Key functions used by the SIR team
First make sure you have devtools installed (if not run
install.pacakges("devtools")). Then run the following command:
devtools::install_github("nish-kishore/sirfunctions")Remember to update from sirfunctions regularly. If no update is needed
the line of code above will automatically skip.
After, you can use any function developed in this package using
sirfunctions::{function}for example:
sirfunctions::edav_io(io = "list")You can find the documentation for any function by running
?sirfunctions::{function}for example:
?sirfunctions::edav_ioHere is a current list of core functions included in sirfunctions with
brief descriptions.
NOTE: Any "Get Data" functions or those that interact with EDAV require authenticated connection to CDC EDAV resources
1) get_all_polio_data: This is the primary function which loads all
recent polio data. Parameters can be used to specify date ranges,
data selection and user verification.
2) edav_io: Perform key writing/reading/editing functions for EDAV
from your R system.
3) load_clean_{resolution}_sp: 'resolution` can be dist, prov or
ctry. Parameters can be used to specify date or spatial ranges as
well as the output.
4) init_dr: This is the primary function to initialize the desk
review analytic pipeline. This function handles folder organization
and download of data for a specific country.
1) send_teams_message: Send a message to a teams channel with
attachments.
2) upload_to_sharepoint: Upload a document to a sharepoint folder.
3) send_outlook_email: Send an email from the validated microsoft
account.
1) extract_country_data: Expects a 'raw.data' object that is
generated by get_all_polio_data() which includes spatial data.
Generates a country specific data file along with relevant spatial
objects.
2) f.ev.rate.01: Calculate the enterovirus detection rate using CDC
cleaned environmental surveillance data.
3) f.npafp.rate.01: Calculate the non-polio (NP) acute flaccid
paralysis (AFP) rate accounting for person-time at risk using CDC
cleaned AFP data and appropriately matched population data.
4) f.stool.ad.01: Calculate stool adequacy using CDC cleaned acute
flaccid paralysis (AFP) data.
5) f.timely.detection.01: Calculate the timeliness of detection of
cases using CDC cleaned acute flaccid paralysis (AFP) data.
6) f.timely.01: Calculate the timeliness of stool data using only epi
data.
1) test_EDAV_connection: Evaluates the speed of connection that users
have with the CDC EDAV system.
2) f.color.schemes: Adds Standard color schemes used in figure
creation by the SIR team.
3) f.expand.bbox: Expands a geographic bounding box generated for
maps.
4) f.metadata.tag: Adds a tag using information from the CDC
generated 'raw.data' file to ggplot and flextable objects.
5) f.plot.looks: Adds standard themes used in figure creation by the
SIR team.
6) create_emergence_group_gif(): function to visualize the spread of
specific emegrence groups.
Please send a message to Nishant Kishore at ynm2\@cdc.gov{.email} for any questions or queries.
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