The dde package implements solvers for ordinary differential
equations (ODEs) and delay differential equations (DDEs). DDEs
differ from ODEs in that the right hand side depends not only on
time and the current state of the system but also on the previous
state of the system.
This seemingly innocuous dependency can create problems, especially where the delay changes size overtime. In particular, problems where delays are on the order of the step size (vanishing delays) are difficult to solve.
This package is aimed at solving non-stiff ODEs and DDEs with simple delays.
The deSolve package already allows for solving delay differential
equations, though the interface and approach differs; see below for
similarities and differences.
With ODE models you will almost always be better off using
deSolve. The deTestSet package also implements Fortran version
of the Dormand Prince algorithms here (as deTestSet::dopri5 and
deTestSet::dopri853). If you use deSolve then you'll have the
ability to switch between a huge number of different solvers.
The reasons to consider using dde over deSolve/deTestSet
would be if you
Other than that, I would recommend using deSolve (which is what I
do).
For completeness, I will show how below
Models implemented in R look very similar to deSolve. Here is
the Lorenz attractor implemented for dde:
lorenz_dde <- function(t, y, p) {
sigma <- p$sigma
R <- p$R
b <- p$b
y1 <- y[[1L]]
y2 <- y[[2L]]
y3 <- y[[3L]]
c(sigma * (y2 - y1),
R * y1 - y2 - y1 * y3,
-b * y3 + y1 * y2)
}
The p argument is the parameters and can be any R object. Here
I'll use a list to hold the standard Lorenz attractor parameters:
p <- list(sigma = 10.0,
R = 28.0,
b = 8.0 / 3.0)
tt <- seq(0, 100, length.out = 50001)
y0 <- c(1, 1, 1)
yy <- dde::dopri(y0, tt, lorenz_dde, p)
Here is the iconic attractor
par(mar=rep(.5, 4))
plot(yy[, c(2, 4)], type = "l", lwd = 0.5, col = "#00000066",
axes = FALSE, xlab = "", ylab = "")
The approach above is almost identical to implementing this model
using deSolve:
lorenz_ds <- function(t, y, p) {
sigma <- 10.0
R <- 28.0
b <- 8.0 / 3.0
y1 <- y[[1L]]
y2 <- y[[2L]]
y3 <- y[[3L]]
list(c(sigma * (y2 - y1),
R * y1 - y2 - y1 * y3,
-b * y3 + y1 * y2))
}
yy_ds <- deSolve::ode(y0, tt, lorenz_ds, p)
One of the nice things about the dopri solvers is that they do
not need to stop the integration at the times that you request
output at:
yy <- dde::dopri(y0, tt, lorenz_dde, p, return_statistics = TRUE)
attr(yy, "statistics")
## n_eval n_step n_accept n_reject
## 27104 4517 4323 194
Above, the number of function evaluations (~6 per step), steps, and
rejected steps is indicated (a rejected step occurs where the
solver has to reduce step size multiple times to achieve the
required accuracy). The number of steps here is about 1/10 the
number of returned samples. This works because the solver here
returns “dense output” which allows it to interpolate the
solution between points that it has not visited. This is supported
by many of the solvers in deSolve, too.
In contrast with deSolve, the dense output here can be collected
and worked with later, though doing this requires a bit of faff.
Specify the history length; this needs to be an overestimate because once the end of the history buffer is reached it will be silently overwritten to return the last steps in history. (This is the behaviour required to support delay models without running out of memory).
yy2 <- dde::dopri(y0, range(tt), lorenz_dde, p, return_minimal = TRUE,
n_history = 5000, return_history = TRUE)
With these arguments yy2 is a 3 x 1 matrix, but it comes with a
massive “history” matrix":
dim(yy2)
## [1] 3 1
h <- attr(yy2, "history")
dim(h)
## [1] 17 4323
The contents of this matrix are designed to be opaque (i.e., I may change how things are represented at a future time). However, the solution can be interpolated to any number of points using this matrix:
yy2 <- dde::dopri_interpolate(h, tt)
all.equal(yy2, yy[, -1], check.attributes = FALSE)
## [1] TRUE
Implementing a delay differential equation model (vs an ODE model)
means that you refer to the model state at a previous point in
time. To do that, you use the the ylag function, of which dde
provides interfaces in both R and C.
