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update test output
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@kingaa
kingaa committed Apr 30, 2024
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1 change: 1 addition & 0 deletions CRAN.md
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Expand Up @@ -31,6 +31,7 @@ git push github v4.6
- perform extra checks:
- `make xcheck`
- `make ycheck`
- `make rchk`
- `make vcheck` and examine `valgrind` output in `pomp-Ex.Rout` for evidence of memory leaks.
- `make revdeps`

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12 changes: 6 additions & 6 deletions tests/R_v_C.Rout
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Expand Down Expand Up @@ -109,16 +109,16 @@ Type 'q()' to quit R.
> ## ----comparison----------------------------------------------------------
> system.time(simulate(gompertz,nsim=10000,format="arrays"))
user system elapsed
6.806 0.114 6.921
5.299 0.032 5.331
> system.time(simulate(Gompertz,nsim=10000,format="arrays"))
user system elapsed
0.161 0.001 0.162
0.141 0.017 0.159
> system.time(pfilter(gompertz,Np=1000))
user system elapsed
0.642 0.013 0.655
0.541 0.000 0.540
> system.time(pfilter(Gompertz,Np=1000))
user system elapsed
0.029 0.001 0.029
0.028 0.000 0.028
>
> dev.off()
null device
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4 changes: 2 additions & 2 deletions tests/abc.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/baddm.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/bake.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/basic_probes.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/betabinom.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/blowflies.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/bsmc2.Rout.save
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@@ -1,7 +1,7 @@

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/bsplines1.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/bsplines2.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/concat.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/covmat.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/csnippet.Rout.save
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@@ -1,7 +1,7 @@

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/dacca.Rout.save
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@@ -1,7 +1,7 @@

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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48 changes: 24 additions & 24 deletions tests/defunct.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Expand All @@ -20,91 +20,91 @@ Type 'q()' to quit R.
> library(pomp)
>
> try(as.pomp())
Error : 'as.pomp' is defunct.
Error in as.pomp() : 'as.pomp' is defunct.
Use 'as_pomp' instead.
See help("Defunct")
> try(bspline.basis())
Error : 'bspline.basis' is defunct.
Error in bspline.basis() : 'bspline.basis' is defunct.
Use 'bspline_basis' instead.
See help("Defunct")
> try(cond.logLik())
Error : 'cond.logLik' is defunct.
Error in cond.logLik() : 'cond.logLik' is defunct.
Use 'cond_logLik' instead.
See help("Defunct")
> try(eff.sample.size())
Error : 'eff.sample.size' is defunct.
Error in eff.sample.size() : 'eff.sample.size' is defunct.
Use 'eff_sample_size' instead.
See help("Defunct")
> try(mvn.diag.rw())
Error : 'mvn.diag.rw' is defunct.
Error in mvn.diag.rw() : 'mvn.diag.rw' is defunct.
Use 'mvn_diag_rw' instead.
See help("Defunct")
> try(mvn.rw())
Error : 'mvn.rw' is defunct.
Error in mvn.rw() : 'mvn.rw' is defunct.
Use 'mvn_rw' instead.
See help("Defunct")
> try(mvn.rw.adaptive())
Error : 'mvn.rw.adaptive' is defunct.
Error in mvn.rw.adaptive() : 'mvn.rw.adaptive' is defunct.
Use 'mvn_rw_adaptive' instead.
See help("Defunct")
> try(periodic.bspline.basis())
Error : 'periodic.bspline.basis' is defunct.
Error in periodic.bspline.basis() : 'periodic.bspline.basis' is defunct.
Use 'periodic_bspline_basis' instead.
See help("Defunct")
> try(pred.mean())
Error : 'pred.mean' is defunct.
Error in pred.mean() : 'pred.mean' is defunct.
Use 'pred_mean' instead.
See help("Defunct")
> try(pred.var())
Error : 'pred.var' is defunct.
Error in pred.var() : 'pred.var' is defunct.
Use 'pred_var' instead.
See help("Defunct")
> try(probe.acf())
Error : 'probe.acf' is defunct.
Error in probe.acf() : 'probe.acf' is defunct.
Use 'probe_acf' instead.
See help("Defunct")
> try(probe.ccf())
Error : 'probe.ccf' is defunct.
Error in probe.ccf() : 'probe.ccf' is defunct.
Use 'probe_ccf' instead.
See help("Defunct")
> try(probe.marginal())
Error : 'probe.marginal' is defunct.
Error in probe.marginal() : 'probe.marginal' is defunct.
Use 'probe_marginal' instead.
See help("Defunct")
> try(probe.mean())
Error : 'probe.mean' is defunct.
Error in probe.mean() : 'probe.mean' is defunct.
Use 'probe_mean' instead.
See help("Defunct")
> try(probe.median())
Error : 'probe.median' is defunct.
Error in probe.median() : 'probe.median' is defunct.
Use 'probe_median' instead.
See help("Defunct")
> try(probe.nlar())
Error : 'probe.nlar' is defunct.
Error in probe.nlar() : 'probe.nlar' is defunct.
Use 'probe_nlar' instead.
See help("Defunct")
> try(probe.period())
Error : 'probe.period' is defunct.
Error in probe.period() : 'probe.period' is defunct.
Use 'probe_period' instead.
See help("Defunct")
> try(probe.quantile())
Error : 'probe.quantile' is defunct.
Error in probe.quantile() : 'probe.quantile' is defunct.
Use 'probe_quantile' instead.
See help("Defunct")
> try(probe.sd())
Error : 'probe.sd' is defunct.
Error in probe.sd() : 'probe.sd' is defunct.
Use 'probe_sd' instead.
See help("Defunct")
> try(probe.var())
Error : 'probe.var' is defunct.
Error in probe.var() : 'probe.var' is defunct.
Use 'probe_var' instead.
See help("Defunct")
> try(rw.sd())
Error : 'rw.sd' is defunct.
Error in rw.sd() : 'rw.sd' is defunct.
Use 'rw_sd' instead.
See help("Defunct")
> try(saved.states())
Error : 'saved.states' is defunct.
Error in saved.states() : 'saved.states' is defunct.
Use 'saved_states' instead.
See help("Defunct")
>
4 changes: 2 additions & 2 deletions tests/dinit.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/dp.Rout.save
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@@ -1,7 +1,7 @@

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Expand Down
4 changes: 2 additions & 2 deletions tests/dprocess.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/ebola.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Expand Down
4 changes: 2 additions & 2 deletions tests/emeasure.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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4 changes: 2 additions & 2 deletions tests/eulermultinom.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Expand Down
4 changes: 2 additions & 2 deletions tests/flow.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Expand Down
4 changes: 2 additions & 2 deletions tests/gillespie.Rout.save
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R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Expand Down
4 changes: 2 additions & 2 deletions tests/gompertz.Rout.save
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@@ -1,7 +1,7 @@

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Expand Down
4 changes: 2 additions & 2 deletions tests/helpers.Rout.save
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@@ -1,7 +1,7 @@

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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