Real-time Rt Estimation, Forecasting and Reporting

Source: R/epinow.R

[Maturing] This function wraps the functionality of estimate_infections() and forecast_infections() in order to estimate Rt and cases by date of infection, forecast into these infections into the future. It also contains additional functionality to convert forecasts to date of report and produce summary output useful for reporting results and interpreting them. See here for an example of using epinow to estimate Rt for Covid-19 in a country from the ECDC data source.

epinow(
  reported_cases,
  generation_time,
  delays = delay_opts(),
  truncation = trunc_opts(),
  rt = rt_opts(),
  backcalc = backcalc_opts(),
  gp = gp_opts(),
  obs = obs_opts(),
  stan = stan_opts(),
  horizon = 7,
  CrIs = c(0.2, 0.5, 0.9),
  zero_threshold = 50,
  return_output = FALSE,
  output = c("samples", "plots", "latest", "fit", "timing"),
  target_folder = NULL,
  target_date,
  forecast_args = NULL,
  logs = tempdir(),
  id = "epinow",
  verbose = interactive()
)

Arguments

reported_cases

A data frame of confirmed cases (confirm) by date (date). confirm must be integer and date must be in date format.
generation_time

A list containing the mean, standard deviation of the mean (mean_sd), standard deviation (sd), standard deviation of the standard deviation and the maximum allowed value for the generation time (assuming a gamma distribution).
delays

A call to delay_opts() defining delay distributions and options. See the documentation of delay_opts() and the examples below for details.
truncation

[Experimental] A list of options as generated by trunc_opts() defining the truncation of observed data. Defaults to trunc_opts(). See estimate_truncation() for an approach to estimating truncation from data.
rt

A list of options as generated by rt_opts() defining Rt estimation. Defaults to rt_opts(). Set to NULL to switch to using back calculation rather than generating infections using Rt.
backcalc

A list of options as generated by backcalc_opts() to define the back calculation. Defaults to backcalc_opts().
gp

A list of options as generated by gp_opts() to define the Gaussian process. Defaults to gp_opts().Set to NULL to disable the Gaussian process.
obs

A list of options as generated by obs_opts() defining the observation model. Defaults to obs_opts().
stan

A list of stan options as generated by stan_opts(). Defaults to stan_opts(). Can be used to override data, init, and verbose settings if desired.
horizon

Numeric, defaults to 7. Number of days into the future to forecast.
CrIs

Numeric vector of credible intervals to calculate.
zero_threshold

[Experimental] Numeric defaults to 50. Indicates if detected zero cases are meaningful by using a threshold of 50 cases on average over the last 7 days. If the average is above this threshold then the zero is replaced with the backwards looking rolling average. If set to infinity then no changes are made.
return_output

Logical, defaults to FALSE. Should output be returned, this automatically updates to TRUE if no directory for saving is specified.
output

A character vector of optional output to return. Supported options are samples ("samples"), plots ("plots"), the run time ("timing"), copying the dated folder into a latest folder (if target_folder is not null, set using "latest"), and the stan fit ("fit"). The default is to return all options. This argument uses partial matching so for example passing "sam" will lead to samples being reported.
target_folder

Character string specifying where to save results (will create if not present).
target_date

Date, defaults to maximum found in the data if not specified.
forecast_args

A list of arguments to pass to forecast_infections(). Unless at a minimum a forecast_model is passed then forecast_infections will be bypassed.
logs

Character path indicating the target folder in which to store log information. Defaults to the temporary directory if not specified. Default logging can be disabled if logs is set to NULL. If specifying a custom logging setup then the code for setup_default_logging and the setup_logging function are a sensible place to start.
id

A character string used to assign logging information on error. Used by regional_epinow to assign errors to regions. Alter the default to run with error catching.
verbose

Logical, defaults to TRUE when used interactively and otherwise FALSE. Should verbose debug progress messages be printed. Corresponds to the "DEBUG" level from futile.logger. See setup_logging for more detailed logging options.

Value

A list of output from estimate_infections, forecast_infections, report_cases, and report_summary.