This is a simple SEIR (Susceptible - Exposed - Infected - Resistant) model from epidemiology. Once exposed to the disease, an individual exists in an “Exposed” state for exactly 14 days before becoming “Infected” (you could model this with a series of compartments and get a distribution of exposed times).
seir <- function(t, y, p) {
b <- 0.1
N <- 1e7
beta <- 10.0
sigma <- 1.0 / 3.0
delta <- 1.0 / 21.0
t_latent <- 14.0
Births <- N * b
surv <- exp(-b * t_latent)
S <- y[[1L]]
E <- y[[2L]]
I <- y[[3L]]
R <- y[[4L]]
tau <- t - t_latent
y_lag <- dde::ylag(tau, c(1L, 3L)) # Here is ylag!
S_lag <- y_lag[[1L]]
I_lag <- y_lag[[2L]]
new_inf <- beta * S * I / N
lag_inf <- beta * S_lag * I_lag * surv / N
c(Births - b * S - new_inf + delta * R,
new_inf - lag_inf - b * E,
lag_inf - (b + sigma) * I,
sigma * I - b * R - delta * R)
}
The model needs to know how many susceptible individuals there were 14 days ago, and how many infected there were 14 days ago. To get this from the model, we use
y_lag <- dde::ylag(tau, c(1L, 3L))
to get the values of the first and third variables (S and I) at time
tau. Alternatively you can get all values with
y_lag <- dde::ylag(tau)
or get them individually
S_lag <- dde::ylag(tau, 1L)
I_lag <- dde::ylag(tau, 3L)
The ylag function can only be called from within an integration;
it will throw an error if you try to call it otherwise.
What happens when we start though? If time starts at 0, then the
first tau is -14 and we have no history then. dde keeps track
of the initial state of the system and if a time before this is
requested it returns the initial state of a variable. This is
going to be reasonable for many applications but will lead to
discontinuities in the derivative of your solution (and the
second derivative and so on). This can make the problem hard to
solve, and it may be preferable to provide your own information
(see the deSolve implementation below for one possible way of
implementing this).
To integrate the problem, use the dde::dopri function (which by
default will use the 5th order method, which is probably the best
bet for most problems). You need to provide arguments:
n_history: number of history elements to retain. If this is
too low then the integration will stop with an error and you can
increase itreturn_history: set this to FALSE if you won't want the
history matrix returned; returning it costs a little time and if
you don't want to inspect it it's better to leave it offy0 <- y0 <- c(1e7 - 1, 0, 1, 0)
tt <- seq(0, 365, length.out = 100)
yy <- dde::dopri(y0, tt, seir, NULL, n_history = 1000L, return_history = FALSE)
matplot(tt, yy[, 2:5], type="l")
deSolve has a function dede that implements a delay differential
equation solver, supporting solutions using lsoda and other
solvers. dde differs in both approach and interface and these
are documented here for users familiar with deSolve. This
section is not needed for basic use of the package, but may be
useful if you have used deSolve, especially with compiled or DDE
models.
By default the delayed variables are computed using interpolation
of the solution using Hermitian (cubic) interpolation along the
time dimension. This works surprisingly well, but we found that
lsoda and other solvers got confused on some large problems
(~2000 equations, 3 delays), possibly because the order of accuracy
of the interpolated solution is much lower than the accuracy of the
actual problem. This manifested in the solver locking up in a
matrix algebra routine involved with approximating the Jacobian of
the solution. The package PBSddesolve, based on solv95, takes
a similar approach and may have similar limitations.
The dde solver uses the “dense output” that the Dormand-Prince
solvers generate; this means that the value of lagged variables can
be immediately looked up without any additional interpolation, and
that the accuracy of the lagged variables will be the same as the
integrated variables.
Above, I implemented a derivative function for an SEIR model for dde as
function(t, y, p) {
b <- 0.1
N <- 1e7
beta <- 10.0
sigma <- 1.0 / 3.0
delta <- 1.0 / 21.0
t_latent <- 14.0
Births <- N * b
surv <- exp(-b * t_latent)
S <- y[[1L]]
E <- y[[2L]]
I <- y[[3L]]
R <- y[[4L]]
tau <- t - t_latent
y_lag <- dde::ylag(tau, c(1L, 3L)) # Here is ylag!
