macpan

Interface Principles

Another component of speed
More difficult to solve than run-time speed
Identifying best practices is harder than writing code
If you cannot do it manually, you cannot automate it
Different interfaces for different roles

Interface for macpan 1.5

macpan1 had no interface for model definition
macpan1.5 was the first attempt to expose model definitions to the user

Interface for macpan 1.5

state = c(S = 20000, I = 100, R = 0)
params = c(gamma = 0.06, beta = 0.15, N = sum(state))

Interface for macpan 1.5

state = c(S = 20000, I = 100, R = 0)
params = c(gamma = 0.06, beta = 0.15, N = sum(state))
sir_model = (
  flexmodel(
    params = params,
    state = state
  )
)

Interface for macpan 1.5

state = c(S = 20000, I = 100, R = 0)
params = c(gamma = 0.06, beta = 0.15, N = sum(state))
sir_model = (
  flexmodel(
    params = params,
    state = state,
    start_date = "2000-01-01",
    end_date = "2000-05-01"
  )
)

Interface for macpan 1.5

state = c(S = 20000, I = 100, R = 0)
params = c(gamma = 0.06, beta = 0.15, N = sum(state))
sir_model = (
  flexmodel(
    params = params,
    state = state,
    start_date = "2000-01-01",
    end_date = "2000-05-01"
  )  
  %>% add_rate("S", "I", ~ (1/N) * (beta) * (I))
  %>% add_rate("I", "R", ~ (gamma))
)

Interface for macpan 1.5

state = c(S = 20000, I = 100, R = 0)
params = c(gamma = 0.06, beta = 0.15, N = sum(state))
sir_model = (
  flexmodel(
    params = params,
    state = state,
    start_date = "2000-01-01",
    end_date = "2000-05-01"
  )  
  %>% add_rate("S", "I", ~ (1/N) * (beta) * (I))
  %>% add_rate("I", "R", ~ (gamma))
)

Interface for macpan 1.5

Advantages
- Modellers can make their own fast models
- Easy to read and define simple models
Lessons
- Limited model definition flexibility/extensibility
- No underlying data structure
- Challenging to maintain in real pipelines
- Difficult to experiment with new interface designs

Interface for macpan 2

Goals:

Retain speed gains of macpan 1.5
Address flexibility/extensibility
Address pipeline maintenance issues
Architecture expects ideas about interface to change

Model Readability

Model definitions as directories of files
File format human-readable and computer-consumable
See the differences between two model versions
Stay organized with a revision history

Model Definition Files

List of variables
States, parameters, derived quantities
Separate from numerical values

Model Definition Files

List of variables
States, parameters, derived quantities
Separate from numerical values
Classify in different ways
Useful for structured models

Model Definition Files

Who Makes the Definition Files?

Depends on the user’s role
Build different interfaces
- Point-and-click
- Tidyverse-style
- Model products
For now – Steve makes the files while talking to modellers

Readable Model Definitions

Model Definition Files – The Point

Establish a standard specification
Build different interfaces on top
Interfaces can change as we learn
Interfaces can be tailored

Extensibility

Easy-flexible trade-off
Easier tools tend to be less flexible
Better tools soften this trade-off
Modellers value flexibility more
Role-based interfaces

Extensible – model definition files

Extensible – model products

(in development)

Extensible – general model operations

(in development)

Extensible – general model operations

(in development)

Extensible – general model operations

(in development)

Extensible – general model operations

(in development)

Extensible – math expressions

Simple Birth Process

simple_sims(iteration_exprs = list(x ~ x + 0.01 * x)
  , time_steps = 10
  , x = 1
)$value

 [1] 1.000000 1.010000 1.020100 1.030301 1.040604 1.051010 1.061520 1.072135
 [9] 1.082857 1.093685 1.104622

Extensible – math expressions

Fibonacci

s = simple_sims(iteration_exprs = list(x ~ A %*% x)
  , time_steps = 10
  , A = matrix(c(1, 1, 1, 0), 2, 2)
  , x = c(1, 0)
)
dplyr::filter(s, row == 0)$value

 [1]  1  1  2  3  5  8 13 21 34 55 89

Extensible – edit model expressions

ExprList(
  before = list(),
  during = list(),
  after = list()
)

