Extract Model Data for Stochastic Models — as.data.frame.seiqhrf • sirplus

This function extracts model simulations for objects of classes seiqhrf into a data frame using the generic as.data.frame function.

# S3 method for seiqhrf
as.data.frame(
  x,
  row.names = NULL,
  optional = FALSE,
  out = "vals",
  sim,
  qval,
  ...
)

Arguments

x	An `EpiModel` object of class `icm` or `netsim`.
row.names	See `as.data.frame.default`.
optional	See `as.data.frame.default`.
out	Data output to data frame: `"mean"` for row means across simulations, `"sd"` for row standard deviations across simulations, `"qnt"` for row quantiles at the level specified in `qval`, or `"vals"` for values from individual simulations.
sim	If `out="vals"`, the simulation number to output. If not specified, then data from all simulations will be output.
qval	Quantile value required when `out="qnt"`.
...	See `as.data.frame.default`.

Details

These methods work for both seiqhrf class models. The available output includes time-specific means, standard deviations, quantiles, and simulation values (compartment and flow sizes) from these stochastic model classes. Means, standard deviations, and quantiles are calculated by taking the row summary (i.e., each row of data is corresponds to a time step) across all simulations in the model output.

Examples

## Stochastic SEIQHRF model
param <- param_seiqhrf()
init <- init_seiqhrf(s.num = 500, i.num = 1)
control <- control_seiqhrf(nsteps = 10, nsims = 3)
mod <- seiqhrf(init, control, param)

