Package 'montagu'

Description

Burden estimate sets define a set of results for a modelling group. They are specific to a touchstone and scenario. Usually, they will be the populated version of the burden estimate set template, which a modelling group can download, and defines the columns and rows for all the countries, ages and years that are expected from that group, for that scenario. The modelling group then overwrites the missing values with results from their model, and submits the results to Montagu.

Usage

montagu_burden_estimate_set_clear(modelling_group_id, touchstone_id,
  scenario_id, burden_estimate_set_id, location = NULL)

Arguments

Value

The id of the burden estimate set

Description

Burden estimate sets define a set of results for a modelling group. They are specific to a touchstone and scenario. Usually, they will be the populated version of the burden estimate set template, which a modelling group can download, and defines the columns and rows for all the countries, ages and years that are expected from that group, for that scenario. The modelling group then overwrites the missing values with results from their model, and submits the results to Montagu.

Usage

montagu_burden_estimate_set_close(modelling_group_id, touchstone_id,
  scenario_id, burden_estimate_set_id, location = NULL)

Arguments

Value

The id of the burden estimate set

Description

Burden estimate sets define a set of results for a modelling group. They are specific to a touchstone and scenario. Usually, they will be the populated version of the burden estimate set template, which a modelling group can download, and defines the columns and rows for all the countries, ages and years that are expected from that group, for that scenario. The modelling group then overwrites the missing values with results from their model, and submits the results to Montagu.

Usage

montagu_burden_estimate_set_create(modelling_group_id, touchstone_id,
  scenario_id, type, details = NULL, location = NULL)

Arguments

Value

The id of the burden estimate set

Description

Burden estimate sets define a set of results for a modelling group. They are specific to a touchstone and scenario. Usually, they will be the populated version of the burden estimate set template, which a modelling group can download, and defines the columns and rows for all the countries, ages and years that are expected from that group, for that scenario. The modelling group then overwrites the missing values with results from their model, and submits the results to Montagu.

Usage

montagu_burden_estimate_set_data(modelling_group_id, touchstone_id,
  scenario_id, burden_estimate_set_id, location = NULL)

Arguments

Value

A list of information about a specific estimate set.

Description

Burden estimate sets define a set of results for a modelling group. They are specific to a touchstone and scenario. Usually, they will be the populated version of the burden estimate set template, which a modelling group can download, and defines the columns and rows for all the countries, ages and years that are expected from that group, for that scenario. The modelling group then overwrites the missing values with results from their model, and submits the results to Montagu.

Usage

montagu_burden_estimate_set_info(modelling_group_id, touchstone_id,
  scenario_id, burden_estimate_set_id, location = NULL)

Arguments

Value

A list of information about a specific estimate set.

Description

Burden estimate sets define a set of results for a modelling group. They are specific to a touchstone and scenario. Usually, they will be the populated version of the burden estimate set template, which a modelling group can download, and defines the columns and rows for all the countries, ages and years that are expected from that group, for that scenario. The modelling group then overwrites the missing values with results from their model, and submits the results to Montagu.

Usage

montagu_burden_estimate_set_outcome_data(modelling_group_id, touchstone_id,
  scenario_id, burden_estimate_set_id, outcome_code, group_by = "age",
  location = NULL)

Arguments

Value

A data frame with columns age or year (depending on group_by),

Description

Burden estimate sets define a set of results for a modelling group. They are specific to a touchstone and scenario. Usually, they will be the populated version of the burden estimate set template, which a modelling group can download, and defines the columns and rows for all the countries, ages and years that are expected from that group, for that scenario. The modelling group then overwrites the missing values with results from their model, and submits the results to Montagu.

Usage

montagu_burden_estimate_set_problems(modelling_group_id, touchstone_id,
  scenario_id, burden_estimate_set_id, location = NULL)

Arguments

Value

A list of any problems with this burden estimate set

Description

Burden estimate sets define a set of results for a modelling group. They are specific to a touchstone and scenario. Usually, they will be the populated version of the burden estimate set template, which a modelling group can download, and defines the columns and rows for all the countries, ages and years that are expected from that group, for that scenario. The modelling group then overwrites the missing values with results from their model, and submits the results to Montagu.

Usage

montagu_burden_estimate_set_upload(modelling_group_id, touchstone_id,
  scenario_id, burden_estimate_set_id, data, lines = 10000L,
  keep_open = FALSE, location = NULL)

Arguments

Value

The id of the burden estimate set

Description

Burden estimate sets define a set of results for a modelling group. They are specific to a touchstone and scenario. Usually, they will be the populated version of the burden estimate set template, which a modelling group can download, and defines the columns and rows for all the countries, ages and years that are expected from that group, for that scenario. The modelling group then overwrites the missing values with results from their model, and submits the results to Montagu.