Extensible – edit model expressions

ExprList(
  before = list(N ~ sum(state_vector)),
  during = list(),
  after = list()
)

Extensible – edit model expressions

ExprList(
  before = list(N ~ sum(state_vector)),
  
  during = list(
    # force of infection
    flow_vector[foi_index] ~ beta * state_vector[I_index] / N
  ),
  
  after = list()
)

Extensible – edit model expressions

ExprList(
  before = list(N ~ sum(state_vector)),
  
  during = list(
    
    # force of infection
    flow_vector[foi_index] ~ beta * state_vector[I_index] / N,
    
    # state-update expressions common to a large class of models
    flows ~ flow_vector * state_vector[from_index],
    incidence_vector ~ groupSums(flows, to_index, n_states),
    outflow_vector ~ groupSums(flows, from_index, n_states),
    state_vector ~ state_vector + incidence_vector - outflow_vector
  ),
  
  after = list()
)

Extensible – C++ Level

engine_eval(~ log(1))

     [,1]
[1,]    0

Extensible – C++ Level

engine_eval(~ sin(1))

Error in TMBSimulator(m) : 
The tmb_model object is malformed,
with the following explanation:
Error in get_indices(x_char[is_func], vec = names(valid_funcs), vec_type = "functions",  : 
  
the expression given by:
sin(1)

contained the following functions:
sin

 that were not found in the list of available functions:
+ - * / ^ exp log ( c matrix %*% sum rep rowSums colSums groupSums [ block t rbind_time rbind_lag cbind_time cbind_lag : seq convolution cbind rbind time_step assign unpack recycle clamp dpois dnbinom dnorm rpois rnbinom rnorm
Please see ?engine_functions for more information on the available functions.