# Default output all simulation runs, default to all in stacked data.frame
as.data.frame(mod)
#>    sim time s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow ds.flow
#> 1    1    1   500     1 501       0       0       0         0       0       0
#> 2    1    2   499     1 501       1       0       0         0       0       0
#> 3    1    3   499     1 501       0       0       0         0       0       0
#> 4    1    4   499     1 501       0       0       0         0       0       0
#> 5    1    5   498     1 501       1       0       0         0       0       0
#> 6    1    6   495     2 501       1       1       0         0       0       0
#> 7    1    7   493     2 501       2       0       0         0       0       0
#> 8    1    8   490     3 501       3       0       0         0       0       0
#> 9    1    9   485     4 501       4       0       0         0       0       0
#> 10   1   10   479     6 501       4       1       0         0       0       0
#> 11   2    1   500     1 501       0       0       0         0       0       0
#> 12   2    2   499     1 501       1       0       0         0       0       0
#> 13   2    3   499     1 501       0       1       0         0       0       0
#> 14   2    4   499     1 501       0       0       0         0       0       0
#> 15   2    5   499     1 501       0       0       0         0       0       0
#> 16   2    6   499     1 501       0       0       0         0       0       0
#> 17   2    7   498     1 501       1       0       0         0       0       0
#> 18   2    8   498     1 501       0       0       0         0       0       0
#> 19   2    9   496     1 501       1       0       0         0       0       0
#> 20   2   10   494     2 501       1       0       0         0       0       0
#> 21   3    1   500     1 501       0       0       0         0       0       0
#> 22   3    2   499     1 501       1       0       0         0       0       0
#> 23   3    3   499     0 501       0       1       1         0       0       0
#> 24   3    4   499     0 501       0       0       0         0       0       0
#> 25   3    5   499     0 501       0       0       0         0       0       0
#> 26   3    6   499     0 501       0       0       0         0       0       0
#> 27   3    7   499     0 501       0       0       0         0       0       0
#> 28   3    8   499     0 501       0       0       0         0       0       0
#> 29   3    9   498     0 501       1       0       0         0       0       0
#> 30   3   10   498     0 501       0       0       0         0       0       0
#>    de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow a.q.flow
#> 1        0       0       0       0       0      0        0        0        0
#> 2        0       0       0       0       0      0        0        0        0
#> 3        0       0       0       0       0      0        0        0        0
#> 4        0       0       0       0       0      0        0        0        0
#> 5        0       0       0       0       0      0        0        0        0
#> 6        0       0       0       0       0      0        0        0        0
#> 7        0       0       0       0       0      0        0        0        0
#> 8        0       0       0       0       0      0        0        0        0
#> 9        0       0       0       0       0      0        0        0        0
#> 10       0       0       0       0       0      0        0        0        0
#> 11       0       0       0       0       0      0        0        0        0
#> 12       0       0       0       0       0      0        0        0        0
#> 13       0       0       0       0       0      0        0        0        0
#> 14       0       0       0       0       0      0        0        0        0
#> 15       0       0       0       0       0      0        0        0        0
#> 16       0       0       0       0       0      0        0        0        0
#> 17       0       0       0       0       0      0        0        0        0
#> 18       0       0       0       0       0      0        0        0        0
#> 19       0       0       0       0       0      0        0        0        0
#> 20       0       0       0       0       0      0        0        0        0
#> 21       0       0       0       0       0      0        0        0        0
#> 22       0       0       0       0       0      0        0        0        0
#> 23       0       0       0       0       0      0        0        0        0
#> 24       0       0       0       0       0      0        0        0        0
#> 25       0       0       0       0       0      0        0        0        0
#> 26       0       0       0       0       0      0        0        0        0
#> 27       0       0       0       0       0      0        0        0        0
#> 28       0       0       0       0       0      0        0        0        0
#> 29       0       0       0       0       0      0        0        0        0
#> 30       0       0       0       0       0      0        0        0        0
#>    e.num r.num q.num h.num f.num
#> 1     NA    NA    NA    NA    NA
#> 2      1     0     0     0     0
#> 3      1     0     0     0     0
#> 4      1     0     0     0     0
#> 5      2     0     0     0     0
#> 6      3     1     0     0     0
#> 7      5     1     0     0     0
#> 8      7     1     0     0     0
#> 9     11     1     0     0     0
#> 10    14     2     0     0     0
#> 11    NA    NA    NA    NA    NA
#> 12     1     0     0     0     0
#> 13     0     1     0     0     0
#> 14     0     1     0     0     0
#> 15     0     1     0     0     0
#> 16     0     1     0     0     0
#> 17     1     1     0     0     0
#> 18     1     1     0     0     0
#> 19     3     1     0     0     0
#> 20     4     1     0     0     0
#> 21    NA    NA    NA    NA    NA
#> 22     1     0     0     0     0
#> 23     0     1     1     0     0
#> 24     0     1     1     0     0
#> 25     0     1     1     0     0
#> 26     0     1     1     0     0
#> 27     0     1     1     0     0
#> 28     0     1     1     0     0
#> 29     1     1     1     0     0
#> 30     1     1     1     0     0
as.data.frame(mod, sim = 2)
#>    sim time s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow ds.flow
#> 1    2    1   500     1 501       0       0       0         0       0       0
#> 2    2    2   499     1 501       1       0       0         0       0       0
#> 3    2    3   499     1 501       0       1       0         0       0       0
#> 4    2    4   499     1 501       0       0       0         0       0       0
#> 5    2    5   499     1 501       0       0       0         0       0       0
#> 6    2    6   499     1 501       0       0       0         0       0       0
#> 7    2    7   498     1 501       1       0       0         0       0       0
#> 8    2    8   498     1 501       0       0       0         0       0       0
#> 9    2    9   496     1 501       1       0       0         0       0       0
#> 10   2   10   494     2 501       1       0       0         0       0       0
#>    de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow a.q.flow
#> 1        0       0       0       0       0      0        0        0        0
#> 2        0       0       0       0       0      0        0        0        0
#> 3        0       0       0       0       0      0        0        0        0
#> 4        0       0       0       0       0      0        0        0        0
#> 5        0       0       0       0       0      0        0        0        0
#> 6        0       0       0       0       0      0        0        0        0
#> 7        0       0       0       0       0      0        0        0        0
#> 8        0       0       0       0       0      0        0        0        0
#> 9        0       0       0       0       0      0        0        0        0
#> 10       0       0       0       0       0      0        0        0        0
#>    e.num r.num q.num h.num f.num
#> 1     NA    NA    NA    NA    NA
#> 2      1     0     0     0     0
#> 3      0     1     0     0     0
#> 4      0     1     0     0     0
#> 5      0     1     0     0     0
#> 6      0     1     0     0     0
#> 7      1     1     0     0     0
#> 8      1     1     0     0     0
#> 9      3     1     0     0     0
#> 10     4     1     0     0     0

