Efficient model #5
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
storopoli
suggested changes
Jul 27, 2021
runEval.Rmd
Outdated
| # Data Generating Process | ||
|
|
||
| The data generating process simulates a fixed population at the individual level on a daily basis. Larger or smaller uniform units could be used. | ||
| The data generating process simulates a fixed population at the individual level on a daily basis. There are a series of simulating DGPs with varied properties. This document covers a DGP that closely mirrors the compartment model structure with real valued compartments with population transfers between states computed via real valued multiplication on each day of the simulation. There is no stochastic element at all in this simulation since it serves as a baseline for more complex models which will have stochastic (random) elements as well as operating on different scales, e.g., agent-based models. |
Contributor
There was a problem hiding this comment.
What is real-valued multiplication? Very confusing...
| # Running simulation and fitting a model | ||
|
|
||
| ```{r echo=TRUE} | ||
| Below we go over how to setup and run the simulation code that generates data and runs experiments. The central code is in `R/runEval.R` with use of functions in `R/util.R` for printing/graphing functions, `R/data_configs.R` for code that creates data via simulation or provides actual data, `R/modeling_configs.R` for code that configures parameters for modeling software and `R/SIRTDsim.R` that contains simulation software and is called from functions in `R/data_configs.R`. The libraries and dependencies are: |
Contributor
There was a problem hiding this comment.
I could'n find data_configs.R. Aren't you mistaken it for sim_configs.R?
| The `sim_brazil_1` is a parameterization that roughly mimics the shape of the COVID-19 outbreak with corresponding simulated values as determined by trying values by hand. Look at the source for more info. Note that the prefix on the function is 'sim', which means that it is part of simulation. There is still one row in the dataframe but with simulation data and the generating paramaterzation. | ||
|
|
||
| ### Adding simulation parameters | ||
| The, remember transposed, dataframe is: |
Contributor
There was a problem hiding this comment.
Aren't you being pedantic? This is the third time you mention "transposed" in less than 10 lines?
runEval.Rmd
Outdated
| kable(t(run_df), digits=3) | ||
| ``` | ||
|
|
||
| We now have simulation data from the SIRTD model for `n_days`. But still only one row--remember transposed above. |
Contributor
There was a problem hiding this comment.
Again, 4th time in less than 15 lines
runEval.Rmd
Outdated
| ``` | ||
|
|
||
| ## Running the simulation | ||
| Above are transposed output for two draws for slight variations of the Brazil hand parameterization. |
Contributor
There was a problem hiding this comment.
What is "Brazil hand parameterization"? Isn't it better to say "custom"?
runEval.Rmd
Outdated
| ## Running non-simulated data | ||
| ## Setting up modeling | ||
|
|
||
| At this point we have three sets of data, one hand configured to mirror Brazil data and two that vary simulation parameters from the hand configured model. Now we apply modeling configurations with subroutines from `R/modeling_configs.R`. |
Contributor
There was a problem hiding this comment.
"custom" instead of "hand"?
runEval.Rmd
Outdated
| ``` | ||
|
|
||
| ## Configuring modeling | ||
| There are two model configurations which apply to the three rows uniformly so we end up with 6 configurations total. One model applies tweets to the task, and one does not. The final result is: |
| ```{r} | ||
| cat(pull_section('# section 5', here::here('R','runEval.R'))) | ||
| cat(pull_section('# run models', here::here('R','runEval.R'))) | ||
| ``` |
Contributor
There was a problem hiding this comment.
Which models are these? Maybe add them?
storopoli
suggested changes
Jul 27, 2021
Contributor
storopoli
left a comment
storopoli
left a comment
There was a problem hiding this comment.
Breck, I did some changes and added some comments. See if you agree. Also please address the comments. They are stuff that either I got confused reading or I am pointing that should be careful thought...
…ratingProcess1 into efficient_model
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fairly large overhaul of the simulation code, runEval.R, runEval.Rmd and so on.