flumodelsutil_data: Internal and external data for flumodelsutil
In HHS/ASPR-flumodelsutil: Flumodels helper utilities
Description
Usage
Format
Source
Description
A collection of data for use with flumodelsutil. Most are used by internal functions but are exposed here for use by
external parties. Those items most likely to be used externally are pandemic.deaths and population.US.total.
Usage
1
Format
A list of data. The named entries are described below:
- ILI.data
-
A data.frame with the following columns:
REGION TYPE: Only value is National
REGION: Only value is NA (since it's national data)
YEAR: Integers with values 1997 to 2015 corresponding to calendar year
Season: Integers with values 1997 to 2015 corresponding to the start of the year X/X+1 flu season.
WEEK: ILINet week
Date: Start date of the week.
% WEIGHTED ILI: ILINet reported
%UNWEIGHTED ILI: ILINet reported
AGE 0-4: Number of ILI cases in the 0-4 age bracket.
AGE 25-49: Number of ILI cases in the 25-49 age bracket.
AGE 25-64: Number of ILI cases in the 24-64 age bracket.
AGE 5-24: Number of ILI cases in the 5-24 age bracket.
AGE 50-64: Number of ILI cases in the 50-64 age bracket.
AGE 65: Number of ILI cases in the 64+ age bracket.
ILITOTAL: Total number of ILI reported cases.
NUM. OF PROVIDERS: Number of providers reporting to ILINet.
TOTAL PATIENTS: Total number of patients reported to ILINet.
- pandemic.deaths
-
A data.frame with 63 rows and 5 variables:
yearYear corresponding to data. integer
weekCDC ILI week. integer
week.of.pandemicHow many weeks since the beginning of the pandemic. Starts at 1 for the first recorded element of the given pandemic. integer
pandemicYear of pandemic. Included pandemics are 1918, 1957, 1968, 2009. integer
deathsEstimated mortality. Please note that not all estimates are for the entire US. integer
- 1918 data
Excess death rates (annual basis) per 100k from influenza and pneumonia in 47 US cities.
- 1957 data
Influenza and pneumonia deaths in the United States.
- 1968 data
Influenza and pneumonia deaths in 122 cities in the United States.
- 2009 data
Influenza deaths in the United States. This includes both waves. For wave 2 only, just use 2009 week 31 (week.of.pandemic 18) and onwards.
- POLYMOD.age.ranges
-
A data.frame, where each column corresponds to an age range. The
column names denote the age ranges. The two rows are AgeStart and AgeEnd.
The given age range corresponds to individuals in the range [AgeStart, AgeEnd].
A value of NA for AgeEnd corresponds to no upper bound, so [70,NA] corresponds
to all individuals aged 70 or more.
- POLYMOD.matrix
-
A double matrix, matrix where k_ij is proportional to the observed number of contacts
(both physical and nonphysical) that a respondent in age band j makes with other
individuals in age band i. The names of both columns and rows denote the
age ranges.
- population.UK
-
An integer array, one entry per age range.
The names denote the age ranges.
- population.US
-
A data.frame with many columns. Those of interest for this package are:
YEAR: Which year the data corresponds to. Currently only 2015 data is provided.
AGE: Age of the population of interest. Age of X corresponds to [X,X+1),
so 0 means infants under one year of age. Age of 999 corresponds to the entire population.
TOT_POP: Total population in the given age bin (or entire US population if AGE == 999).
- population.US.total
-
A numeric of total 2015 US population.
Source
- ILI.data
-
CDC ILINet
- pandemic.deaths
-
Mossong J, Hens N, Jit M, Beutels P, Auranen K, et al. (2008)
Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases.
PLOS Medicine 5(3): e74. https://doi.org/10.1371/journal.pmed.0050074
- POLYMOD.age.ranges
-
Mossong J, Hens N, Jit M, Beutels P, Auranen K, et al. (2008)
Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases.
PLOS Medicine 5(3): e74. https://doi.org/10.1371/journal.pmed.0050074
- POLYMOD.matrix
-
Mossong J, Hens N, Jit M, Beutels P, Auranen K, et al. (2008)
Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases.
PLOS Medicine 5(3): e74. https://doi.org/10.1371/journal.pmed.0050074
- population.US
-
US Census
- population.US.total
-
US Census
HHS/ASPR-flumodelsutil documentation built on Dec. 31, 2020, 12:58 p.m.