Extensible – C++ Level

Extensible – plug into tidyverse

              matrix time row col        value
1       state_vector    0   S     1.000000e+02
2       state_vector    0   E     1.000000e+00
3       state_vector    0   I     0.000000e+00
4       state_vector    0   R     0.000000e+00
5       state_vector    1   S     1.000000e+02
6       state_vector    1   E     9.000000e-01
7       state_vector    1   I     1.000000e-01
8       state_vector    1   R     0.000000e+00
9       state_vector    2   S     9.996040e+01
10      state_vector    2   E     8.496040e-01
11      state_vector    2   I     1.840000e-01
12      state_vector    2   R     6.000000e-03
13      state_vector    3   S     9.988755e+01
14      state_vector    3   E     8.374860e-01
15      state_vector    3   I     2.579204e-01
16      state_vector    3   R     1.704000e-02
17      state_vector    4   S     9.978552e+01
18      state_vector    4   E     8.557692e-01
19      state_vector    4   I     3.261938e-01
20      state_vector    4   R     3.251522e-02
21      state_vector    5   S     9.965661e+01
22      state_vector    5   E     8.991009e-01
23      state_vector    5   I     3.921991e-01
24      state_vector    5   R     5.208685e-02
25      state_vector    6   S     9.950182e+01
26      state_vector    6   E     9.639838e-01
27      state_vector    6   I     4.585772e-01
28      state_vector    6   R     7.561879e-02
29      state_vector    7   S     9.932111e+01
30      state_vector    7   E     1.048295e+00
31      state_vector    7   I     5.274610e-01
32      state_vector    7   R     1.031334e-01
33      state_vector    8   S     9.911363e+01
34      state_vector    8   E     1.150943e+00
35      state_vector    8   I     6.006428e-01
36      state_vector    8   R     1.347811e-01
37      state_vector    9   S     9.887786e+01
38      state_vector    9   E     1.271619e+00
39      state_vector    9   I     6.796986e-01
40      state_vector    9   R     1.708197e-01
41      state_vector   10   S     9.861170e+01
42      state_vector   10   E     1.410624e+00
43      state_vector   10   I     7.660785e-01
44      state_vector   10   R     2.116016e-01
45      state_vector   11   S     9.831251e+01
46      state_vector   11   E     1.568747e+00
47      state_vector   11   I     8.611762e-01
48      state_vector   11   R     2.575663e-01
49      state_vector   12   S     9.797721e+01
50      state_vector   12   E     1.747177e+00
51      state_vector   12   I     9.663803e-01
52      state_vector   12   R     3.092369e-01
53      state_vector   13   S     9.760222e+01
54      state_vector   13   E     1.947442e+00
55      state_vector   13   I     1.083115e+00
56      state_vector   13   R     3.672197e-01
57      state_vector   14   S     9.718355e+01
58      state_vector   14   E     2.171369e+00
59      state_vector   14   I     1.212872e+00
60      state_vector   14   R     4.322066e-01
61      state_vector   15   S     9.671674e+01
62      state_vector   15   E     2.421049e+00
63      state_vector   15   I     1.357237e+00
64      state_vector   15   R     5.049789e-01
65      state_vector   16   S     9.619686e+01
66      state_vector   16   E     2.698815e+00
67      state_vector   16   I     1.517908e+00
68      state_vector   16   R     5.864131e-01
69      state_vector   17   S     9.561857e+01
70      state_vector   17   E     3.007223e+00
71      state_vector   17   I     1.696715e+00
72      state_vector   17   R     6.774876e-01
73      state_vector   18   S     9.497605e+01
74      state_vector   18   E     3.349025e+00
75      state_vector   18   I     1.895634e+00
76      state_vector   18   R     7.792905e-01
77      state_vector   19   S     9.426302e+01
78      state_vector   19   E     3.727152e+00
79      state_vector   19   I     2.116799e+00
80      state_vector   19   R     8.930285e-01
81      state_vector   20   S     9.347278e+01
82      state_vector   20   E     4.144677e+00
83      state_vector   20   I     2.362506e+00
84      state_vector   20   R     1.020036e+00
85      state_vector   21   S     9.259821e+01
86      state_vector   21   E     4.604784e+00
87      state_vector   21   I     2.635223e+00
88      state_vector   21   R     1.161787e+00
89      state_vector   22   S     9.163180e+01
90      state_vector   22   E     5.110709e+00
91      state_vector   22   I     2.937588e+00
92      state_vector   22   R     1.319900e+00
93      state_vector   23   S     9.056576e+01
94      state_vector   23   E     5.665684e+00
95      state_vector   23   I     3.272404e+00
96      state_vector   23   R     1.496155e+00
97      state_vector   24   S     8.939202e+01
98      state_vector   24   E     6.272849e+00
99      state_vector   24   I     3.642628e+00
100     state_vector   24   R     1.692500e+00
101     state_vector   25   S     8.810243e+01
102     state_vector   25   E     6.935156e+00
103     state_vector   25   I     4.051355e+00
104     state_vector   25   R     1.911057e+00
105     state_vector   26   S     8.668883e+01
106     state_vector   26   E     7.655241e+00
107     state_vector   26   I     4.501789e+00
108     state_vector   26   R     2.154139e+00
109     state_vector   27   S     8.514327e+01
110     state_vector   27   E     8.435281e+00
111     state_vector   27   I     4.997206e+00
112     state_vector   27   R     2.424246e+00
113     state_vector   28   S     8.345820e+01
114     state_vector   28   E     9.276816e+00
115     state_vector   28   I     5.540902e+00
116     state_vector   28   R     2.724078e+00
117     state_vector   29   S     8.162678e+01
118     state_vector   29   E     1.018055e+01
119     state_vector   29   I     6.136129e+00
120     state_vector   29   R     3.056533e+00
121     state_vector   30   S     7.964313e+01
