Package 'montagu'

Title: Interface with 'montagu'
Description: Client for interacting with the montagu API, and authentication with the montagu OrderlyWeb instance. This package is part of montagu.
Authors: Rich FitzJohn [aut, cre], Wes Hinsley [aut]
Maintainer: Rich FitzJohn <[email protected]>
License: MIT + file LICENSE
Version: 0.6.1
Built: 2024-10-31 04:35:22 UTC
Source: https://github.com/vimc/montagu-r

Help Index


Deletes all uploaded rows from an incomplete 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_clear(modelling_group_id, touchstone_id,
  scenario_id, burden_estimate_set_id, location = NULL)

Arguments

modelling_group_id

Modelling group identifier

touchstone_id

Touchstone identifier

scenario_id

Scenario identifier

burden_estimate_set_id

Burden estimate set created by montagu_burden_estimate_set_crete

location

The montagu server to connect to.

Value

The id of the burden estimate set


Closes a burden estimate set, marking it as complete.

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

modelling_group_id

Modelling group identifier

touchstone_id

Touchstone identifier

scenario_id

Scenario identifier

burden_estimate_set_id

Burden estimate set created by montagu_burden_estimate_set_create

location

The montagu server to connect to.

Value

The id of the burden estimate set


Create a new 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

modelling_group_id

Modelling group identifier

touchstone_id

Touchstone identifier

scenario_id

Scenario identifier

type

Can be 'central-single-run' or 'central-averaged'

details

Optional details string

location

The montagu server to connect to.

Value

The id of the burden estimate set


Retrieves the data for a specific 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

modelling_group_id

Modelling group identifier

touchstone_id

Touchstone identifier

scenario_id

Scenario identifier

burden_estimate_set_id

the integer id of a burden estimate set

location

The montagu server to connect to.

Value

A list of information about a specific estimate set.


Retrieves information about a specific 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_info(modelling_group_id, touchstone_id,
  scenario_id, burden_estimate_set_id, location = NULL)

Arguments

modelling_group_id

Modelling group identifier

touchstone_id

Touchstone identifier

scenario_id

Scenario identifier

burden_estimate_set_id

The integer id of a burden estimate set

location

The montagu server to connect to.

Value

A list of information about a specific estimate set.


Retrieve data for a particular outcoe of a burden estimate set, aggregated across country and disaggregated by either age or year.

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

modelling_group_id

Modelling group identifier

touchstone_id

Touchstone identifier

scenario_id

Scenario identifier

burden_estimate_set_id

The integer id of a burden estimate set

outcome_code

The name of an outcome, such as 'cases' or 'deaths'.

group_by

Set to 'age' (the default) or 'year', to set the

location

The montagu server to connect to.

Value

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


Retrieves information about a specific 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_problems(modelling_group_id, touchstone_id,
  scenario_id, burden_estimate_set_id, location = NULL)

Arguments

modelling_group_id

Modelling group identifier

touchstone_id

Touchstone identifier

scenario_id

Scenario identifier

burden_estimate_set_id

The integer id of a burden estimate set

location

The montagu server to connect to.

Value

A list of any problems with this burden estimate set


Deletes all uploaded rows from an incomplete 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

modelling_group_id

Modelling group identifier

touchstone_id

Touchstone identifier

scenario_id

Scenario identifier

burden_estimate_set_id

Burden estimate set created by montagu_burden_estimate_set_crete

data

Data frame containing burden estimates.

lines

Number of lines to chunk the files into

keep_open

Keep the burden estimate set open after upload?

location

The montagu server to connect to.

Value

The id of the burden estimate set


Retrieves list of estimate sets for a group, touchstone and scenario.

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

modelling_group_id

Modelling group identifier

touchstone_id

Touchstone identifier

scenario_id

Scenario identifier

location

The montagu server to connect to.

Value

A data frame of information about all relevant estimate sets.


Get central burden estimate template for an expectation

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

expectation_id

id of the expectation (integer)

location

The montagu server to connect to.

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.


Retrieve coverage data for a scenario, touchstone and modelling group.

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

modelling_group

id of modelling group; if omitted or NULL, then return coverage info for all modelling groups.

touchstone_id

id of touchstone (including version)

scenario_id

id of scenario within touchstone

format

"wide" or "long" csv format. Long format contains a row per year per country; wide format contains a row per country, with year-specific columns for target population and coverage.

all_countries

Include all countries, instead of just those for which burden estimates are required.

location

The montagu server to connect to.

Value

A data frame of the coverage data.


Retrieve metadata for coverage sets for a particularly group, touchstone and scenario.

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

modelling_group

id of modelling group

touchstone_id

id of touchstone (including version)

scenario_id

id of scenario within touchstone

location

The montagu server to connect to.

Value

A data frame of metadata about all associated coverage sets


Get information on current estimate set for a scenario.

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

scenario_id

id of the scenario

location

The montagu server to connect to.

Value

A list of fields about the current estimate set


Retrieve list of any problems in current estimate set for a scenario.

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

scenario_id

id of the scenario

location

The montagu server to connect to.

Value

A list of problem text.


Download demographic data for a given touchstone.

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

type_code

The demographic type code (something like cbr for Fertility: Crude birth rate (CBR). Get the possible values from montagu_demographics_list

touchstone_id

Touchstone identifier

gender_code

One of "male", "female" or "both" (if omitted montagu will return "both"). Not applicable to all statistics.

wide

Logical, if TRUE returns data in wide format rather than long.

source_code

Optional source code, may be useful if one type_code can come from two sources within a touchstone.

location

The location of the montagu api server.

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.