S_lag <- y_lag[[1L]]
I_lag <- y_lag[[2L]]
new_inf <- beta * S * I / N
lag_inf <- beta * S_lag * I_lag * surv / N
c(Births - b * S - new_inf + delta * R,
new_inf - lag_inf - b * E,
lag_inf - (b + sigma) * I,
sigma * I - b * R - delta * R)
}
<bytecode: 0x55cd98caa338>
The implementation using deSolve looks very similar:
seir_deSolve <- function(t, y, parms) {
b <- 0.1
N <- 1e7
beta <- 10
sigma <- 1 / 3
delta <- 1 / 21
t_latent <- 14.0
I0 <- 1
Births <- N * b
surv <- exp(-b * t_latent)
S <- y[[1L]]
E <- y[[2L]]
I <- y[[3L]]
R <- y[[4L]]
tau <- t - t_latent
if (tau < 0.0) { # NOTE: assuming that t0 is always zero
S_lag <- parms$S0
I_lag <- parms$I0
} else {
y_lag <- deSolve::lagvalue(tau, c(1L, 3L))
S_lag <- y_lag[[1L]]
I_lag <- y_lag[[2L]]
}
new_inf <- beta * S * I / N
lag_inf <- beta * S_lag * I_lag * surv / N
list(c(Births - b * S - new_inf + delta * R,
new_inf - lag_inf - b * E,
lag_inf - (b + sigma) * I,
sigma * I - b * R - delta * R))
}
The differences are that:
deSolve requires that the derivatives are returned as a list,
whereas dde uses a numeric vector (see below for details about this)deSolve requires that you provide the initial values for the
lagged values (and we also need to know what the initial time
is too, but I'm assuming that as zero)deSolve::lagvalue (for dde it is
dde::ylag)Aside from this the code is essentially identical.
To run the model with deSolve, use deSolve::dede which
automatically sets up a history buffer of 10000 elements (the
mxhist element of the control list alters this).
y0 <- y0 <- c(1e7 - 1, 0, 1, 0)
tt <- seq(0, 365, length.out = 100)
initial <- list(S0 = y0[[1]], I0 = y0[[3]])
yy_ds <- deSolve::dede(y0, tt, seir_deSolve, initial)
This produces output that the same as dde:
yy_dde <- dde::dopri(y0, tt, seir, NULL, n_history = 1000L,
return_history = FALSE)
op <- par(mfrow=c(1, 2), mar=c(4, .5, 1.4, .5), oma=c(0, 2, 0, 0))
matplot(tt, yy_dde[, -1], type="l", main = "dde")
matplot(tt, yy_ds[, -1], type="l", main = "deSolve", yaxt="n")
The performance of both packages is fairly similar, taking a few tens of milliseconds to run on my machines
tR <- microbenchmark::microbenchmark(times = 30,
deSolve = deSolve::dede(y0, tt, seir_deSolve, initial),
dde = dde::dopri(y0, tt, seir, NULL, n_history = 1000L,
return_history = FALSE))
tR
## Unit: milliseconds
## expr min lq mean median uq max neval
## deSolve 29.38835 31.69870 32.08285 32.01664 32.41737 35.94031 30
## dde 15.17311 15.41519 16.32605 16.35025 17.18696 17.85124 30
The compiled code interface for deSolve has greatly influenced
dde and models implemented in either framework will be similar.
Eventually dde may support a fully deSolve compatible interface
but for now there are a few differences.
#include <R.h>
#include <R_ext/Rdynload.h>
void lagvalue(double tau, int *nr, int N, double *ytau);
// The parameters are going to be arranged:
//
// t0
// S0, I0
// (b, N, beta, sigma, delta, t_latent)
//
// See below for why t0, S0 and I0 are stored
static double parms[3];
// The standard deSolve initialisation function
void seir_initmod(void (* odeparms)(int *, double *)) {
int N = 3;
odeparms(&N, parms);
}
// The RHS
void seir_deSolve(int *n, double *t, double *y, double *dydt,
double *yout, int *ip) {
// again, hard-coded parameters for now; will change this shortly
// once I get the same working with the dde impementation.
double b = 0.1, N = 1e7, beta = 10.0, sigma = 1.0 / 3.0,
delta = 1.0 / 21.0, t_latent = 14.0;
double Births = N * b, surv = exp(-b * t_latent);
// Because of the way that deSolve implements delays we need to
// store the initial time and values in the parameters vector; if
// the requested time is earlier than the time we started at then
// the initial values need to be used, which we also store in the
// parameters.