See also

estimate_infections simulate_infections forecast_infections regional_epinow

Examples

# \donttest{
# set number of cores to use
options(mc.cores = ifelse(interactive(), 4, 1))
# construct example distributions
generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
incubation_period <- get_incubation_period(disease = "SARS-CoV-2", source = "lauer")
reporting_delay <- list(
  mean = convert_to_logmean(2, 1),
  mean_sd = 0.1,
  sd = convert_to_logsd(2, 1),
  sd_sd = 0.1,
  max = 10
)

# example case data
reported_cases <- example_confirmed[1:40]

# estimate Rt and nowcast/forecast cases by date of infection
out <- epinow(
  reported_cases = reported_cases, generation_time = generation_time,
  rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
  delays = delay_opts(incubation_period, reporting_delay)
)
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpw97Blo/regional-epinow/2020-04-01.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to the console and: /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//Rtmpw97Blo/epinow/2020-04-01.log
#> WARN [2021-06-17 03:02:19] epinow: There were 19 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them. - 
#> WARN [2021-06-17 03:02:19] epinow: Examine the pairs() plot to diagnose sampling problems
#>  - 
# summary of the latest estimates
summary(out)
#>                                  measure               estimate
#> 1: New confirmed cases by infection date    3102 (1297 -- 6910)
#> 2:        Expected change in daily cases      Likely decreasing
#> 3:            Effective reproduction no.     0.75 (0.49 -- 1.1)
#> 4:                        Rate of growth -0.07 (-0.16 -- 0.022)
#> 5:          Doubling/halving time (days)      -9.9 (31 -- -4.4)
# plot estimates
plot(out)


