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 |
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.
montagu_burden_estimate_set_clear(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, location = NULL)
montagu_burden_estimate_set_clear(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, location = NULL)
modelling_group_id |
Modelling group identifier |
touchstone_id |
Touchstone identifier |
scenario_id |
Scenario identifier |
burden_estimate_set_id |
Burden estimate set created by
|
location |
The montagu server to connect to. |
The id of the burden estimate set
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.
montagu_burden_estimate_set_close(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, location = NULL)
montagu_burden_estimate_set_close(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, location = NULL)
modelling_group_id |
Modelling group identifier |
touchstone_id |
Touchstone identifier |
scenario_id |
Scenario identifier |
burden_estimate_set_id |
Burden estimate set created by
|
location |
The montagu server to connect to. |
The id of the burden estimate set
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.
montagu_burden_estimate_set_create(modelling_group_id, touchstone_id, scenario_id, type, details = NULL, location = NULL)
montagu_burden_estimate_set_create(modelling_group_id, touchstone_id, scenario_id, type, details = NULL, location = NULL)
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. |
The id of the burden estimate set
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.
montagu_burden_estimate_set_data(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, location = NULL)
montagu_burden_estimate_set_data(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, location = NULL)
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. |
A list of information about a specific estimate set.
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.
montagu_burden_estimate_set_info(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, location = NULL)
montagu_burden_estimate_set_info(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, location = NULL)
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. |
A list of information about a specific estimate set.
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.
montagu_burden_estimate_set_outcome_data(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, outcome_code, group_by = "age", location = NULL)
montagu_burden_estimate_set_outcome_data(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, outcome_code, group_by = "age", location = NULL)
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. |
A data frame with columns age or year (depending on group_by),
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.
montagu_burden_estimate_set_problems(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, location = NULL)
montagu_burden_estimate_set_problems(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, location = NULL)
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. |
A list of any problems with this burden estimate set
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.
montagu_burden_estimate_set_upload(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, data, lines = 10000L, keep_open = FALSE, location = NULL)
montagu_burden_estimate_set_upload(modelling_group_id, touchstone_id, scenario_id, burden_estimate_set_id, data, lines = 10000L, keep_open = FALSE, location = NULL)
modelling_group_id |
Modelling group identifier |
touchstone_id |
Touchstone identifier |
scenario_id |
Scenario identifier |
burden_estimate_set_id |
Burden estimate set created by
|
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. |
The id of the burden estimate set
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.
montagu_burden_estimate_sets(modelling_group_id, touchstone_id, scenario_id, location = NULL)
montagu_burden_estimate_sets(modelling_group_id, touchstone_id, scenario_id, location = NULL)
modelling_group_id |
Modelling group identifier |
touchstone_id |
Touchstone identifier |
scenario_id |
Scenario identifier |
location |
The montagu server to connect to. |
A data frame of information about all relevant estimate sets.
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.
montagu_central_burden_estimate_template(modelling_group_id, touchstone_id, expectation_id, location = NULL)
montagu_central_burden_estimate_template(modelling_group_id, touchstone_id, expectation_id, location = NULL)
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. |
A data frame with columns disease, year, age, country, and country_name with given values, then cohort_size, deaths, cases and dalys, all NA.
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.
montagu_coverage_data(modelling_group = NULL, touchstone_id, scenario_id, format = "long", all_countries = FALSE, location = NULL)
montagu_coverage_data(modelling_group = NULL, touchstone_id, scenario_id, format = "long", all_countries = FALSE, location = NULL)
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. |
A data frame of the coverage data.
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.
montagu_coverage_info(modelling_group, touchstone_id, scenario_id, location = NULL)
montagu_coverage_info(modelling_group, touchstone_id, scenario_id, location = NULL)
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. |
A data frame of metadata about all associated coverage sets
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.
montagu_current_estimate_set_info(modelling_group_id, touchstone_id, scenario_id, location = NULL)
montagu_current_estimate_set_info(modelling_group_id, touchstone_id, scenario_id, location = NULL)
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. |
A list of fields about the current estimate set
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.
montagu_current_estimate_set_problems(modelling_group_id, touchstone_id, scenario_id, location = NULL)
montagu_current_estimate_set_problems(modelling_group_id, touchstone_id, scenario_id, location = NULL)
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. |
A list of problem text.