Usage

montagu_burden_estimate_sets(modelling_group_id, touchstone_id,
  scenario_id, location = NULL)

Arguments

Value

A data frame of information about all relevant estimate sets.

Description

The burden estimate set is the list of burden estimates for a particular scenario for a touchstone. Montagu provides csv templates including rows for all the countries, years and ages, and columns for all the burden outcomes expected. These templates can then be filled in by the modelling groups, and uploaded to Montagu as their results submission.

Usage

montagu_central_burden_estimate_template(modelling_group_id, touchstone_id,
  expectation_id, location = NULL)

Arguments

Value

A data frame with columns disease, year, age, country, and country_name with given values, then cohort_size, deaths, cases and dalys, all NA.

Description

The coverage data describes for each country, over time and age, the efforts to vaccinate people against each disease. Routine activities involve the regular vaccination that is in place, whereas campaigns are specifically targeted towards a certain disease or people group for a certain time period.

Usage

montagu_coverage_data(modelling_group = NULL, touchstone_id, scenario_id,
  format = "long", all_countries = FALSE, location = NULL)

Arguments

Value

A data frame of the coverage data.

Description

The coverage data describes for each country, over time and age, the efforts to vaccinate people against each disease. Routine activities involve the regular vaccination that is in place, whereas campaigns are specifically targeted towards a certain disease or people group for a certain time period.

Usage

montagu_coverage_info(modelling_group, touchstone_id, scenario_id,
  location = NULL)

Arguments

Value

A data frame of metadata about all associated coverage sets

Description

Groups upload estimate sets to Montagu. The most recent set of results uploaded by a group for a given scenario can be queried for its status, or retrieved.

Usage

montagu_current_estimate_set_info(modelling_group_id, touchstone_id,
  scenario_id, location = NULL)

Arguments

Value

A list of fields about the current estimate set

Description

Groups upload estimate sets to Montagu. The most recent set of results uploaded by a group for a given scenario can be queried for its status, or retrieved.

Usage

montagu_current_estimate_set_problems(modelling_group_id, touchstone_id,
  scenario_id, location = NULL)

Arguments

Value

A list of problem text.

Description

Montagu provides standardised demographic data for the groups to use in their models. The source of the data is UNWPP, although various procedures are applied for convenience, including work on some smaller countries, people above the age of 80 in certain time periods, and extrapolating both cohorts backwards in time to their origins before 1950. Internal documents in the reporting portal describe the methods and motivations for these extensions.

Usage

montagu_demographic_data(type_code, touchstone_id, gender_code = NULL,
  wide = FALSE, source_code = NULL, location = NULL)

Arguments

Value

A data frame, giving the code and description for each demographic statistic, whether the data are stratified by gender, and a code indicating the source of the demographic data, which will change if there are future updates to any of the demographic data fields.

Description

Montagu provides standardised demographic data for the groups to use in their models. The source of the data is UNWPP, although various procedures are applied for convenience, including work on some smaller countries, people above the age of 80 in certain time periods, and extrapolating both cohorts backwards in time to their origins before 1950. Internal documents in the reporting portal describe the methods and motivations for these extensions.

Usage

montagu_demographics_list(touchstone_id, location = NULL)

Arguments

Value

A data frame, giving the code and description for each demographic statistic, whether the data are stratified by gender, and a code indicating the source of the demographic data, which will change if there are future updates to any of the demographic data fields.

Description

Diseases have an internal id and a name in Montagu, which are generally, but not always the same. Occasionally, it is necessary to provide the disease id to Montagu functions.

Usage

montagu_disease(disease_id, location = NULL)

Arguments

Value

a list of an id and a disease name

Description

Diseases have an internal id and a name in Montagu, which are generally, but not always the same. Occasionally, it is necessary to provide the disease id to Montagu functions.

Usage

montagu_diseases(location = NULL)

Arguments

Value

data frame containing ids and names of diseases

Description

The expectations, for a modelling group for a particular touchstone, indicate the range of chronological years, ages and countries for which burden estimates are expected, and what burden outcomes are required.

Usage

montagu_expectation(modelling_group_id, touchstone_id, expectation_id,
  location = NULL)

Arguments

Value

list of information about the expectation, including a description and ranges of age and time required.

Description

Different scenarios may have different expectations. For example, for Hepatitis B, different countries are required for different scenarios, since the different HepB vaccination initiatives have been carried out in different sets of countries. For other diseases, the same expectation might be equally valid in different scenarios. Here, we can query which scenarios a particular expectation applies to.

