R Under development (unstable) (2024-01-28 r85838 ucrt) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(ern)

ern version: 1.3.1 

If not already installed, software JAGS is recommended. 
(https://sourceforge.net/projects/mcmc-jags/files/)

> 
> test_check("ern")
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 8
   Unobserved stochastic nodes: 58
   Total graph size: 790

Initializing model

Wastewater data smoothed using loess method
iterations Richardson-Lucy deconvolution:  20
-----
The clinical testing data you input is not daily. `ern` requires daily data to compute Rt. `ern` will infer daily reports from your inputs. See `prm.daily` and `prm.daily.check` arguments of `estimate_R_cl()` for daily inference options.
-----
Assuming the first observed report (from 2020-03-14)
is aggregated over 7 previous days
(second observation's aggregation period).
This can be changed in `estimate_R_cl()`, using the
`prm.daily` argument (set a value for `first.agg.period`
in this parameter list).
-----
Running MCMC model to infer daily reports from aggregated reports...

Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 8
   Unobserved stochastic nodes: 58
   Total graph size: 790

Initializing model

- Filtering out any daily inferred reports associated
with inferred aggregates outside of the specified tolerance of 10%...
Before filtering: 56 daily reports
After filtering:  42 daily reports
To reduce the number of observations dropped in filtering, either:
  - adjust MCMC parameters in prm.daily (burn, iter, chains) to
      improve chances of MCMC convergence,
  - increase tolerance for this check (prm.daily.check$agg.reldiff.tol)
Using default config in `EpiEstim::estimate_R()`.
Deconvolution reporting delays...
iterations Richardson-Lucy deconvolution:  10
Deconvolution incubation period...
iterations Richardson-Lucy deconvolution:  10
Using default config in `EpiEstim::estimate_R()`.
Deconvolution reporting delays...
iterations Richardson-Lucy deconvolution:  10
Deconvolution incubation period...
iterations Richardson-Lucy deconvolution:  10
Deconvolution reporting delays...
iterations Richardson-Lucy deconvolution:  8
Deconvolution incubation period...
iterations Richardson-Lucy deconvolution:  10
Using default config in `EpiEstim::estimate_R()`.
Deconvolution reporting delays...
iterations Richardson-Lucy deconvolution:  10
Deconvolution incubation period...
iterations Richardson-Lucy deconvolution:  10
Deconvolution reporting delays...
iterations Richardson-Lucy deconvolution:  10
Deconvolution incubation period...
iterations Richardson-Lucy deconvolution:  10
iterations Richardson-Lucy deconvolution:  9
Deconvolution incubation period...
iterations Richardson-Lucy deconvolution:  9
Wastewater data smoothed using loess method
Wastewater data smoothed using loess method
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9
iterations Richardson-Lucy deconvolution:  9

ERROR: `si_distr` must be specified in `config.EpiEstim`. ABORTING!
Wastewater data smoothed using loess method
Wastewater data smoothed using rollmean method
[ FAIL 0 | WARN 300 | SKIP 0 | PASS 176 ]

[ FAIL 0 | WARN 300 | SKIP 0 | PASS 176 ]
> 
> proc.time()
   user  system elapsed 
  65.23    1.31   69.67