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.
montagu_demographic_data(type_code, touchstone_id, gender_code = NULL, wide = FALSE, source_code = NULL, location = NULL)
montagu_demographic_data(type_code, touchstone_id, gender_code = NULL, wide = FALSE, source_code = NULL, location = NULL)
type_code |
The demographic type code (something like
|
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 |
source_code |
Optional source code, may be useful if one
|
location |
The location of the montagu api server. |
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.
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.
montagu_demographics_list(touchstone_id, location = NULL)
montagu_demographics_list(touchstone_id, location = NULL)
touchstone_id |
Touchstone identifier |
location |
The location of the montagu api server. |
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.
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.
montagu_disease(disease_id, location = NULL)
montagu_disease(disease_id, location = NULL)
disease_id |
The disease id. |
location |
the montagu server to connect to. |
a list of an id and a disease name
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.
montagu_diseases(location = NULL)
montagu_diseases(location = NULL)
location |
the montagu server to connect to. |
data frame containing ids and names of diseases
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.
montagu_expectation(modelling_group_id, touchstone_id, expectation_id, location = NULL)
montagu_expectation(modelling_group_id, touchstone_id, expectation_id, location = NULL)
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. |
list of information about the expectation, including a description and ranges of age and time required.
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.
montagu_expectation_applicable_scenarios(modelling_group_id, touchstone_id, expectation_id, location = NULL)
montagu_expectation_applicable_scenarios(modelling_group_id, touchstone_id, expectation_id, location = NULL)
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. |
A vector of scenario names
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.
montagu_expectation_countries(modelling_group_id, touchstone_id, expectation_id, location = NULL)
montagu_expectation_countries(modelling_group_id, touchstone_id, expectation_id, location = NULL)
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. |
A data frame of country id and name, for all expected countries.
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.
montagu_expectation_outcomes(modelling_group_id, touchstone_id, expectation_id, location = NULL)
montagu_expectation_outcomes(modelling_group_id, touchstone_id, expectation_id, location = NULL)
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. |
A vector of outcome names
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.
montagu_expectations(modelling_group_id, touchstone_id, location = NULL)
montagu_expectations(modelling_group_id, touchstone_id, location = NULL)
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. |
A data frame of information about the expectation
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.
montagu_model(model_id, location = NULL)
montagu_model(model_id, location = NULL)
model_id |
The model id. |
location |
The montagu server to connect to. |
List containing information about one model
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.
montagu_model_list(modelling_group_id, location = NULL)
montagu_model_list(modelling_group_id, location = NULL)
modelling_group_id |
The id of the modelling group |
location |
The montagu server to connect to. |
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.
montagu_model_run_parameter_set_data(modelling_group_id, touchstone_id, model_run_parameter_set_id, location = NULL)
montagu_model_run_parameter_set_data(modelling_group_id, touchstone_id, model_run_parameter_set_id, location = NULL)
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. |
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.
a csv of parameter values for each run_id.
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.
montagu_model_run_parameter_set_info(modelling_group_id, touchstone_id, model_run_parameter_set_id, location = NULL)
montagu_model_run_parameter_set_info(modelling_group_id, touchstone_id, model_run_parameter_set_id, location = NULL)
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. |
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.
a list of info about one model run parameter set.
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.
montagu_model_run_parameter_set_upload(modelling_group_id, touchstone_id, disease_id, data, location = NULL)
montagu_model_run_parameter_set_upload(modelling_group_id, touchstone_id, disease_id, data, location = NULL)
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. |
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.
the id of the newly created model_run_parameter_set
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.
montagu_model_run_parameter_sets(modelling_group_id, touchstone_id, location = NULL)
montagu_model_run_parameter_sets(modelling_group_id, touchstone_id, location = NULL)
modelling_group_id |
The id of the modelling group |
touchstone_id |
The id of the touchstone |
location |
The montagu server to connect to. |
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.
a data frame of info about the model run parameter sets.
