Data on the parameters identified in the systematic review of articles related to Marburg virus disease.
Source:R/data.R
marburg_parameter.RdThis data set provides all extracted parameters for Marburg virus disease (MVD).
Format
A csv file containing the following parameters:
parameter_data_id = ID variable for the parameter.
article_id = ID variable for the article the outbreak data came from.
parameter_type = extracted parameter (see marburg_dropdown_parameters for the full list of parameters extracted).
parameter_value = extracted parameter value as stated in the article.
parameter_unit = units of the extracted parameter (see marburg_dropdown_parameters for the full list of parameter units).
parameter_lower_bound = minimum value of the parameter across any dimension of disaggregation.
parameter_upper_bound = maximum value of the parameter across any dimension of disaggregation.
parameter_value_type = whether the parameter value is the mean, median, standard deviation.
parameter_uncertainty_single_value = extracted uncertainty if only a single value provided.
parameter_uncertainty_single_type = uncertainty type if only a single value is reported e.g. "Standard Error (SE)" (see marburg_dropdown_parameters for the full list of options).
parameter_uncertainty_lower_value = lower value of paired uncertainty.
parameter_uncertainty_upper_value = upper value of paired uncertainty.
parameter_uncertainty_type = uncertainty type if a pair of values are provided, e.g. "CI90%", "CRI95%" (see marburg_dropdown_parameters for the full list of options).
cfr_ifr_numerator = numerator of the cfr or ifr provided in the article.
cfr_ifr_denominator = denominator of the cfr or ifr provided in the article.
distribution_type = if uncertainty is given as a distribution (see marburg_dropdown_parameters for the full list of options).
distribution_par1_value = value for distribution parameter 1.
distribution_par1_type = distribution parameter 1 type, e.g. shape, scale (see marburg_dropdown_parameters for the full list of options).
distribution_par1_uncertainty = whether the article reported uncertainty for the distribution parameter estimates (TRUE/FALSE).
distribution_par2_value = value for distribution parameter 2.
distribution_par2_type = distribution parameter 2 type, e.g. shape, scale (see marburg_dropdown_parameters for the full list of options).
distribution_par2_uncertainty = whether the article reported uncertainty for the distribution parameter estimates (TRUE/FALSE).
method_from_supplement = whether the parameter was taken from the supplementary material of the article. TRUE/FALSE.
method_moment_value = time period, either "Pre outbreak", Start outbreak", "Mid outbreak", "Post Outbreak", or "Other", if specified in the article.
cfr_ifr_method = whether the method used to calculate the cfr/ifr was "Naive", "Adjusted", "Unknown".
method_r = method used to estimate the reproduction number (see marburg_dropdown_parameters for the full list of options).
method_disaggregated_by = how the parameter is disaggregated e.g. by Age, Sex, Region.
method_disaggregated = whether the parameter is disaggregated (TRUE/FALSE).
method_disaggregated_only = whether only disaggregated data is available (TRUE/FALSE).
riskfactor_outcome = the outcome(s) for which the risk factor was evaluated e.g. "Death" or "Infection" (see marburg_dropdown_parameters for the full list of options).
riskfactor_name = the potential risk factor(s) evaluated e.g. "Age" (see marburg_dropdown_parameters for the full list of options).
riskfactor_occupation = specific occupation(s) if occupation is a risk factor (see marburg_dropdown_parameters for the full list of options).
riskfactor_significant = either "Significant", "Not significant", "Unspecified" or NA.
riskfactor_adjusted = either "Adjusted", "Not adjusted", "Unspecified".
population_sex = the sex of the study population, either "Female", "Male", "Both", "Unspecified".
population_sample_type = how the study was conducted e.g. "Hospital based", "Population based" (see 'Setting' in marburg_dropdown_parameters for the full list of options).
population_group = population group e.g. "Healthcare workers" (see marburg_dropdown_parameters for the full list of options).
population_age_min = minimum age in sample (if reported).
population_age_max = maximum age in the sample (if reported).
population_sample_size = total number of participants/samples tested.
population_country = country/countries that the study took place in.
population_location = location that the study took place e.g. region, city.
population_study_start_day = day study started (numeric - DD)
population_study_start_month = month study started (three letter abbreviation e.g. "Feb")
population_study_start_year = year study started (numeric - YYYY)
population_study_end_day = day study ended (numeric - DD)
population_study_end_month = month study ended (three letter abbreviation e.g. "Feb")
population_study_end_year = year study ended (numeric - YYYY)
genome_site = the portion of the pathogen’s genome used to estimate any extracted parameters. I.e. the gene, gene segment, codon position, or a more generic description (‘whole genome’ or ‘intergenic positions’).
genomic_sequence_available = whether the study sequenced new pathogen isolates and their accession numbers have been provided for retrieval from a public database. TRUE/FALSE.
parameter_class = class of the extracted parameter. Either "Human delay", "Seroprevalence", "Severity", "Reproduction number", "Mutations", "Risk factors", or "Other transmission parameters".
covidence_id = article identifier used by the Imperial team.