Usage

montagu_expectation_applicable_scenarios(modelling_group_id, touchstone_id,
  expectation_id, location = NULL)

Arguments

Value

A vector of scenario names

Description

The expectations, for a modelling group for a particular touchstone, indicate the range of chronological years, ages and countries for which burden estimates are expected, and what burden outcomes are required.

Usage

montagu_expectation_countries(modelling_group_id, touchstone_id,
  expectation_id, location = NULL)

Arguments

Value

A data frame of country id and name, for all expected countries.

Description

The expectations, for a modelling group for a particular touchstone, indicate the range of chronological years, ages and countries for which burden estimates are expected, and what burden outcomes are required.

Usage

montagu_expectation_outcomes(modelling_group_id, touchstone_id,
  expectation_id, location = NULL)

Arguments

Value

A vector of outcome names

Description

The expectations, for a modelling group for a particular touchstone, indicate the range of chronological years, ages and countries for which burden estimates are expected. These are also per-disease, so groups that model multiple diseases will see multiple rows of expectations.

Usage

montagu_expectations(modelling_group_id, touchstone_id, location = NULL)

Arguments

Value

A data frame of information about the expectation

Description

Models and modelling groups have text ids in Montagu. Here we can look up the relationships between groups and models, with description and citation information.

Usage

montagu_model(model_id, location = NULL)

Arguments

Value

List containing information about one model

Description

Modelling group ids generally consist of an identifier for the institution where the group is based, a hyphen, and the principal investigor for that group. Groups will be informed of their internal id when joining the consortium, but for convenience, we provide functions to look up the modelling group id, and associated models.

Usage

montagu_model_list(modelling_group_id, location = NULL)

Arguments

Description

A model run parameter set is a list of parameters that is required for a set of stochastic model runs. In a stochastic ensemble, modelling groups are requested to perform a number of model runs. Each model run executes with a unique set of parameters, and for a given run, all scenarios are run with the same parameters, so that we can calculate impact between them. The spread of parameters across the different runs should capture the range of sensible behaviour of the model. The model run parameter set then contains as many rows as there are model runs. Each row must contain a run_id, and the value for each parameter that is varied.

Usage

montagu_model_run_parameter_set_data(modelling_group_id, touchstone_id,
  model_run_parameter_set_id, location = NULL)

Arguments

Details

Adding, and querying existing model_run_parameter_sets is supported, and when creating a stochastic burden estimate set, the id of the associated model_run_parameter_set is required as a parameter.

Value

a csv of parameter values for each run_id.

Description

A model run parameter set is a list of parameters that is required for a set of stochastic model runs. In a stochastic ensemble, modelling groups are requested to perform a number of model runs. Each model run executes with a unique set of parameters, and for a given run, all scenarios are run with the same parameters, so that we can calculate impact between them. The spread of parameters across the different runs should capture the range of sensible behaviour of the model. The model run parameter set then contains as many rows as there are model runs. Each row must contain a run_id, and the value for each parameter that is varied.

Usage

montagu_model_run_parameter_set_info(modelling_group_id, touchstone_id,
  model_run_parameter_set_id, location = NULL)

Arguments

Details

Adding, and querying existing model_run_parameter_sets is supported, and when creating a stochastic burden estimate set, the id of the associated model_run_parameter_set is required as a parameter.

Value

a list of info about one model run parameter set.

Description

A model run parameter set is a list of parameters that is required for a set of stochastic model runs. In a stochastic ensemble, modelling groups are requested to perform a number of model runs. Each model run executes with a unique set of parameters, and for a given run, all scenarios are run with the same parameters, so that we can calculate impact between them. The spread of parameters across the different runs should capture the range of sensible behaviour of the model. The model run parameter set then contains as many rows as there are model runs. Each row must contain a run_id, and the value for each parameter that is varied.

Usage

montagu_model_run_parameter_set_upload(modelling_group_id, touchstone_id,
  disease_id, data, location = NULL)

Arguments

Details

Adding, and querying existing model_run_parameter_sets is supported, and when creating a stochastic burden estimate set, the id of the associated model_run_parameter_set is required as a parameter.

Value

the id of the newly created model_run_parameter_set

Description

A model run parameter set is a list of parameters that is required for a set of stochastic model runs. In a stochastic ensemble, modelling groups are requested to perform a number of model runs. Each model run executes with a unique set of parameters, and for a given run, all scenarios are run with the same parameters, so that we can calculate impact between them. The spread of parameters across the different runs should capture the range of sensible behaviour of the model. The model run parameter set then contains as many rows as there are model runs. Each row must contain a run_id, and the value for each parameter that is varied.