# Time-specific means across simulations
as.data.frame(mod, out = "mean")
#>    time    s.num     i.num num   se.flow   is.flow   iq.flow iq2h.flow hf.flow
#> 1     1 500.0000 1.0000000 501 0.0000000 0.0000000 0.0000000         0       0
#> 2     2 499.0000 1.0000000 501 1.0000000 0.0000000 0.0000000         0       0
#> 3     3 499.0000 0.6666667 501 0.0000000 0.6666667 0.3333333         0       0
#> 4     4 499.0000 0.6666667 501 0.0000000 0.0000000 0.0000000         0       0
#> 5     5 498.6667 0.6666667 501 0.3333333 0.0000000 0.0000000         0       0
#> 6     6 497.6667 1.0000000 501 0.3333333 0.3333333 0.0000000         0       0
#> 7     7 496.6667 1.0000000 501 1.0000000 0.0000000 0.0000000         0       0
#> 8     8 495.6667 1.3333333 501 1.0000000 0.0000000 0.0000000         0       0
#> 9     9 493.0000 1.6666667 501 2.0000000 0.0000000 0.0000000         0       0
#> 10   10 490.3333 2.6666667 501 1.6666667 0.3333333 0.0000000         0       0
#>    ds.flow de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow
#> 1        0       0       0       0       0       0      0        0        0
#> 2        0       0       0       0       0       0      0        0        0
#> 3        0       0       0       0       0       0      0        0        0
#> 4        0       0       0       0       0       0      0        0        0
#> 5        0       0       0       0       0       0      0        0        0
#> 6        0       0       0       0       0       0      0        0        0
#> 7        0       0       0       0       0       0      0        0        0
#> 8        0       0       0       0       0       0      0        0        0
#> 9        0       0       0       0       0       0      0        0        0
#> 10       0       0       0       0       0       0      0        0        0
#>    a.q.flow     e.num     r.num     q.num h.num f.num
#> 1         0       NaN       NaN       NaN   NaN   NaN
#> 2         0 1.0000000 0.0000000 0.0000000     0     0
#> 3         0 0.3333333 0.6666667 0.3333333     0     0
#> 4         0 0.3333333 0.6666667 0.3333333     0     0
#> 5         0 0.6666667 0.6666667 0.3333333     0     0
#> 6         0 1.0000000 1.0000000 0.3333333     0     0
#> 7         0 2.0000000 1.0000000 0.3333333     0     0
#> 8         0 2.6666667 1.0000000 0.3333333     0     0
#> 9         0 5.0000000 1.0000000 0.3333333     0     0
#> 10        0 6.3333333 1.3333333 0.3333333     0     0

# Time-specific standard deviations across simulations
as.data.frame(mod, out = "sd")
#>    time      s.num     i.num num   se.flow   is.flow   iq.flow iq2h.flow
#> 1     1  0.0000000 0.0000000   0 0.0000000 0.0000000 0.0000000         0
#> 2     2  0.0000000 0.0000000   0 0.0000000 0.0000000 0.0000000         0
#> 3     3  0.0000000 0.5773503   0 0.0000000 0.5773503 0.5773503         0
#> 4     4  0.0000000 0.5773503   0 0.0000000 0.0000000 0.0000000         0
#> 5     5  0.5773503 0.5773503   0 0.5773503 0.0000000 0.0000000         0
#> 6     6  2.3094011 1.0000000   0 0.5773503 0.5773503 0.0000000         0
#> 7     7  3.2145503 1.0000000   0 1.0000000 0.0000000 0.0000000         0
#> 8     8  4.9328829 1.5275252   0 1.7320508 0.0000000 0.0000000         0
#> 9     9  7.0000000 2.0816660   0 1.7320508 0.0000000 0.0000000         0
#> 10   10 10.0166528 3.0550505   0 2.0816660 0.5773503 0.0000000         0
#>    hf.flow ds.flow de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow
#> 1        0       0       0       0       0       0       0      0        0
#> 2        0       0       0       0       0       0       0      0        0
#> 3        0       0       0       0       0       0       0      0        0
#> 4        0       0       0       0       0       0       0      0        0
#> 5        0       0       0       0       0       0       0      0        0
#> 6        0       0       0       0       0       0       0      0        0
#> 7        0       0       0       0       0       0       0      0        0
#> 8        0       0       0       0       0       0       0      0        0
#> 9        0       0       0       0       0       0       0      0        0
#> 10       0       0       0       0       0       0       0      0        0
#>    a.i.flow a.q.flow     e.num     r.num     q.num h.num f.num
#> 1         0        0        NA        NA        NA    NA    NA
#> 2         0        0 0.0000000 0.0000000 0.0000000     0     0
#> 3         0        0 0.5773503 0.5773503 0.5773503     0     0
#> 4         0        0 0.5773503 0.5773503 0.5773503     0     0
#> 5         0        0 1.1547005 0.5773503 0.5773503     0     0
#> 6         0        0 1.7320508 0.0000000 0.5773503     0     0
#> 7         0        0 2.6457513 0.0000000 0.5773503     0     0
#> 8         0        0 3.7859389 0.0000000 0.5773503     0     0
#> 9         0        0 5.2915026 0.0000000 0.5773503     0     0
#> 10        0        0 6.8068593 0.5773503 0.5773503     0     0