122     state_vector   30   E     1.114615e+01
123     state_vector   30   I     6.786017e+00
124     state_vector   30   R     3.424700e+00
125     state_vector   31   S     7.750270e+01
126     state_vector   31   E     1.217197e+01
127     state_vector   31   I     7.493471e+00
128     state_vector   31   R     3.831861e+00
129     state_vector   32   S     7.520264e+01
130     state_vector   32   E     1.325483e+01
131     state_vector   32   I     8.261060e+00
132     state_vector   32   R     4.281470e+00
133     state_vector   33   S     7.274223e+01
134     state_vector   33   E     1.438976e+01
135     state_vector   33   I     9.090880e+00
136     state_vector   33   R     4.777133e+00
137     state_vector   34   S     7.012326e+01
138     state_vector   34   E     1.556976e+01
139     state_vector   34   I     9.984403e+00
140     state_vector   34   R     5.322586e+00
141     state_vector   35   S     6.735043e+01
142     state_vector   35   E     1.678561e+01
143     state_vector   35   I     1.094231e+01
144     state_vector   35   R     5.921650e+00
145     state_vector   36   S     6.443174e+01
146     state_vector   36   E     1.802574e+01
147     state_vector   36   I     1.196434e+01
148     state_vector   36   R     6.578189e+00
149     state_vector   37   S     6.137874e+01
150     state_vector   37   E     1.927617e+01
151     state_vector   37   I     1.304905e+01
152     state_vector   37   R     7.296049e+00
153     state_vector   38   S     5.820672e+01
154     state_vector   38   E     2.052057e+01
155     state_vector   38   I     1.419372e+01
156     state_vector   38   R     8.078992e+00
157     state_vector   39   S     5.493476e+01
158     state_vector   39   E     2.174047e+01
159     state_vector   39   I     1.539416e+01
160     state_vector   39   R     8.930616e+00
161     state_vector   40   S     5.158555e+01
162     state_vector   40   E     2.291563e+01
163     state_vector   40   I     1.664455e+01
164     state_vector   40   R     9.854265e+00
165     state_vector   41   S     4.818508e+01
166     state_vector   41   E     2.402453e+01
167     state_vector   41   I     1.793744e+01
168     state_vector   41   R     1.085294e+01
169     state_vector   42   S     4.476205e+01
170     state_vector   42   E     2.504512e+01
171     state_vector   42   I     1.926365e+01
172     state_vector   42   R     1.192918e+01
173     state_vector   43   S     4.134707e+01
174     state_vector   43   E     2.595558e+01
175     state_vector   43   I     2.061234e+01
176     state_vector   43   R     1.308500e+01
177     state_vector   44   S     3.797179e+01
178     state_vector   44   E     2.673531e+01
179     state_vector   44   I     2.197116e+01
180     state_vector   44   R     1.432174e+01
181     state_vector   45   S     3.466769e+01
182     state_vector   45   E     2.736587e+01
183     state_vector   45   I     2.332642e+01
184     state_vector   45   R     1.564001e+01
185     state_vector   46   S     3.146502e+01
186     state_vector   46   E     2.783195e+01
187     state_vector   46   I     2.466342e+01
188     state_vector   46   R     1.703960e+01
189     state_vector   47   S     2.839162e+01
190     state_vector   47   E     2.812216e+01
191     state_vector   47   I     2.596681e+01
192     state_vector   47   R     1.851940e+01
193     state_vector   48   S     2.547186e+01
194     state_vector   48   E     2.822971e+01
195     state_vector   48   I     2.722102e+01
196     state_vector   48   R     2.007741e+01
197     state_vector   49   S     2.272584e+01
198     state_vector   49   E     2.815276e+01
199     state_vector   49   I     2.841073e+01
200     state_vector   49   R     2.171067e+01
201     state_vector   50   S     2.016878e+01
202     state_vector   50   E     2.789454e+01
203     state_vector   50   I     2.952136e+01
204     state_vector   50   R     2.341532e+01
205     state_vector   51   S     1.781072e+01
206     state_vector   51   E     2.746315e+01
207     state_vector   51   I     3.053954e+01
208     state_vector   51   R     2.518660e+01
209     state_vector   52   S     1.565654e+01
210     state_vector   52   E     2.687101e+01
211     state_vector   52   I     3.145348e+01
212     state_vector   52   R     2.701897e+01
213     state_vector   53   S     1.370623e+01
214     state_vector   53   E     2.613422e+01
215     state_vector   53   I     3.225337e+01
216     state_vector   53   R     2.890618e+01
217     state_vector   54   S     1.195545e+01
218     state_vector   54   E     2.527158e+01
219     state_vector   54   I     3.293159e+01
220     state_vector   54   R     3.084138e+01
221     state_vector   55   S     1.039619e+01
222     state_vector   55   E     2.430368e+01
223     state_vector   55   I     3.348285e+01
224     state_vector   55   R     3.281728e+01
225     state_vector   56   S     9.017602e+00
226     state_vector   56   E     2.325190e+01
227     state_vector   56   I     3.390425e+01
228     state_vector   56   R     3.482625e+01
229     state_vector   57   S     7.806770e+00
230     state_vector   57   E     2.213754e+01
231     state_vector   57   I     3.419518e+01
232     state_vector   57   R     3.686051e+01
233     state_vector   58   S     6.749527e+00
234     state_vector   58   E     2.098103e+01
235     state_vector   58   I     3.435723e+01
236     state_vector   58   R     3.891222e+01
237     state_vector   59   S     5.831131e+00
238     state_vector   59   E     1.980132e+01
239     state_vector   59   I     3.439390e+01
240     state_vector   59   R     4.097365e+01
241     state_vector   60   S     5.036852e+00
242     state_vector   60   E     1.861547e+01
243     state_vector   60   I     3.431039e+01
244     state_vector   60   R     4.303728e+01
245     state_vector   61   S     4.352431e+00