Usage

montagu_model_run_parameter_sets(modelling_group_id, touchstone_id,
  location = NULL)

Arguments

Details

Adding, and querying existing model_run_parameter_sets is supported, and when creating a stochastic burden estimate set, the id of the associated model_run_parameter_set is required as a parameter.

Value

a data frame of info about the model run parameter sets.

Description

Modelling group ids generally consist of an identifier for the institution where the group is based, a hyphen, and the principal investigor for that group. Groups will be informed of their internal id when joining the consortium, but for convenience, we provide functions to look up the modelling group id, and associated models.

Usage

montagu_modelling_group(modelling_group_id, location = NULL)

Arguments

Value

A list of id and description for the given group id.

Description

Retrieve list of members for a given modelling_group_id.

Usage

montagu_modelling_group_members(modelling_group_id, location = NULL)

Arguments

Description

Modelling group ids generally consist of an identifier for the institution where the group is based, a hyphen, and the principal investigor for that group. Groups will be informed of their internal id when joining the consortium, but for convenience, we provide functions to look up the modelling group id, and associated models.

Usage

montagu_modelling_groups(location = NULL)

Arguments

Value

A dataframe of id and description for each group

Description

Models and modelling groups have text ids in Montagu. Here we can look up the relationships between groups and models, with description and citation information.

Usage

montagu_models(location = NULL)

Arguments

Value

Data frame containing information about models.

Description

An orderlyweb remote driver for montagu

Usage

montagu_orderlyweb_remote(name, host, port, ...)

Arguments

Description

A scenario describes the vaccination conditions for a particular run of a model. Typical examples include a scenario where there is no vaccination, a scenario where there is routine (background) vaccination, or a scenario in which there are targetted campaigns to vaccinate particularly ages. Depending on disease, modelling groups may be asked to model various scenarios, for a particular touchstone.

Usage

montagu_scenario_problems(modelling_group_id, touchstone_id, scenario_id,
  location = NULL)

Arguments

Value

A list of problem text.

Description

A scenario describes the vaccination conditions for a particular run of a model. Typical examples include a scenario where there is no vaccination, a scenario where there is routine (background) vaccination, or a scenario in which there are targetted campaigns to vaccinate particularly ages. Depending on disease, modelling groups may be asked to model various scenarios, for a particular touchstone.

Usage

montagu_scenario_status(modelling_group_id, touchstone_id, scenario_id,
  location = NULL)

Arguments

Value

"invalid", "complete", "valid", or "empty"

Description

A scenario describes the vaccination conditions for a particular run of a model. Typical examples include a scenario where there is no vaccination, a scenario where there is routine (background) vaccination, or a scenario in which there are targetted campaigns to vaccinate particularly ages. Depending on disease, modelling groups may be asked to model various scenarios, for a particular touchstone.

Usage

montagu_scenarios(modelling_group_id = NULL, touchstone_id,
  location = NULL)

Arguments

Value

Data frame of scenario_id, description and disease.

Description

Create a handle to a montagu server

Usage

montagu_server(name, host, port = 443, username = NULL,
  password = NULL, verbose = FALSE, global = TRUE,
  overwrite = FALSE)

Arguments

Value

Invisibly, a montagu_server object.

Description

Set a global default montagu server

Usage

montagu_server_global_default_set(location)

Arguments

Description

List known montagu servers

Usage

montagu_server_global_list()

Description

Montagu provides the stochastic burden estimate set, which along with the columns of the central-estimate set, also includes a run_id column.

Usage

montagu_stochastic_burden_estimate_template(modelling_group_id,
  touchstone_id, expectation_id, location = NULL)

Arguments

Value

A data frame with columns disease (given), run_id (NA), year, age, country, and country_name (all given), and finally cohort_size, deaths, cases and dalys, (NA).

Description

Touchstones are versioned; errata in the input or coverage data may be addressed with a new version of the existing touchstone. When interacting with Montagu, a touchstone_id will consist of a basename, and a version.

Usage

montagu_touchstone_versions(modelling_group_id = NULL,
  touchstone_name = NULL, require_open = FALSE, location = NULL)

Arguments

Value

Data frame of touchstone id, name, version, description and status

Description

Touchstones are created by the VIMC management. The touchstone id associates a particular call for burden estimates, with the input data (coverage and demography) required to produce those estimates, and with the results that the modelling groups provide. A touchstone has a base name, and a version.

Usage

montagu_touchstones(modelling_group_id = NULL, location = NULL)

Arguments

Value

Data frame of touchstone name, description and comment.

Description

Given a particular touchstone and scenario, we can loookup all the other touchstones that also contain this scenario.

Usage

montagu_touchstones_for_scenario(modelling_group_id, touchstone_id,
  scenario_id, location = NULL)

Arguments

Value

vector of touchstone ids