# Time-specific quantile values across simulations
as.data.frame(mod, out = "qnt", qval = 0.25)
#>    time s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow ds.flow
#> 1     1 500.0   1.0 501     0.0     0.0       0         0       0       0
#> 2     2 499.0   1.0 501     1.0     0.0       0         0       0       0
#> 3     3 499.0   0.5 501     0.0     0.5       0         0       0       0
#> 4     4 499.0   0.5 501     0.0     0.0       0         0       0       0
#> 5     5 498.5   0.5 501     0.0     0.0       0         0       0       0
#> 6     6 497.0   0.5 501     0.0     0.0       0         0       0       0
#> 7     7 495.5   0.5 501     0.5     0.0       0         0       0       0
#> 8     8 494.0   0.5 501     0.0     0.0       0         0       0       0
#> 9     9 490.5   0.5 501     1.0     0.0       0         0       0       0
#> 10   10 486.5   1.0 501     0.5     0.0       0         0       0       0
#>    de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow a.q.flow
#> 1        0       0       0       0       0      0        0        0        0
#> 2        0       0       0       0       0      0        0        0        0
#> 3        0       0       0       0       0      0        0        0        0
#> 4        0       0       0       0       0      0        0        0        0
#> 5        0       0       0       0       0      0        0        0        0
#> 6        0       0       0       0       0      0        0        0        0
#> 7        0       0       0       0       0      0        0        0        0
#> 8        0       0       0       0       0      0        0        0        0
#> 9        0       0       0       0       0      0        0        0        0
#> 10       0       0       0       0       0      0        0        0        0
#>    e.num r.num q.num h.num f.num
#> 1     NA    NA    NA    NA    NA
#> 2    1.0   0.0     0     0     0
#> 3    0.0   0.5     0     0     0
#> 4    0.0   0.5     0     0     0
#> 5    0.0   0.5     0     0     0
#> 6    0.0   1.0     0     0     0
#> 7    0.5   1.0     0     0     0
#> 8    0.5   1.0     0     0     0
#> 9    2.0   1.0     0     0     0
#> 10   2.5   1.0     0     0     0
as.data.frame(mod, out = "qnt", qval = 0.75)
#>    time s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow ds.flow
#> 1     1 500.0   1.0 501     0.0     0.0     0.0         0       0       0
#> 2     2 499.0   1.0 501     1.0     0.0     0.0         0       0       0
#> 3     3 499.0   1.0 501     0.0     1.0     0.5         0       0       0
#> 4     4 499.0   1.0 501     0.0     0.0     0.0         0       0       0
#> 5     5 499.0   1.0 501     0.5     0.0     0.0         0       0       0
#> 6     6 499.0   1.5 501     0.5     0.5     0.0         0       0       0
#> 7     7 498.5   1.5 501     1.5     0.0     0.0         0       0       0
#> 8     8 498.5   2.0 501     1.5     0.0     0.0         0       0       0
#> 9     9 497.0   2.5 501     2.5     0.0     0.0         0       0       0
#> 10   10 496.0   4.0 501     2.5     0.5     0.0         0       0       0
#>    de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow a.q.flow
#> 1        0       0       0       0       0      0        0        0        0
#> 2        0       0       0       0       0      0        0        0        0
#> 3        0       0       0       0       0      0        0        0        0
#> 4        0       0       0       0       0      0        0        0        0
#> 5        0       0       0       0       0      0        0        0        0
#> 6        0       0       0       0       0      0        0        0        0
#> 7        0       0       0       0       0      0        0        0        0
#> 8        0       0       0       0       0      0        0        0        0
#> 9        0       0       0       0       0      0        0        0        0
#> 10       0       0       0       0       0      0        0        0        0
#>    e.num r.num q.num h.num f.num
#> 1     NA    NA    NA    NA    NA
#> 2    1.0   0.0   0.0     0     0
#> 3    0.5   1.0   0.5     0     0
#> 4    0.5   1.0   0.5     0     0
#> 5    1.0   1.0   0.5     0     0
#> 6    1.5   1.0   0.5     0     0
#> 7    3.0   1.0   0.5     0     0
#> 8    4.0   1.0   0.5     0     0
#> 9    7.0   1.0   0.5     0     0
#> 10   9.0   1.5   0.5     0     0