double t0 = parms[0];
const double tau = *t - t_latent;
static int idx[2] = {0, 2};
double S_lag, I_lag;
if (tau <= t0) {
S_lag = parms[1];
I_lag = parms[2];
} else {
double ylag[2];
lagvalue(tau, idx, 2, ylag);
S_lag = ylag[0];
I_lag = ylag[1];
}
const double S = y[0], E = y[1], I = y[2], R = y[3];
const double new_inf = beta * S * I / N;
const double lag_inf = beta * S_lag * I_lag * surv / N;
dydt[0] = Births - b * S - new_inf + delta * R;
dydt[1] = new_inf - lag_inf - b * E;
dydt[2] = lag_inf - (b + sigma) * I;
dydt[3] = sigma * I - b * R - delta * R;
}
// This is the interface to deSolve's lag functions. Note that unlike
// dde you are responsible for checking for underflows and providing
// values for underflowed times.
void lagvalue(double tau, int *nr, int N, double *ytau) {
typedef void lagvalue_t(double, int *, int, double *);
static lagvalue_t *fun = NULL;
if (fun == NULL) {
fun = (lagvalue_t*) R_GetCCallable("deSolve", "lagvalue");
}
fun(tau, nr, N, ytau);
}
This looks very similar to the dde version above but:
parms (or whatever parameters are called) are handled as a
global variable that is updated via a model initialisation
function, whereas in dde they're passed in as a void pointert0 and initial conditions for S and I * There is
an argument double *yout for additional output variables (of
length *ip; in dde these are handled via a separate function.dde this is achieved by
including <dde/dde.h> and <dde/dde.c>.Apart from these details, the model definition should appear very similar.
initial <- c(0.0, y0[[1]], y0[[3]])
zz_ds <- deSolve::dede(y0, tt, "seir_deSolve", initial,
initfunc = "seir_initmod", dllname = "dde_seir_ds")
zz_dde <- dde::dopri(y0, tt, "seir", numeric(), dllname = "dde_seir",
n_history = 1000L, return_history = FALSE)
Check that outputs of these models are the same as the R version above:
all.equal(zz_ds, yy_ds, check.attributes = FALSE)
## [1] TRUE
all.equal(zz_dde, yy_dde, check.attributes = FALSE)
## [1] TRUE
Here, the timings are even closer and have dropped from on the order of 20 milliseconds to 0.5 milliseconds; so we're getting a ~40x speed up from using compiled code.
tC <- microbenchmark::microbenchmark(
deSolve = deSolve::dede(y0, tt, "seir_deSolve", initial,
initfunc = "seir_initmod", dllname = "dde_seir_ds"),
dde = dde::dopri(y0, tt, "seir", numeric(), dllname = "dde_seir",
n_history = 1000L, return_history = FALSE))
tC
## Unit: microseconds
## expr min lq mean median uq max neval
## deSolve 655.379 665.4885 693.0394 672.055 677.6115 2457.890 100
## dde 996.819 1008.5775 1034.2613 1028.179 1055.4235 1137.123 100
The difference in speed will tend to increase as the models become larger (in terms of numbers of equations and parameters). On the other hand, constructing large models in C can be a hassle (but see odin for a possible solution).
You can extract a little more performance by tweaking options to
dde::dopri; in particular, adding return_minimal = TRUE
will avoid transposing the output, binding the times on, and (if
given) avoiding binding output variables. These costs may be
nontrivial with bigger models, though the cost of running a larger
model will likely be larger still. Previous version of R suffered
from a large cost of looking up the address of the compiled
function (Windows may still take longer to do this than macOS/Linux).
In that case, use getNativeSymbolInfo("seir") and pass that
through to dopri as the func argument.
ptr <- getNativeSymbolInfo("seir")
tC2 <- microbenchmark::microbenchmark(
deSolve = deSolve::dede(y0, tt, "seir_deSolve", initial,
initfunc = "seir_initmod", dllname = "dde_seir_ds"),
dde = dde::dopri(y0, tt, "seir", numeric(), dllname = "dde_seir",
n_history = 1000L, return_history = FALSE),
dde2 = dde::dopri(y0, tt, ptr, numeric(), n_history = 1000L,
return_history = FALSE, return_minimal = TRUE))
tC2
## Unit: microseconds
## expr min lq mean median uq max neval
## deSolve 646.311 651.7895 678.8803 655.944 667.3380 2383.152 100
## dde 997.534 1007.4970 1018.3352 1012.630 1019.5760 1138.806 100
## dde2 962.943 971.2535 984.0095 975.405 983.6715 1102.526 100