Merge pull request #1 from CDCgov/dev

Migrating to Rnssp v 0.1.0

DESCRIPTION

@@ -1,54 +1,57 @@
-Package: Rnssp
-Type: Package
-Title: A Signature R package for the National Syndromic and Surveillance Program (NSSP)
-Version: 0.0.2
-Date: 2021-01-27
-Authors@R: c(
-    person("Gbedegnon Roseric", "Azondekon", email = "[email protected]",
-                  role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9155-4153")),
-    person("Michael", "Sheppard", email = "[email protected]",
-                  role = c("ctb"), comment = c(ORCID = "0000-0003-3660-575X")))
-Maintainer: Gbedegnon Roseric Azondekon <[email protected]>
-Description: A collection of tools, functions, and Rmarkdown templates 
-    that supports the National Syndromic and Surveillance Program Community of Practice.
-Depends: 
-    R (>= 3.6.0),
-    magrittr,
-    purrr,
-    dplyr,
-    data.table,
-    stringr,
-    tidyr,
-    slider,
-    sf
-License: Apache License (>= 2)
-URL: https://github.com/CDCgov/Rnssp, https://cdcgov.github.io/Rnssp
-Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.1.1
-Suggests: 
-    testthat,
-    knitr,
-    rmarkdown,
-    scales,
-    forcats,
-    ggplot2,
-    ggpubr,
-    ggraph,
-    ggthemes,
-    igraph,
-    tidytext,
-    widyr
-Imports: 
-    R6,
-    stringi,
-    assertive.types,
-    safer,
-    jsonlite,
-    httr,
-    askpass,
-    readr,
-    janitor,
-    tibble,
-    yaml
-VignetteBuilder: knitr
+Package: Rnssp
+Type: Package
+Title: A Signature R package for the National Syndromic Surveillance Program (NSSP)
+Version: 0.1.0
+Date: 2021-01-27
+Authors@R: c(
+    person("Gbedegnon Roseric", "Azondekon", email = "[email protected]",
+                  role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9155-4153")),
+    person("Michael", "Sheppard", email = "[email protected]",
+                  role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-3660-575X")))
+Maintainer: Gbedegnon Roseric Azondekon <[email protected]>
+Description: A collection of tools, functions, and Rmarkdown templates 
+    that supports the National Syndromic Surveillance Program Community of Practice.
+Depends: 
+    R (>= 3.6.0),
+    magrittr,
+    purrr,
+    dplyr,
+    data.table,
+    stringr,
+    tidyr,
+    sf
+License: Apache License (>= 2)
+URL: https://github.com/CDCgov/Rnssp, https://cdcgov.github.io/Rnssp
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.1.1
+Suggests: 
+    testthat,
+    knitr,
+    rmarkdown,
+    scales,
+    forcats,
+    ggplot2,
+    ggpubr,
+    ggraph,
+    ggthemes,
+    igraph,
+    tidytext,
+    widyr
+Imports: 
+    R6,
+    stringi,
+    assertive.types,
+    safer,
+    jsonlite,
+    httr,
+    askpass,
+    readr,
+    janitor,
+    tibble,
+    yaml,
+    cli,
+    shiny (>= 0.13),
+    miniUI (>= 0.1.1),
+    rstudioapi (>= 0.5)
+VignetteBuilder: knitr