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Description Usage Format Source
Description
A collection of data for use with flumodelsutil. Most are used by internal functions but are exposed here for use by
external parties. Those items most likely to be used externally are pandemic.deaths and population.US.total.
Usage
1 |
Format
A list of data. The named entries are described below:
- ILI.data
-
A
data.framewith the following columns:REGION TYPE: Only value is National
REGION: Only value is NA (since it's national data)
YEAR: Integers with values 1997 to 2015 corresponding to calendar year
Season: Integers with values 1997 to 2015 corresponding to the start of the year X/X+1 flu season.
WEEK: ILINet week
Date: Start date of the week.
% WEIGHTED ILI: ILINet reported
%UNWEIGHTED ILI: ILINet reported
AGE 0-4: Number of ILI cases in the 0-4 age bracket.
AGE 25-49: Number of ILI cases in the 25-49 age bracket.
AGE 25-64: Number of ILI cases in the 24-64 age bracket.
AGE 5-24: Number of ILI cases in the 5-24 age bracket.
AGE 50-64: Number of ILI cases in the 50-64 age bracket.
AGE 65: Number of ILI cases in the 64+ age bracket.
ILITOTAL: Total number of ILI reported cases.
NUM. OF PROVIDERS: Number of providers reporting to ILINet.
TOTAL PATIENTS: Total number of patients reported to ILINet.
- pandemic.deaths
-
A
data.framewith 63 rows and 5 variables:yearYear corresponding to data.
integerweekCDC ILI week.
integerweek.of.pandemicHow many weeks since the beginning of the pandemic. Starts at 1 for the first recorded element of the given pandemic.
integerpandemicYear of pandemic. Included pandemics are 1918, 1957, 1968, 2009.
integerdeathsEstimated mortality. Please note that not all estimates are for the entire US.
integer- 1918 data
Excess death rates (annual basis) per 100k from influenza and pneumonia in 47 US cities.
- 1957 data
Influenza and pneumonia deaths in the United States.
- 1968 data
Influenza and pneumonia deaths in 122 cities in the United States.
- 2009 data
Influenza deaths in the United States. This includes both waves. For wave 2 only, just use 2009 week 31 (week.of.pandemic 18) and onwards.
- POLYMOD.age.ranges
-
A
data.frame, where each column corresponds to an age range. The column names denote the age ranges. The two rows are AgeStart and AgeEnd. The given age range corresponds to individuals in the range [AgeStart, AgeEnd]. A value of NA for AgeEnd corresponds to no upper bound, so [70,NA] corresponds to all individuals aged 70 or more. - POLYMOD.matrix
-
A
doublematrix, matrix where k_ij is proportional to the observed number of contacts (both physical and nonphysical) that a respondent in age band j makes with other individuals in age band i. The names of both columns and rows denote the age ranges. - population.UK
-
An
integerarray, one entry per age range. Thenamesdenote the age ranges. - population.US
-
A
data.framewith many columns. Those of interest for this package are:YEAR: Which year the data corresponds to. Currently only 2015 data is provided.
AGE: Age of the population of interest. Age of X corresponds to [X,X+1), so 0 means infants under one year of age. Age of 999 corresponds to the entire population.
TOT_POP: Total population in the given age bin (or entire US population if AGE == 999).
- population.US.total
-
A
numericof total 2015 US population.
Source
- ILI.data
-
CDC ILINet
- pandemic.deaths
-
Mossong J, Hens N, Jit M, Beutels P, Auranen K, et al. (2008) Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases. PLOS Medicine 5(3): e74. https://doi.org/10.1371/journal.pmed.0050074
- POLYMOD.age.ranges
-
Mossong J, Hens N, Jit M, Beutels P, Auranen K, et al. (2008) Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases. PLOS Medicine 5(3): e74. https://doi.org/10.1371/journal.pmed.0050074
- POLYMOD.matrix
-
Mossong J, Hens N, Jit M, Beutels P, Auranen K, et al. (2008) Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases. PLOS Medicine 5(3): e74. https://doi.org/10.1371/journal.pmed.0050074
- population.US
-
US Census
- population.US.total
-
US Census
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