NEWS.md

In CDCgov/Rnssp: A Signature R package for the National Syndromic Surveillance Program (NSSP)

Rnssp 0.3.0

New Features

• The Rnssp R package has a new hexsticker.
• Rnssp webassembly build now available for webr and shinylive.
• Custom built shiny applications from the Rnssp-shiny-apps Github repository are seamlessly integrated to Rnssp.
• New function list_apps() lists available custom-built shiny apps from the Rnssp-shiny-apps Github repository.
• New addin added for RStudio users to run Rnssp shiny apps (run_app_gui()).

Updates

• The deprecated $get_api_tsgraph() method has been removed.
• The get_api_tsgraph function has been removed as a consequence of the removal of the deprecated $get_api_tsgraph method.

Bug Fixes

• The Credentials class has been updated. It now interfaces with API services no authorization requirement.
• The get_essence_data() function has been upgraded to accommodate the table builder ESSENCE API.
• The change_dates() function has been upgraded to fix flip-flopping start and end date values (#13)
• The assertive.types package dependency has been replaced by the assertions package (#14).
• The webscrape_icd() function has been fixed to webscrape 2024 ICD10 code sets.

Rnssp 0.2.0

New Features

• New function create_profile() added as a wrapper to the $new() method defined in the Credentials class.
• New function get_essence_data() added to specifically pull data using the NSSP-ESSENCE API.
• Negative binomial detection algorithm alert_nbinom() added for weekly time series of counts spanning multiple years.
• run_app() has been added as a utility to run embedded shiny apps.
• New Token class added for API services token use. The Token class has the same methods as the Credentials class.
• New function create_token_profile() added as a wrapper to the $new() method defined in the Token class.
• Rnssp detects new version and suggests package upgrade.

Updates

• New test test-create_profile.R added for create_profile().
• New test test-create_token_profile.R added for create_token_profile().
• New test test-alert_nbinom.R added for alert_nbinom().
• New test test-alert_serfling.R added for alert_serfling().
• New test test-get_essence_data.R added for get_essence_data().
• New test test-get_api_graph.R added for get_api_graph().
• New test test-get_api_tsgraph.R added for get_api_tsgraph().
• slider package added as a dependency.
• lubridate package added as a dependency.
• Deprecated alert_mar() function has been removed.
• add_rmd_template() has been improved with additional arguments and better error handling.
• remove_rmd_template() has been improved with additional arguments and better error handling.
• Rnssp:::add_rmd_template_gui() has been improved with additional arguments and better error handling.
• Rnssp:::remove_rmd_template_gui() has been improved with additional arguments and better error handling.
• $get_api_response() has been improved and now prints HTTP status code.
• $get_api_tsgraph() has been improved with additional arguments and now prints HTTP status code.
• The $get_api_tsgraph() method has been deprecated and will be removed in the next release of Rnssp.
• New method $get_api_graph() has been added as a replacement to the $get_api_tsgraph().

Bug Fixes

• Abstracted critical user credentials from the $get_api_ts_graph() method.
• Fix the get_api_tsgraph() function which was previously returning an API response object.

Rnssp 0.1.0

New Features

• New function get_api_response() added as a wrapper to the $get_api_response() method defined in the Credentials class.
• New function get_api_data() added as a wrapper to the $get_api_data() method defined in the Credentials class.
• New function get_api_tsgraph() added as a wrapper to the $get_api_tsgraph() method defined in the Credentials class.
• Regression/EWMA Switch algorithm alert_switch() added for anomaly detection.
• Adaptive Multiple Regression algorithm alert_regression() added for anomaly detection.
• Farrington Temporal Detector algorithm alert_farrington() added for weekly time series of counts spanning multiple years.
• ICD Code Web Scraper function webscrape_icd() added to web scrape ICD discharge diagnosis code sets from the CDC FTP server (for ICD-10) or CMS website (for ICD-9).
• The following Addins have been added for RStudio users:
• Create User Profile via a Graphical User Interface (Rnssp:::create_user_profile_gui())
• Create a User Profile with a script skeleton (Rnssp:::create_user_profile())
• List available Rnssp templates (list_templates())
• Add or Update Rnssp templates (Rnssp:::add_rmd_template_gui())
• Remove Rnssp templates (Rnssp:::remove_rmd_template_gui())
• Open Rnssp templates online documentation (Rnssp:::rnssp_templates_manual())
• Open Rnssp package online documentation (Rnssp:::rnssp_manual())

Updates

• add_rmd_template() no longer has a template_name argument. The argument template_name has been replaced by template which is the first argument in the function call.
• New test test-alert_farrington.R added for alert_farrington().
• New test test-alert_regression.R added for alert_regression().
• New test test-alert_switch.R added for alert_switch().
• New test test-add_rmd_template.R added for add_rmd_template().
• New test test-remove_rmd_template.R added for remove_rmd_template().
• New test test-get_api_data.R added for the get_api_data() function.
• New test test-get_api_response.R added for the get_api_response() function.
• New test test-get_api_tsgraph.R added for the get_api_tsgraph() function.
• New test test-get_api_data_method.R added for the $get_api_data() method.
• New test test-get_api_response_method.R added for the $get_api_response() method.
• New test test-get_api_tsgraph_method.R added for the $get_api_tsgraph() method.
• New test test-webscrape_icd.R added for webscrape_icd()
• Added shapefile for US Hospital Service Area (HSA) Shapefile (hsa_sf)
• Added Rnssp stopwords (rnssp_stopwords)
• alert_mar() is depecrated. Use alert_regression instead.
• Test test_alert_mar.R has been removed for alert_mar().
• Regression models in alert_regression() are fit using lm.fit() instead of lm() to reduce computation time associated with extraneous computations made by lm().
• New vignette added to demonstrate the use of Rnssp addins.

Other News

• slider package dependency no longer needed.
• cli package is now a dependency for attractive Command Line Interfaces (CLIs)

Rnssp 0.0.2

New Features

• All vignettes can be browsed with the Rnssp_vignettes() function
• list_templates() lists available templates from the Rnssp-rmd-templates Github repository
• add_rmd_template() can now add RMarkdown templates from Rnssp-rmd-templates Github repository
• add_rmd_template() can now run in non-interactive mode
• remove_rmd_template() removes an existing RMarkdown template from an existing Rnssp package template list.
• change_dates() changes the start and/or end dates in an ESSENCE API URL

Bug Fixes

• Abstracted critical user credentials from response object.
• The $get_api_data() method has been extended to accept further arguments to parse CSV files.

Other News

• Added CI/CD pipeline
• Updated all Rnssp vignettes.
• Rnssp Online documentation website is now available.
• Added new hex sticker for Rnssp package branding.
• Added a THANKS.md to acknowledge various supports and other contributions.

Rnssp 0.0.1

New Features

• alert_ewma() implements EWMA time series anomaly detection algorithm
• alert_mar() implements MAR time series anomaly detection algorithm
• classify_trend() implements a time series trend classification algorithm
• Added a vignette for time series anomaly detection and trend classification
• Added a NEWS.md file to track changes to the package.

Rnssp 0.0.0.9000

CDCgov/Rnssp documentation built on May 12, 2024, 1:32 a.m.