joshwlambert
commented
5 months ago Thanks for reporting this issue! Here is a reproducible example of the issue using the most up-to-date versions of the {epiparameter} and {epireview} packages (there have been some updates to the packages since the issue was first opened).
library(epiparameter)
library(epireview)
#> Loading required package: epitrix
#> Loading required package: ggplot2
#> Loading required package: ggforcelibrary(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, unionebola_data <- epireview::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 epireview::load_epidata("ebola"): No outbreaks information found for
#> ebola
#> Data loaded for ebola
ebola_si <- (ebola_data$params
%>% filter(parameter_type == "Human delay - serial interval")
%>% filter(distribution_type == "Gamma")
)
print(as.data.frame(ebola_si[1,]))
#> id parameter_data_id
#> 1 86e39ecd9f503068d69402cbf1395cca 5c8d68c39d1c3b9870ecaaff0280d02e
#> covidence_id pathogen parameter_type parameter_value
#> 1 15896 Ebola virus Human delay - serial interval 15.3
#> exponent parameter_unit parameter_lower_bound parameter_upper_bound
#> 1 0 Days NA NA
#> parameter_value_type parameter_uncertainty_single_value
#> 1 Mean NA
#> parameter_uncertainty_singe_type parameter_uncertainty_lower_value
#> 1 <NA> NA
#> parameter_uncertainty_upper_value parameter_uncertainty_type
#> 1 NA <NA>
#> cfr_ifr_numerator cfr_ifr_denominator distribution_type
#> 1 NA NA Gamma
#> distribution_par1_value distribution_par1_type distribution_par1_uncertainty
#> 1 15.3 Mean TRUE
#> distribution_par2_value distribution_par2_type distribution_par2_uncertainty
#> 1 2.3 Mean sd TRUE
#> method_from_supplement method_moment_value cfr_ifr_method method_r
#> 1 FALSE Post outbreak <NA> <NA>
#> method_disaggregated_by method_disaggregated method_disaggregated_only
#> 1 <NA> FALSE FALSE
#> riskfactor_outcome riskfactor_name riskfactor_occupation
#> 1 <NA> <NA> <NA>
#> riskfactor_significant riskfactor_adjusted population_sex
#> 1 <NA> <NA> Unspecified
#> population_sample_type population_group population_age_min population_age_max
#> 1 Unspecified Unspecified NA NA
#> population_sample_size population_country population_location
#> 1 20 Nigeria <NA>
#> population_study_start_day population_study_start_month
#> 1 17 Jul
#> population_study_start_year population_study_end_day
#> 1 2014 20
#> population_study_end_month population_study_end_year genome_site
#> 1 Oct 2014 <NA>
#> genomic_sequence_available other_delay_start other_delay_end inverse_param
#> 1 FALSE <NA> <NA> FALSE
#> parameter_from_figure parameter_class ebola_variant other_delay
#> 1 FALSE Human delay Unspecified <NA>
#> delay_short delay_start other_rf_outcome attack_rate_type
#> 1 Serial interval Infection process <NA> <NA>
#> survey_start_date survey_end_date survey_date parameter_bounds
#> 1 17 Jul 2014 20 Oct 2014 17 Jul 2014 - 20 Oct 2014 <NA>
#> comb_uncertainty_type comb_uncertainty article_qa_score outbreak
#> 1 <NA> <NA> 85.71429 West Africa 2013-2016
#> ebola_species parameter_type_short first_author_surname year_publication
#> 1 Zaire <NA> Chan 2020
#> article_label
#> 1 Chan 2020 (1)
epiobj <- as_epidist(ebola_si[1,])
#> Using Chan (2020). "<title not available>." _<journal not available>_.
#> To retrieve the citation use the 'get_citation' function
#> Warning: Cannot create full citation for epidemiological parameters without bibliographic information
#> see ?as_epidist for help.
#> Error in extract_param(type = "range", values = median_range, distribution = prob_dist, : values vector should be c(median, min, max) check valuesCreated on 2024-06-14 with reprex v2.1.0
The issue persists, but the error message is now different.
Please include a brief description of the issue and any proposed solutions you may have.
Error message: Error in is_epidist_params(prob_dist, prob_dist_params) : Assertion on 'prob_dist_params' failed: Must have unique names, but element 3 is duplicated. Calls: as_epidist ... is_epidist_params -> -> makeAssertion -> mstop
Code:
ebola_data <- epireview::load_epidata("ebola")
ebola_si <- (ebola_data$params %>% filter(parameter_type == "Human delay - serial interval") %>% filter(distribution_type == "Gamma") )
print(as.data.frame(ebola_si[1,]))
epiobj <- as_epidist(ebola_si[1,])
Here is a zoomed in version.
Some parameter_data_id worked and some doesn't.
ebola_si <- (ebola_data$params %>% filter(parameter_type == "Human delay - serial interval") %>% filter(parameter_data_id == "5c8d68c39d1c3b9870ecaaff0280d02e") ## failed )
epiobj <- as_epidist(ebola_si[1,])
Here is an parameter_data_id that works:
ebola_si <- (ebola_data$params %>% filter(parameter_type == "Human delay - serial interval") %>% filter(parameter_data_id == "0c3e02f80addfccc1017fa619fba76c5") ## work )
epiobj <- as_epidist(ebola_si[1,])