NEWS.md

@@ -1,32 +1,76 @@
-# 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](https://github.com/CDCgov/Rnssp-rmd-templates) Github repository
-* `add_rmd_template()` can now add RMarkdown templates from [Rnssp-rmd-templates](https://github.com/CDCgov/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 `$get_api_data()` method has been extended to accept further arguments to parse CSV files.
-
-## Other News
-* Added CI/CD pipeline
-* Updated all `Rnssp` vignettes.
-* [Rnssp Online documentation](https://cdcgov.github.io/Rnssp/) website is now available.
-* Added new hex sticker for Rnssp package branding.
-* Added a `THANKS.md` to acknowledge various supports and other contributions.
-
-# Rnssp 0.0.1
-
-## New Features
-
-* `alert_ewma()` implements EWMA time series anomaly detection algorithm
-* `alert_mar()` implements MAR time series anomaly detection algorithm
-* `classify_trend()` implements a time series trend classification algorithm
-* Added a vignette for time series anomaly detection and trend classification
-* Added a `NEWS.md` file to track changes to the package.
-
-# Rnssp 0.0.0.9000
+# Rnssp 0.1.0
+
+## New Features
+* New function `get_api_data()` added as a wrapper to the `$get_api_response()` method defined in the `Credentials` class.
+* New function `get_api_response()` 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 `$get_api_tsgraph()` method.
+* New test `test-webscrape_icd.R` added for `webscrape_icd()`
+* Added shapefile for US Hospital Service Area (HSA) Shapefile (`hsa_sf`)
+* Added Rnssp stopwords (`rnssp_stopwords`)
+* `alert_mar()` is depecrated. Use `alert_regression` instead.
+* Test `test_alert_mar.R` has been removed for `alert_mar()`.
+* Regression models in `alert_regression()` are fit using `lm.fit()` instead of `lm()` to reduce computation time associated with extraneous computations made by `lm()`.
+* New vignette added to demonstrate the use of Rnssp addins.
+
+## Other News
+* `slider` package dependency no longer needed.
+* `cli` package is now a dependency for attractive Command Line Interfaces (CLIs)
+
+# Rnssp 0.0.2
+
+## New Features
+* All vignettes can be browsed with the `Rnssp_vignettes()` function
+* `list_templates()` lists available templates from the [Rnssp-rmd-templates](https://github.com/CDCgov/Rnssp-rmd-templates) Github repository
+* `add_rmd_template()` can now add RMarkdown templates from [Rnssp-rmd-templates](https://github.com/CDCgov/Rnssp-rmd-templates) Github repository
+* `add_rmd_template()` can now run in non-interactive mode
+* `remove_rmd_template()` removes an existing RMarkdown template from an existing `Rnssp` package template list.
+* `change_dates()` changes the start and/or end dates in an ESSENCE API URL
+
+## Bug Fixes
+* Abstracted critical user credentials from response object.
+* The `$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](https://cdcgov.github.io/Rnssp/) 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

R/Rnssp-package.R

@@ -2,7 +2,11 @@
 "_PACKAGE"
 #' Tools, Functions, Shapefiles data, and Rmarkdown templates to work with Syndromic Surveillance data via NSSP ESSENCE
 #'
+<<<<<<< HEAD
+#' The National Syndromic Surveillance Program (NSSP) at the Centers for Disease and Control has a large Community of Practice (CoP)
+=======
 #' The National Syndromic and Surveillance Program (NSSP) at the Centers for Disease and Control has a large Community of Practice (CoP)
+>>>>>>> master
 #' including state and local Departments of Health. The NSSP has developed multiple resources including analysis reports,
 #' analytic tools, and assisted with scripts to interface with ESSENCE. The \code{Rnssp} R package is built in an attempt to
 #' improve reusability, reproducibility, and distribution of the analytical resources developed at the CDC NSSP.
@@ -28,8 +32,14 @@
 #'
 #' @docType package
 #' @name Rnssp
+<<<<<<< HEAD
+#' @author Gbedegnon Roseric Azondekon (\email{[email protected]})
+#' @import dplyr, readr, magrittr, R6, stringi, assertive.types, safer, jsonlite, httr, askpass, yaml
+#' @import sf, shiny (>= 0.13), miniUI (>= 0.1.1), rstudioapi (>= 0.5)
+=======
 #' @author Gbedegnon Roseric Azondekon (\href{mailto:[email protected]}{[email protected]})
 #' @import dplyr, readr, magrittr, R6, stringi, assertive.types, safer, jsonlite, httr, askpass, yaml
 #' @import sf
+>>>>>>> master
 NULL
 # > NULL