246     state_vector   61   E     1.743834e+01
247     state_vector   61   I     3.411332e+01
248     state_vector   61   R     4.509591e+01
249     state_vector   62   S     3.764408e+00
250     state_vector   62   E     1.628253e+01
251     state_vector   62   I     3.381035e+01
252     state_vector   62   R     4.714271e+01
253     state_vector   63   S     3.260345e+00
254     state_vector   63   E     1.515834e+01
255     state_vector   63   I     3.340999e+01
256     state_vector   63   R     4.917133e+01
257     state_vector   64   S     2.828946e+00
258     state_vector   64   E     1.407391e+01
259     state_vector   64   I     3.292122e+01
260     state_vector   64   R     5.117593e+01
261     state_vector   65   S     2.460105e+00
262     state_vector   65   E     1.303536e+01
263     state_vector   65   I     3.235334e+01
264     state_vector   65   R     5.315120e+01
265     state_vector   66   S     2.144887e+00
266     state_vector   66   E     1.204704e+01
267     state_vector   66   I     3.171567e+01
268     state_vector   66   R     5.509240e+01
269     state_vector   67   S     1.875475e+00
270     state_vector   67   E     1.111175e+01
271     state_vector   67   I     3.101744e+01
272     state_vector   67   R     5.699534e+01
273     state_vector   68   S     1.645089e+00
274     state_vector   68   E     1.023096e+01
275     state_vector   68   I     3.026757e+01
276     state_vector   68   R     5.885639e+01
277     state_vector   69   S     1.447890e+00
278     state_vector   69   E     9.405062e+00
279     state_vector   69   I     2.947461e+01
280     state_vector   69   R     6.067244e+01
281     state_vector   70   S     1.278876e+00
282     state_vector   70   E     8.633570e+00
283     state_vector   70   I     2.864664e+01
284     state_vector   70   R     6.244092e+01
285     state_vector   71   S     1.133785e+00
286     state_vector   71   E     7.915304e+00
287     state_vector   71   I     2.779120e+01
288     state_vector   71   R     6.415972e+01
289     state_vector   72   S     1.008996e+00
290     state_vector   72   E     7.248562e+00
291     state_vector   72   I     2.691525e+01
292     state_vector   72   R     6.582719e+01
293     state_vector   73   S     9.014418e-01
294     state_vector   73   E     6.631260e+00
295     state_vector   73   I     2.602520e+01
296     state_vector   73   R     6.744210e+01
297     state_vector   74   S     8.085301e-01
298     state_vector   74   E     6.061046e+00
299     state_vector   74   I     2.512681e+01
300     state_vector   74   R     6.900361e+01
301     state_vector   75   S     7.280716e-01
302     state_vector   75   E     5.535400e+00
303     state_vector   75   I     2.422531e+01
304     state_vector   75   R     7.051122e+01
305     state_vector   76   S     6.582191e-01
306     state_vector   76   E     5.051712e+00
307     state_vector   76   I     2.332533e+01
308     state_vector   76   R     7.196474e+01
309     state_vector   77   S     5.974144e-01
310     state_vector   77   E     4.607346e+00
311     state_vector   77   I     2.243098e+01
312     state_vector   77   R     7.336426e+01
313     state_vector   78   S     5.443428e-01
314     state_vector   78   E     4.199683e+00
315     state_vector   78   I     2.154585e+01
316     state_vector   78   R     7.471012e+01
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758 incidence_vector   88   E     1.579122e-02
759 incidence_vector   88   I     1.794052e-01
760 incidence_vector   88   R     8.627294e-01
761 incidence_vector   89   S     0.000000e+00
762 incidence_vector   89   E     1.418427e-02
763 incidence_vector   89   I     1.630438e-01
764 incidence_vector   89   R     8.217299e-01
765 incidence_vector   90   S     0.000000e+00
766 incidence_vector   90   E     1.276973e-02
767 incidence_vector   90   I     1.481578e-01
768 incidence_vector   90   R     7.822088e-01
769 incidence_vector   91   S     0.000000e+00
770 incidence_vector   91   E     1.152142e-02
771 incidence_vector   91   I     1.346190e-01
772 incidence_vector   91   R     7.441657e-01
773 incidence_vector   92   S     0.000000e+00
774 incidence_vector   92   E     1.041707e-02
775 incidence_vector   92   I     1.223093e-01
776 incidence_vector   92   R     7.075929e-01
777 incidence_vector   93   S     0.000000e+00
778 incidence_vector   93   E     9.437690e-03
779 incidence_vector   93   I     1.111200e-01
780 incidence_vector   93   R     6.724759e-01
781 incidence_vector   94   S     0.000000e+00
782 incidence_vector   94   E     8.567061e-03
783 incidence_vector   94   I     1.009518e-01
784 incidence_vector   94   R     6.387945e-01
785 incidence_vector   95   S     0.000000e+00
786 incidence_vector   95   E     7.791292e-03
787 incidence_vector   95   I     9.171334e-02
788 incidence_vector   95   R     6.065240e-01
789 incidence_vector   96   S     0.000000e+00
790 incidence_vector   96   E     7.098467e-03
791 incidence_vector   96   I     8.332113e-02
792 incidence_vector   96   R     5.756353e-01
793 incidence_vector   97   S     0.000000e+00
794 incidence_vector   97   E     6.478336e-03
795 incidence_vector   97   I     7.569887e-02
796 incidence_vector   97   R     5.460965e-01
797 incidence_vector   98   S     0.000000e+00
798 incidence_vector   98   E     5.922068e-03
799 incidence_vector   98   I     6.877681e-02
800 incidence_vector   98   R     5.178726e-01
801 incidence_vector   99   S     0.000000e+00
802 incidence_vector   99   E     5.422032e-03
803 incidence_vector   99   I     6.249134e-02
804 incidence_vector   99   R     4.909269e-01
805 incidence_vector  100   S     0.000000e+00
806 incidence_vector  100   E     4.971623e-03
807 incidence_vector  100   I     5.678441e-02
808 incidence_vector  100   R     4.652208e-01

