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Higher contact rate error #14

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sima-u1418987 opened this issue Apr 6, 2024 · 8 comments · Fixed by #15
Closed

Higher contact rate error #14

sima-u1418987 opened this issue Apr 6, 2024 · 8 comments · Fixed by #15

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@sima-u1418987
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sima-u1418987 commented Apr 6, 2024 •
edited by gvegayon
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result <- suppressWarnings(suppressMessages(invisible({
  
  library(epiworldR)
  
  library(data.table)
  library(EpiEstim)
  library(dplyr)
  library(ggplot2)
  library(tidyverse)
  library(EpiNow2)
})))


model_seircon=ModelSEIRCONN(name="covid",n=50000,prevalence = 0.001,contact_rate = 20,transmission_rate = 0.5,recovery_rate = 1/7,incubation_days = 3)





run(model_seircon,ndays=50,seed=1912)
#> _________________________________________________________________________
#> |Running the model...
#> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
#> | done.
summary(model_seircon)
#> ________________________________________________________________________________
#> ________________________________________________________________________________
#> SIMULATION STUDY
#> 
#> Name of the model   : Susceptible-Exposed-Infected-Removed (SEIR) (connected)
#> Population size     : 50000
#> Agents' data        : (none)
#> Number of entities  : 0
#> Days (duration)     : 50 (of 50)
#> Number of viruses   : 1
#> Last run elapsed t  : 473.00ms
#> Last run speed      : 5.28 million agents x day / second
#> Rewiring            : off
#> 
#> Global events:
#>  (none)
#> 
#> Virus(es):
#>  - covid (baseline prevalence: 0.10%)
#> 
#> Tool(s):
#>  (none)
#> 
#> Model parameters:
#>  - Avg. Incubation days : 3.0000
#>  - Contact rate         : 20.0000
#>  - Prob. Recovery       : 0.1429
#>  - Prob. Transmission   : 0.5000
#> 
#> Distribution of the population at time 50:
#>   - (0) Susceptible : 49950 -> 0
#>   - (1) Exposed     :    50 -> 0
#>   - (2) Infected    :     0 -> 140
#>   - (3) Recovered   :     0 -> 49860
#> 
#> Transition Probabilities:
#>  - Susceptible  0.60  0.40  0.00  0.00
#>  - Exposed      0.00  0.66  0.34  0.00
#>  - Infected     0.00  0.00  0.86  0.14
#>  - Recovered    0.00  0.00  0.00  1.00



plot(model_seircon)



saver <- make_saver(
  "total_hist",
  "transmission",
  "transition",
  "reproductive",
  "generation"
)
run_multiple(model_seircon,ndays=50,nsim=100,seed=1972,saver=saver)
#> Starting multiple runs (100) using 1 thread(s)
#> _________________________________________________________________________
#> _________________________________________________________________________
#> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
#>  done.


res1 <- run_multiple_get_results(model_seircon)
#> Warning in run_multiple_get_results(model_seircon): When retrieving the saved
#> results, for the case of transmission, there were no observations.
#> Error in attributes(.Data) <- c(attributes(.Data), attrib): all attributes must have names [4 does not]
res1$reproductive
#> Error in eval(expr, envir, enclos): object 'res1' not found
@gvegayon
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gvegayon commented Apr 7, 2024

Thanks for posting this, @sima-u1418987!

@gvegayon gvegayon transferred this issue from UofUEpiBio/covid19-abm Apr 7, 2024
@gvegayon
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gvegayon commented Apr 7, 2024

The issue happens when run_multiple is run after run(). It may have something to do with reset.

gvegayon added a commit that referenced this issue Apr 7, 2024
@gvegayon
Adding test for run_multiple after run [skip ci] (see #14)
7b21bde
@sima-u1418987
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sima-u1418987 commented Apr 7, 2024 via email

@gvegayon gvegayon linked a pull request Apr 7, 2024 that will close this issue
14 higher contact rate error #15
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gvegayon added a commit that referenced this issue Apr 7, 2024
@gvegayon
14 higher contact rate error (#15)
47a9c80 
* Adding proper way to handle classes

* Adding test for run_multiple after run [skip ci] (see #14)

* Updating version and adding test
@gvegayon
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gvegayon commented Apr 7, 2024

OK @sima-u1418987. I've fixed the issue. The problem was that agents' states were not being reset. This only happened when you called run() before run_multiple(). The bug is now fixed (agents' states are always reset). You can either try to install the development version following the instructions here. @derekmeyer37, we need to upload the patch soon. I'll send you the targz file.

@sima-u1418987
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sima-u1418987 commented Apr 8, 2024 via email

@gvegayon
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gvegayon commented Apr 8, 2024

Did you install the GitHub version? I don't get Rt=0

@derekmeyer37
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derekmeyer37 commented Apr 8, 2024 •
edited
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@sima-u1418987
You will want to run the github version of the package until the fixed version is available on CRAN. You can do this by installing the package using:
devtools::install_github("UofUEpiBio/epiworldR")

Then, load the epiworldR library using: 
library(epiworldR)

Let us know if this works for you. 

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sima-u1418987 commented Apr 8, 2024 via email

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14 higher contact rate error UofUEpiBio/epiworldR
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@gvegayon @derekmeyer37 @sima-u1418987