/or non-linear relationship. To that end, I’ve calculated SPEI, a measure of drought, where more negative numbers represent more severe drought. SPEI is monthly while the demography data is yearly. For every observation of a plant, there is an entire history of SPEI for the past 36 months from that observation.

head(ha)
## # A tibble: 6 x 11
##   plot  ha_id_number  year  size size_next log_size log_size_next  flwr  surv
##   <fct> <fct>        <dbl> <dbl>     <dbl>    <dbl>         <dbl> <dbl> <dbl>
## 1 2107  107           1998    66       112     4.19          4.72     0     1
## 2 2107  107           1999   112       102     4.72          4.62     0     1
## 3 2107  107           2000   102        68     4.62          4.22     0     1
## 4 2107  107           2001    68        96     4.22          4.56     0     1
## 5 2107  107           2002    96       164     4.56          5.10     0     1
## 6 2107  107           2003   164       114     5.10          4.74     0     1
## # … with 74 more variables: spei_history[,1] <dbl>, [,2] <dbl>, [,3] <dbl>,
## #   [,4] <dbl>, [,5] <dbl>, [,6] <dbl>, [,7] <dbl>, [,8] <dbl>, [,9] <dbl>,
## #   [,10] <dbl>, [,11] <dbl>, [,12] <dbl>, [,13] <dbl>, [,14] <dbl>,
## #   [,15] <dbl>, [,16] <dbl>, [,17] <dbl>, [,18] <dbl>, [,19] <dbl>,
## #   [,20] <dbl>, [,21] <dbl>, [,22] <dbl>, [,23] <dbl>, [,24] <dbl>,
## #   [,25] <dbl>, [,26] <dbl>, [,27] <dbl>, [,28] <dbl>, [,29] <dbl>,
## #   [,30] <dbl>, [,31] <dbl>, [,32] <dbl>, [,33] <dbl>, [,34] <dbl>,
## #   [,35] <dbl>, [,36] <dbl>, [,37] <dbl>, L[,1] <int>, [,2] <int>, [,3] <int>,
## #   [,4] <int>, [,5] <int>, [,6] <int>, [,7] <int>, [,8] <int>, [,9] <int>,
## #   [,10] <int>, [,11] <int>, [,12] <int>, [,13] <int>, [,14] <int>,
## #   [,15] <int>, [,16] <int>, [,17] <int>, [,18] <int>, [,19] <int>,
## #   [,20] <int>, [,21] <int>, [,22] <int>, [,23] <int>, [,24] <int>,
## #   [,25] <int>, [,26] <int>, [,27] <int>, [,28] <int>, [,29] <int>,
## #   [,30] <int>, [,31] <int>, [,32] <int>, [,33] <int>, [,34] <int>,
## #   [,35] <int>, [,36] <int>, [,37] <int>
  • plot (factor): A plot ID
  • ha_id_number (factor): A unique plant ID
  • year (numeric): year of census
  • size (numeric): number of shoots x height in cm
  • size_next (numeric): size in the next year
  • log_size (numeric): log transformed size
  • log_size_next (numeric): log transformed size next year
  • flwr (numeric): Did a plant flower? 1 = yes, 0 = no
  • surv (numeric): Did a plant survive? 1 = yes, 0 = no
  • spei_history (c(“matrix”, “array”)): A matrix column of the drought history starting in the current month (spei_history[,1] = February) and going back 24 months (spei_history[,25] = February 2 years ago)
  • L (c(“matrix”, “array”)): A matrix column describing the lag structure of spei_history. Literally just 0:24 for every row.

Fit a DLNM

library(mgcv) #for gam()
library(dlnm) #for the "cb" basis
growth <-
  gam(log_size_next ~ 
        log_size +
        s(spei_history, L, # <- the two dimensions
          bs = "cb", # <- fit as crossbasis
          k = c(3, 24), # <- knots for each dimension
          xt = list(bs = "cr")), # <- what basis to use for each dimension
      family = gaussian(link = "identity"),
      method = "REML",
      data = ha)

Above is a simple DLNM with survival modeled as a function of number of shoots and the crossbasis function of SPEI over the past 36 months. shts is a fixed effect (i.e. not a smooth, but to be fit as a straight line), and the crossbasis is defined in s(spei_history, L, …). spei_history and L are the two dimensions of the crossbasis function, bs = "cb" tells gam() that this is a crossbasis function from the dlnm package (calls dlnm::smooth.construct.cb.smooth.spec behind the scenes). xt = list(bs = "cr") tells it to use a cubic regression spline as the basis for both dimensions of the crossbasis function (but you can also mix and match marginal basis functions by providing a length 2 vector here).