# summary of R estimates
summary(out, type = "parameters", params = "R")
#>           date variable strat                           type    median
#>  1: 2020-02-22        R  <NA>                       estimate 2.0400235
#>  2: 2020-02-23        R  <NA>                       estimate 2.0317500
#>  3: 2020-02-24        R  <NA>                       estimate 2.0197935
#>  4: 2020-02-25        R  <NA>                       estimate 2.0028885
#>  5: 2020-02-26        R  <NA>                       estimate 1.9846100
#>  6: 2020-02-27        R  <NA>                       estimate 1.9644733
#>  7: 2020-02-28        R  <NA>                       estimate 1.9383530
#>  8: 2020-02-29        R  <NA>                       estimate 1.9104295
#>  9: 2020-03-01        R  <NA>                       estimate 1.8791831
#> 10: 2020-03-02        R  <NA>                       estimate 1.8462847
#> 11: 2020-03-03        R  <NA>                       estimate 1.8111220
#> 12: 2020-03-04        R  <NA>                       estimate 1.7738176
#> 13: 2020-03-05        R  <NA>                       estimate 1.7340597
#> 14: 2020-03-06        R  <NA>                       estimate 1.6940317
#> 15: 2020-03-07        R  <NA>                       estimate 1.6533648
#> 16: 2020-03-08        R  <NA>                       estimate 1.6115351
#> 17: 2020-03-09        R  <NA>                       estimate 1.5688942
#> 18: 2020-03-10        R  <NA>                       estimate 1.5247661
#> 19: 2020-03-11        R  <NA>                       estimate 1.4806071
#> 20: 2020-03-12        R  <NA>                       estimate 1.4340833
#> 21: 2020-03-13        R  <NA>                       estimate 1.3885703
#> 22: 2020-03-14        R  <NA>                       estimate 1.3423512
#> 23: 2020-03-15        R  <NA>                       estimate 1.2957401
#> 24: 2020-03-16        R  <NA>                       estimate 1.2493432
#> 25: 2020-03-17        R  <NA>                       estimate 1.2050926
#> 26: 2020-03-18        R  <NA>                       estimate 1.1612819
#> 27: 2020-03-19        R  <NA>                       estimate 1.1189929
#> 28: 2020-03-20        R  <NA>                       estimate 1.0778897
#> 29: 2020-03-21        R  <NA>                       estimate 1.0386724
#> 30: 2020-03-22        R  <NA>                       estimate 1.0009712
#> 31: 2020-03-23        R  <NA>                       estimate 0.9661975
#> 32: 2020-03-24        R  <NA>                       estimate 0.9337842
#> 33: 2020-03-25        R  <NA>                       estimate 0.9042709
#> 34: 2020-03-26        R  <NA> estimate based on partial data 0.8778950
#> 35: 2020-03-27        R  <NA> estimate based on partial data 0.8524504
#> 36: 2020-03-28        R  <NA> estimate based on partial data 0.8295114
#> 37: 2020-03-29        R  <NA> estimate based on partial data 0.8064282
#> 38: 2020-03-30        R  <NA> estimate based on partial data 0.7872069
#> 39: 2020-03-31        R  <NA> estimate based on partial data 0.7707662
#> 40: 2020-04-01        R  <NA> estimate based on partial data 0.7544764
#> 41: 2020-04-02        R  <NA>                       forecast 0.7544764
#> 42: 2020-04-03        R  <NA>                       forecast 0.7544764
#> 43: 2020-04-04        R  <NA>                       forecast 0.7544764
#> 44: 2020-04-05        R  <NA>                       forecast 0.7544764
#> 45: 2020-04-06        R  <NA>                       forecast 0.7544764
#> 46: 2020-04-07        R  <NA>                       forecast 0.7544764
#> 47: 2020-04-08        R  <NA>                       forecast 0.7544764
#>           date variable strat                           type    median
#>          mean         sd  lower_90  lower_50  lower_20  upper_20  upper_50
#>  1: 2.0431307 0.09247615 1.8970949 1.9792808 2.0170224 2.0644295 2.1048274
#>  2: 2.0336035 0.08236873 1.9050539 1.9751596 2.0116093 2.0524191 2.0885483
#>  3: 2.0212853 0.07770371 1.8989413 1.9686632 2.0012495 2.0378172 2.0717823
#>  4: 2.0058769 0.07624102 1.8832594 1.9544088 1.9855922 2.0219334 2.0544507
#>  5: 1.9872152 0.07578078 1.8667615 1.9367351 1.9676469 2.0052123 2.0335810