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.
montagu_modelling_group(modelling_group_id, location = NULL)
montagu_modelling_group(modelling_group_id, location = NULL)
modelling_group_id |
The id of the modelling group |
location |
The montagu server to connect to. |
A list of id and description for the given group id.
Retrieve list of members for a given modelling_group_id.
montagu_modelling_group_members(modelling_group_id, location = NULL)
montagu_modelling_group_members(modelling_group_id, location = NULL)
modelling_group_id |
The id of the modelling group |
location |
The montagu server to connect to. |
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.
montagu_modelling_groups(location = NULL)
montagu_modelling_groups(location = NULL)
location |
The montagu server to connect to. |
A dataframe of id and description for each group
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.
montagu_models(location = NULL)
montagu_models(location = NULL)
location |
The montagu server to connect to. |
Data frame containing information about models.
An orderlyweb
remote driver for montagu
montagu_orderlyweb_remote(name, host, port, ...)
montagu_orderlyweb_remote(name, host, port, ...)
name |
Name for the remote, shared with the
|
host |
Hostname, shared with the
|
port |
Port, shared with the
|
... |
Additional arguments passed through to
|
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.
montagu_scenario_problems(modelling_group_id, touchstone_id, scenario_id, location = NULL)
montagu_scenario_problems(modelling_group_id, touchstone_id, scenario_id, location = NULL)
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. |
A list of problem text.
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.
montagu_scenario_status(modelling_group_id, touchstone_id, scenario_id, location = NULL)
montagu_scenario_status(modelling_group_id, touchstone_id, scenario_id, location = NULL)
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. |
"invalid", "complete", "valid", or "empty"
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.
montagu_scenarios(modelling_group_id = NULL, touchstone_id, location = NULL)
montagu_scenarios(modelling_group_id = NULL, touchstone_id, location = NULL)
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. |
Data frame of scenario_id, description and disease.
Create a handle to a montagu server
montagu_server(name, host, port = 443, username = NULL, password = NULL, verbose = FALSE, global = TRUE, overwrite = FALSE)
montagu_server(name, host, port = 443, username = NULL, password = NULL, verbose = FALSE, global = TRUE, overwrite = FALSE)
name |
The name to call this server. This appears in a few
places as a "friendly" name. If |
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 |
password |
The password. If not given, then on
authorisation, the user will be prompted. Falls back on the R
global options |
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 |
overwrite |
Logical, and meaningful only if |
Invisibly, a montagu_server
object.
Set a global default montagu server
montagu_server_global_default_set(location)
montagu_server_global_default_set(location)
location |
A server location |
List known montagu servers
montagu_server_global_list()
montagu_server_global_list()
Montagu provides the stochastic burden estimate set, which along with the columns of the central-estimate set, also includes a run_id column.
montagu_stochastic_burden_estimate_template(modelling_group_id, touchstone_id, expectation_id, location = NULL)
montagu_stochastic_burden_estimate_template(modelling_group_id, touchstone_id, expectation_id, location = NULL)
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. |
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).
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.
montagu_touchstone_versions(modelling_group_id = NULL, touchstone_name = NULL, require_open = FALSE, location = NULL)
montagu_touchstone_versions(modelling_group_id = NULL, touchstone_name = NULL, require_open = FALSE, location = NULL)
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. |
Data frame of touchstone id, name, version, description and status
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.
montagu_touchstones(modelling_group_id = NULL, location = NULL)
montagu_touchstones(modelling_group_id = NULL, location = NULL)
modelling_group_id |
id of the modelling group. If omitted or null, then all touchstones are returned. |
location |
The montagu server to connect to. |
Data frame of touchstone name, description and comment.
Given a particular touchstone and scenario, we can loookup all the other touchstones that also contain this scenario.
montagu_touchstones_for_scenario(modelling_group_id, touchstone_id, scenario_id, location = NULL)
montagu_touchstones_for_scenario(modelling_group_id, touchstone_id, scenario_id, location = NULL)
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. |
vector of touchstone ids