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Code and data for influenza in the United States (1998- Jan 2020)

Citation

N/A

Notes on the code

The .R files contain the code to build the data files and some summary figures. In line comments mention some key gaps.

Data

  1. ILINet.csv - US CDC FluView https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html. Downloaded on Jan. 27th 2020.
  2. WHO_NREVSS_Clinical_Labs.csv - US CDC FluView https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html. Downloaded on Jan. 27th 2020.
  3. WHO_NREVSS_Combined_prior_to_2015_16.csv - US CDC FluView https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html. Downloaded on Jan. 27th 2020.
  4. WHO_NREVSS_Public_Health_Labs.csv - US CDC FluView https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html. Downloaded on Jan. 27th 2020.
  5. us_pops.csv - Data were copy/pasted from https://www.multpl.com/united-states-population/table/by-year on Sept. 24th 2019. They ballpark look right, but we should circle back and use US census data.
  6. Biosense2_resp_Dallase_Denton_Ellis_Johnson_Parker_Tarrant.csv - Weekly BioSense 2.0 data were extracted from an online repository (see link). Data are the percent of emergency department visits for upper respiratory infection, based on classification of free-text chief complaint entries. Data were collected from https://www.google.com/publicdata/explore?ds=z46e2n1b69u8mu_

CDC Disclaimer

This was copy/pasted from https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html on Oct 7th 2019

Disclaimer

Viral Surveillance — Data collection from both the U.S. World Health Organization (WHO) Collaborating Laboratories and National Respiratory and Enteric Virus Surveillance System (NREVSS) laboratories began during the 1997-98 season. The volume of tested specimens has greatly increased during this time due to increased participation and increased testing. During the 1997-98 season 43 state public health laboratories participated in surveillance, and by the 2004-05 season all state public health laboratories were participating in surveillance. The addition of NREVSS data during the 1997-98 season roughly doubled the amount of virologic data reported each week.

The number of specimens tested and % positive rate vary by region and season based on different testing practices including triaging of specimens by the reporting labs, therefore it is not appropriate to compare the magnitude of positivity rates or the number of positive specimens between regions or seasons.

The U.S. WHO and NREVSS collaborating laboratories report the total number of respiratory specimens tested and the number positive for influenza types A and B each week to CDC. Most of the U.S. WHO collaborating laboratories also report the influenza A subtype (H1 or H3) of the viruses they have isolated, but the majority of NREVSS laboratories do not report the influenza A subtype.

For more information on virologic surveillance please visit:http://www.cdc.gov/flu/weekly/overview.htm#Viral

Outpatient Illness Surveillance — Information on patient visits to health care providers for influenza-like illness is collected through the U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet). This collaborative effort between CDC, state and local health departments, and health care providers started during the 1997-98 influenza season when approximately 250 providers were enrolled. Enrollment in the system has increased over time and there were >3,000 providers enrolled during the 2010-11 season.

The number and percent of patients presenting with ILI each week will vary by region and season due to many factors, including having different provider type mixes (children present with higher rates of ILI than adults, and therefore regions with a higher percentage of pediatric practices will have higher numbers of cases). Therefore it is not appropriate to compare the magnitude of the percent of visits due to ILI between regions and seasons.

Baseline levels are calculated both nationally and for each region. Percentages at or above the baseline level are considered to be elevated.

For more information on ILI surveillance and baselines please visit:http://www.cdc.gov/flu/weekly/overview.htm#Outpatient

License

(see LICENSE)

Additional license, warranty, and copyright information

We provide a license for our code (see LICENSE) and do not claim ownership, nor the right to license, the data we have obtained. Please cite the appropriate agency, paper, and/or individual in publications and/or derivatives using these data, contact them regarding the legal use of these data, and remember to pass-forward any existing license/warranty/copyright information. As a reminder, THE DATA AND SOFTWARE ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE DATA AND/OR SOFTWARE OR THE USE OR OTHER DEALINGS IN THE DATA AND/OR SOFTWARE.