List the demographic data available for a given touchstone.

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

touchstone_id

Touchstone identifier

location

The location of the montagu api server.

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.


Retrieve disease with given id.

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

disease_id

The disease id.

location

the montagu server to connect to.

Value

a list of an id and a disease name


Retrieve list of all disease ids and names.

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

location

the montagu server to connect to.

Value

data frame containing ids and names of diseases


Get information about an expectation

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

expectation_id

id of the expectation (integer)

location

The montagu server to connect to.

Value

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


Get applicable scenarios for an expectation

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

expectation_id

id of the expectation (integer)

location

The montagu server to connect to.

Value

A vector of scenario names


Get country list for an expectation

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

expectation_id

Integer id of the expectation

location

The montagu server to connect to.

Value

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


Get expected outcomes

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

expectation_id

id of the expectation (integer)

location

The montagu server to connect to.

Value

A vector of outcome names


Get expectations for a modelling group and touchstone

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

location

The montagu server to connect to.

Value

A data frame of information about the expectation


Retrieve model with given id.

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

model_id

The model id.

location

The montagu server to connect to.

Value

List containing information about one model


Retrieve list of models for a given modelling_group_id.

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

modelling_group_id

The id of the modelling group

location

The montagu server to connect to.


Retrieve info about one model run parameter sets for a group and touchstone

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

modelling_group_id

The id of the modelling group

touchstone_id

The id of the touchstone

model_run_parameter_set_id

The id of the model_run_parameter_set.

location

The montagu server to connect to.

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.


Retrieve info about one model run parameter sets for a group and touchstone

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

modelling_group_id

The id of the modelling group

touchstone_id

The id of the touchstone

model_run_parameter_set_id

The id of the model_run_parameter_set.

location

The montagu server to connect to.

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.


Upload a model_run_parameter_set to Montagu.

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

modelling_group_id

The id of the modelling group

touchstone_id

The id of the touchstone

disease_id

The id of the disease associated with this model

data

a data frame with a column 'run_id', and other columns for each parameter that will be varied for each run.

location

The montagu server to connect to.

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


Retrieve a list of model run parameter sets for a group and touchstone

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

modelling_group_id

The id of the modelling group

touchstone_id

The id of the touchstone

location

The montagu server to connect to.

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.


Retrieve modelling_group with given modelling_group_id.

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

modelling_group_id

The id of the modelling group

location

The montagu server to connect to.

Value

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


Retrieve list of members for a given modelling_group_id.

Description

Retrieve list of members for a given modelling_group_id.

Usage

montagu_modelling_group_members(modelling_group_id, location = NULL)

Arguments

modelling_group_id

The id of the modelling group

location

The montagu server to connect to.


Retrieve list of all modelling group ids and names.

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

location

The montagu server to connect to.

Value

A dataframe of id and description for each group


Retrieve list of all model ids, names, citations and groups.

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

location

The montagu server to connect to.

Value

Data frame containing information about models.


orderly remote driver

Description

An orderlyweb remote driver for montagu

Usage

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

Arguments

name

Name for the remote, shared with the montagu_server name.

host

Hostname, shared with the montagu_server host.

port

Port, shared with the montagu_server port.

...

Additional arguments passed through to montagu_server


Retrieve a list of any problems with a scenario.

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

scenario_id

id of the scenario

location

The montagu server to connect to.

Value

A list of problem text.


Retrieve current status of a groups' scenario.

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

scenario_id

id of the scenario

location

The montagu server to connect to.

Value

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


Retrieve information about a scenario

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

location

The montagu server to connect to.

Value

Data frame of scenario_id, description and disease.


Create a handle to a montagu server

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

name

The name to call this server. This appears in a few places as a "friendly" name. If global = TRUE then this will be available from the package using this name.

host

The hostname of the server

port

The port the server is running on (default is 443 which is the standard https port)

username

The username. If not given, then on authorisation, the user will be prompted. Falls back on the R global options montagu.<name>.username and montagu.username in turn.

password

The password. If not given, then on authorisation, the user will be prompted. Falls back on the R global options montagu.<name>.password and montagu.password in turn.

verbose

Logical, indicating if verbose http communication should be used. This is for debugging only.

global

Logical, indicating if the server should be stored in the global set. If true then you can pass location = name to most other functions in the package.

overwrite

Logical, and meaningful only if global = TRUE, indicating if a global configuration should be replaced if it exists.

Value

Invisibly, a montagu_server object.


Set a global default montagu server

Description

Set a global default montagu server

Usage

montagu_server_global_default_set(location)

Arguments

location

A server location


List known montagu servers

Description

List known montagu servers

Usage

montagu_server_global_list()

Get stochastic burden estimate template for an expectation

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

expectation_id

id of the expectation (integer)

location

The montagu server to connect to.

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).


Retrieve list of all versions of a given touchstone.

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

modelling_group_id

id of the modelling group. If omitted or null, then all touchstones are returned.

touchstone_name

Optional base name of the touchstone to filter. (ie, no version suffix)

require_open

If true, include only open touchstones

location

The montagu server to connect to.

Value

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


Retrieve touchstones a modelling group is responsible for.

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

modelling_group_id

id of the modelling group. If omitted or null, then all touchstones are returned.

location

The montagu server to connect to.

Value

Data frame of touchstone name, description and comment.


Get touchstones that include this scenario

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

modelling_group_id

id of the modelling group. If omitted, or null, then all scenarios associated with the touchstone are returned.

touchstone_id

id of the touchstone (including version)

scenario_id

id of the scenario

location

The montagu server to connect to.

Value

vector of touchstone ids