#>  6: 1.9652765 0.07497266 1.8439721 1.9159453 1.9450567 1.9818530 2.0124239
#>  7: 1.9401616 0.07331726 1.8206510 1.8922866 1.9205888 1.9558345 1.9847983
#>  8: 1.9120680 0.07084776 1.7976209 1.8661829 1.8938738 1.9269076 1.9569083
#>  9: 1.8812581 0.06782536 1.7728623 1.8376516 1.8620475 1.8960761 1.9245138
#> 10: 1.8480260 0.06454449 1.7444996 1.8054464 1.8285491 1.8620203 1.8891473
#> 11: 1.8126713 0.06125250 1.7154533 1.7720083 1.7950577 1.8257348 1.8512735
#> 12: 1.7754783 0.05815268 1.6830824 1.7379158 1.7600432 1.7868851 1.8125401
#> 13: 1.7367025 0.05543777 1.6496317 1.7003583 1.7227618 1.7477938 1.7721722
#> 14: 1.6965633 0.05330061 1.6107763 1.6616189 1.6822592 1.7086859 1.7322341
#> 15: 1.6552417 0.05189098 1.5725029 1.6203870 1.6412752 1.6666398 1.6894070
#> 16: 1.6128831 0.05123351 1.5305681 1.5782804 1.5994401 1.6247808 1.6461951
#> 17: 1.5696066 0.05117035 1.4861955 1.5350197 1.5574543 1.5809243 1.6023645
#> 18: 1.5255182 0.05139529 1.4433306 1.4917797 1.5130189 1.5368457 1.5578517
#> 19: 1.4807288 0.05157695 1.3973684 1.4468043 1.4679544 1.4914387 1.5120035
#> 20: 1.4353710 0.05149308 1.3526875 1.4023935 1.4226948 1.4458921 1.4663832
#> 21: 1.3896115 0.05109225 1.3082142 1.3559406 1.3763709 1.3998808 1.4208003
#> 22: 1.3436568 0.05045745 1.2628479 1.3094009 1.3306712 1.3539168 1.3744914
#> 23: 1.2977514 0.04971503 1.2190261 1.2646907 1.2843627 1.3068625 1.3284003
#> 24: 1.2521704 0.04896876 1.1757242 1.2200902 1.2380808 1.2618185 1.2826368
#> 25: 1.2072108 0.04831812 1.1343802 1.1757771 1.1934108 1.2167218 1.2360024
#> 26: 1.1631816 0.04795435 1.0910703 1.1324155 1.1506548 1.1724229 1.1903811
#> 27: 1.1203947 0.04826018 1.0458026 1.0896869 1.1083022 1.1301330 1.1478405
#> 28: 1.0791552 0.04980966 1.0017969 1.0482312 1.0659956 1.0895968 1.1082403
#> 29: 1.0397499 0.05320488 0.9557678 1.0056320 1.0269493 1.0507130 1.0718569
#> 30: 1.0024366 0.05882801 0.9059877 0.9645664 0.9872198 1.0151189 1.0389320
#> 31: 0.9674339 0.06671136 0.8558535 0.9236115 0.9495405 0.9824761 1.0099048
#> 32: 0.9349146 0.07661372 0.8086640 0.8844013 0.9150073 0.9529859 0.9846860
#> 33: 0.9050019 0.08818294 0.7604811 0.8468416 0.8824836 0.9256346 0.9623306
#> 34: 0.8777699 0.10107523 0.7110990 0.8106475 0.8521390 0.9021626 0.9431304
#> 35: 0.8532470 0.11500742 0.6645234 0.7766434 0.8239244 0.8796309 0.9270434
#> 36: 0.8314196 0.12976777 0.6204354 0.7474803 0.7976432 0.8611757 0.9115458
#> 37: 0.8122373 0.14520469 0.5824028 0.7190311 0.7717733 0.8430448 0.9032621
#> 38: 0.7956172 0.16120065 0.5486171 0.6943416 0.7480549 0.8270830 0.8928107
#> 39: 0.7814477 0.17763846 0.5160527 0.6699588 0.7294695 0.8122628 0.8843682
#> 40: 0.7695919 0.19437165 0.4867514 0.6469803 0.7116256 0.7991536 0.8781084
#> 41: 0.7695919 0.19437165 0.4867514 0.6469803 0.7116256 0.7991536 0.8781084
#> 42: 0.7695919 0.19437165 0.4867514 0.6469803 0.7116256 0.7991536 0.8781084
#> 43: 0.7695919 0.19437165 0.4867514 0.6469803 0.7116256 0.7991536 0.8781084
#> 44: 0.7695919 0.19437165 0.4867514 0.6469803 0.7116256 0.7991536 0.8781084
#> 45: 0.7695919 0.19437165 0.4867514 0.6469803 0.7116256 0.7991536 0.8781084
#> 46: 0.7695919 0.19437165 0.4867514 0.6469803 0.7116256 0.7991536 0.8781084
#> 47: 0.7695919 0.19437165 0.4867514 0.6469803 0.7116256 0.7991536 0.8781084
#>          mean         sd  lower_90  lower_50  lower_20  upper_20  upper_50
#>     upper_90
#>  1: 2.200408
#>  2: 2.171737
#>  3: 2.149988
#>  4: 2.130832
#>  5: 2.111638
#>  6: 2.089965
#>  7: 2.065433
#>  8: 2.032571
#>  9: 1.995337
#> 10: 1.958400
#> 11: 1.917753
#> 12: 1.871719
#> 13: 1.829821
#> 14: 1.784894
#> 15: 1.743411
#> 16: 1.700176
#> 17: 1.652454
#> 18: 1.607861
#> 19: 1.563655
#> 20: 1.520413
#> 21: 1.477276
#> 22: 1.430788
#> 23: 1.385297
#> 24: 1.337182
#> 25: 1.290787
#> 26: 1.245013
#> 27: 1.201230
#> 28: 1.163773
#> 29: 1.131899
#> 30: 1.101821
#> 31: 1.077396
#> 32: 1.060440
#> 33: 1.053679
#> 34: 1.046287
#> 35: 1.043351
#> 36: 1.045082
#> 37: 1.050516
#> 38: 1.060150
#> 39: 1.068934
#> 40: 1.084516
#> 41: 1.084516
#> 42: 1.084516
#> 43: 1.084516
#> 44: 1.084516
#> 45: 1.084516
#> 46: 1.084516
#> 47: 1.084516
#>     upper_90
# }