Problem 1: visualizing the results

Unfortunately plot.gam() does not work with these crossbasis functions.

plot.gam(growth)
## Error in plot.gam(growth): No terms to plot - nothing for plot.gam() to do.

The dlnm package provides some functions for visualizing the results of a DLNM, though I don’t like them much.

First you use crosspred() to get predicted values for the DLNM.

pred_dat <- crosspred("spei_history", growth)
## centering value unspecified. Automatically set to 0

Then you plot those with plot.crosspred(). The default is a 3D plot.

plot(pred_dat)

I prefer a heatmap, although the one produced here has some issues.

plot(pred_dat, ptype = "contour", xlab = "SPEI", ylab = "lag(months)")

First obvious problem is the colors. The range is the same for red and blue, despite different number of breaks. Second, the units are not what I’d expect. For a marginal effects plot these should be the size of an average plant in year t+1, all else being equal. This is plotting the size relative to the size at an average value of SPEI, which is a weird thing to think about. That’s because the package was built with epidemiology and relative risk in mind. Here is the plot relative to SPEI = 1.5

pred_dat <- crosspred("spei_history", growth, cen = 1.5)
plot(pred_dat, ptype = "contour", xlab = "SPEI", ylab = "lag(months)")

## Solution (?)

So, I spent a lot of time writing a complicated function, cb_margeff(), to create data for a marginal effects plot. It creates a newdata data frame to be passed to predict() and loops across different matrixes with all columns of spei_history set to average except for one, representing a range of possible SPEI values.

plotdata <- cb_margeff(growth, spei_history, L)
ggplot(plotdata, aes(x = x, y = lag, fill = fitted)) +
  geom_raster() +
  scale_fill_viridis_c("size in year t+1", option = "A") +
  scale_x_continuous("SPEI", expand = c(0,0)) +
  scale_y_continuous("lag (months)", expand = c(0,0))

Yeah, this is looking better.

The interpretation of this type of plot (which I would describe as a marginal effects plot, but correct me if I’m wrong) makes more sense to me. If there was drought (low SPEI) about 8 months prior to the census, that’s bad for growth. Drought 20 months prior is good for growth though.

BUT WAIT

I poked around in plot.gam with debug() and it turns out the reason the plotting doesn’t work is only because the author of dlnm, Gasparrini, didn’t want it to work.

I can change a simple flag inside the growth model, and then it produces something very similar (identical?) to what I have above:

growth$smooth[[1]]$plot.me
## [1] FALSE
growth$smooth[[1]]$plot.me <- TRUE
plot.gam(growth, scheme = 2)

Why is this default plot not available? It’s literally exactly what I wanted, and I’m pretty sure there’s nothing incorrect about it, but it worries me that the author of dlnm didn’t want me to make it.

UPDATE

I think I better understand what is going on here now. plot.gam(), and the ggplot2 implementation of it, gratia::draw(), plot the smooth itself, not the predicted values. By “the smooth itself”, I mean the function that is acting sort of like one of the coefficients in a GLM. Instead of \(y = \beta_0 + \beta_1 x_1\), we have \(y = \beta_0 + f_1(x_1)\). To further clarify, look at the options for predict.gam(). To get predicted \(y\) values, you can use type = "link" or type = "response". But if you just want the values for \(f_1(x_1)\), then you can use type = "terms". The plot above looks like the one I want, but the scale is actually not in units of plant size. See the gratia version, which includes a scale bar:

gratia::draw(growth, select = 1)
## Warning: Removed 423 rows containing non-finite values (stat_contour).

So my efforts in creating cb_margeff() weren’t for nothing, afterall, and are not in conflict with the views of the dlnm package authors. Some day I should probably figure out how to “manually” calculate values of \(y\) from the GAM coefficients, but today is not that day.

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Postdoctoral Researcher

I’m a postdoctoral researcher in Emilio Bruna’s lab at University of Florida working on the effects of drought and habitat fragmentation on a tropical plant. I’m interested in the mechanisms of plant responses to stress and their consequences for natural and agricultural ecosystems.

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