This issue is to request a "Quick start" section in the Readme to show users how to get started with accessing and extracting parameters from the database for use in downstream analyses. A small example of conversion to the {epiparameter} class <epidist> is shown here.
library(epireview)
#> Loading required package: epitrix
#> Loading required package: ggplot2
#> Loading required package: ggforce
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
data = load_epidata("ebola")
#> Warning: One or more parsing issues, call `problems()` on your data frame for details,
#> e.g.:
#> dat <- vroom(...)
#> problems(dat)
#> Warning in load_epidata_raw(pathogen, "outbreak"): No data found for ebola
#> Warning: One or more parsing issues, call `problems()` on your data frame for details,
#> e.g.:
#> dat <- vroom(...)
#> problems(dat)
#> Warning in load_epidata("ebola"): No outbreaks information found for ebola
#> Data loaded for ebola
names(data)
#> [1] "articles" "params" "models" "outbreaks"
param_data = data$params
# get all onset to death distribution data
# select high quality with Gamma dist
param_data = filter(
param_data,
parameter_type == "Human delay - Symptom Onset/Fever to Death",
distribution_type == "Gamma",
article_qa_score > 50
) %>%
head(1)
# transform to epidist
# NOTE which parameters are used for uncertainty
# this differs between studies/entries
onset_to_death_mean = pull(param_data, parameter_value)
onset_to_death_sd = pull(param_data, distribution_par2_value)
# assume a Gamma distribution?
dist_params = epiparameter::convert_summary_stats_to_params(
x = "gamma",
mean = onset_to_death_mean,
sd = onset_to_death_sd
)
# select one with shape and scale
epidist_ebola_otd = epiparameter::epidist(
"Ebola virus disease",
"Ebolavirus",
epi_dist = "onset_to_death",
prob_distribution = "gamma",
prob_distribution_params = unlist(dist_params)
)
#> Citation cannot be created as author, year, journal or title is missing
epidist_ebola_otd
#> Disease: Ebola virus disease
#> Pathogen: Ebolavirus
#> Epi Distribution: onset to death
#> Study: (????). "No citation."
#> Distribution: gamma
#> Parameters:
#> shape: 4.549
#> scale: 2.082
Thanks for your suggestion Pratik! I have added a Quick Start section to the README. We also plan to add more documentation and vignettes in the near future.
This issue is to request a "Quick start" section in the Readme to show users how to get started with accessing and extracting parameters from the database for use in downstream analyses. A small example of conversion to the {epiparameter} class
<epidist>
is shown here.Created on 2024-03-27 with reprex v2.0.2