Extensible – plug into stan/tmb

sir_tmb = tmb_fun(sir_macpan)

tmb is a model fitting package
stan is a Bayesian inference package
Better confidence intervals
Flexible inference
No need to make stan model

Extensible – plug into stan/tmb

sir_tmb = tmb_fun(sir_macpan)
sir_stan = tmbstan(sir_tmb, chains = 1)

tmb is a model fitting package
stan is a Bayesian inference package
Better confidence intervals
Flexible inference
No need to make stan model

Extensible – plug into stan/tmb

sir_tmb = tmb_fun(sir_macpan)
sir_stan = tmbstan(sir_tmb, chains = 1)
traceplot(sir_stan, ncol = 1)

tmb is a model fitting package
stan is a Bayesian inference package
Better confidence intervals
Flexible inference
No need to make stan model

Take-Home

Compartmental modelling R package
Free and open source
McMasterPandemic reboot
Blazing Fast
Team-produced

Take-Home

Team-produced

Contributions, Contributors, Community

Original developers were real modellers (Ben Bolker, Jonathan Dushoff, David Earn, Mike Li, Irena Papst)
Pipeline development for delivering PHAC, OMT, and PHO forecasts (Irena Papst, Mike Li)
Sharcnet C++ expertise (Weiguang Guan)
Current R development (Darren Flynn-Primrose)
Gather requirements from public health modellers and academics (Amy Hurford, Lisa Kanary, Caroline Colijn, Zahra Mohammadi, Claude Nadeau, Philippe Berthiaume)
Mathematical rigor (Jonathan Dushoff, Darren Flynn-Primrose)
Workshop this summer (Irena Papst)