cases_weekly: Produce Weekly Summary of Cases
In mrc-ide/esft: WHO ESFT Calculations

cases_weekly

R Documentation

Produce Weekly Summary of Cases

Description

Replicates the calculations in the 'Weekly Summary' tab of the ESFT depending on the input data source (WHO or Imperial). There are elements of these calculations, such as the assumption that hospital incidence = number of severe cases in the Imperial calculations, that the ICL team does not make in its calculations. Therefore, keep in mind that this is just a duplicate of the calculations in the ESFT, and not a critical appraisal of these calculations. This calculation does not yield an output where the first row contains the start date, as rows previous to the start date are needed for the patient calculations.

Note: since proportion of mild and moderate are the same, the estimates of these categories will be the same.

Usage

cases_weekly(
  params,
  capacity,
  test_strategy_params,
  data,
  data_source = "Imperial",
  user
)

Arguments

`params`	Includes both estimates of beds and case severity proportions.
`capacity`	From get_country_capacity
`test_strategy_params`	From set_testing_strategy
`data`	Specific country fit data, from the imperial model fits or from WHO data
`data_source`	Either WHO or Imperial.
`user`	From user_input function

Value

Dataframe of weekly summary, if data_source = "Imperial". If the data_source = "WHO", the ICU and hospital columns will not be included.

week_begins: Date the week summarized begins
week_ends: Date the week summarized ends
hospital_demand: Summed hospital demand: number of people who would be using a hospital bed given enough healthcare capacity but won't necessarily have it
ICU_demand: Summed ICU demand: number of people who would be using a hospital bed given enough healthcare capacity but won't necessarily have it
hospital_incidence: Summed hospital incidence: the total number of new people who need a new hospital bed at the current time. This does not include those recovering from ICU in a hospital bed or who already have access to a bed.
ICU_incidence: Summed ICU incidence: the total number of new people who need a new ICU bed at the current time. This does not include those who already have access to a bed.
infections: Estimated number of new infections, from model fits
cumulative_infections: Cumulative number of infections
new_critical_cases: For Imperial input = new critical cases per week as defined by as the ICU incidence. For WHO input, this is equal to the number of new cases per week multiplied by the proportion of infections that are critical
new_severe_cases: For Imperial input = new severe cases per week as defined by as the hospital incidence. For WHO input, this is equal to the number of new cases per week multiplied by the proportion of infections that are severe
new_mod_cases: New moderate cases every week, found by doing a transformation of the critical and severe cases and multiplying by the moderate case proportion
new_mild_cases: New mild cases every week, found by doing a transformation of the critical and severe cases and multiplying by the mild case proportion
cum_critical_cases: Cumulative critical cases per week as defined by the ESFT: cumulative ICU incidence
cum_severe_cases: Cumulative severe cases per week as defined by the ESFT: cumulative hospital incidence
cum_mod_cases: Cumulative moderate cases, using the first moderate case calculation
cum_mild_cases: Cumulative mild cases, using the first mild case calculation
sus_cases_but_negative: Sum of all new cases multiplied by the number of negative tests per positive case