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Type 'q()' to quit R. > # 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) INFORMATION: Es konnten keine Dateien mit dem angegebenen Muster gefunden werden. JAGS version 4.3.1 installed. rjags version 4-15 installed. > > 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: 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: 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: 8 iterations Richardson-Lucy deconvolution: 9 iterations Richardson-Lucy deconvolution: 9 iterations Richardson-Lucy deconvolution: 8 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 0 | SKIP 0 | PASS 176 ] > > proc.time() user system elapsed 38.85 0.70 42.60