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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,35 +1,35 @@ | ||
| #' @keywords internal | ||
| "_PACKAGE" | ||
| #' Tools, Functions, Shapefiles data, and Rmarkdown templates to work with Syndromic Surveillance data via NSSP ESSENCE | ||
| #' | ||
| #' The National Syndromic and Surveillance Program (NSSP) at the Centers for Disease and Control has a large Community of Practice (CoP) | ||
| #' 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 `Rnnsp` R package is built in an attempt to | ||
| #' improve reusability, reproducibility, and distribution of the analytical resources developed at the CDC NSSP. | ||
| #' | ||
| #' @section Rnssp functions: | ||
| #' The Rnssp functions include: | ||
| #' \itemize{ | ||
| #' \item API functions to pull data from the ESSENCE system | ||
| #' \item Various utility functions to securely set user credentials, add or remove R Markdown templates, or set new dates in API urls. | ||
| #' \item Anomaly detection and Time Series Trend classification algorithms | ||
| #' } | ||
| #' | ||
| #' @section Rnssp vignettes: | ||
| #' The vignettes serve as instructive tutorials demonstrating practical uses of the | ||
| #' Rnssp package. Please run the `Rnssp_vignettes()` function to browse all available vignettes. | ||
| #' | ||
| #' @section Rnssp Rmarkdown templates: | ||
| #' By default, the Rnssp package comes with one R Markdown template. We leave it up | ||
| #' to users to decide which template to extend the package with post-installation. | ||
| #' To list all available template, run the `list_templates()` function. Please, check | ||
| #' the Rnssp R markdown template Github repository at | ||
| #' https://github.com/cdcgov/rnssp-rmd-templates. | ||
| #' | ||
| #' @docType package | ||
| #' @name Rnssp | ||
| #' @author Gbedegnon Roseric Azondekon ([email protected]) | ||
| #' @import dplyr, readr, magrittr, R6, stringi, assertive.types, safer, jsonlite, httr, askpass, yaml | ||
| #' @import sf | ||
| NULL | ||
| # > NULL | ||
| #' @keywords internal | ||
| "_PACKAGE" | ||
| #' Tools, Functions, Shapefiles data, and Rmarkdown templates to work with Syndromic Surveillance data via NSSP ESSENCE | ||
| #' | ||
| #' The National Syndromic and Surveillance Program (NSSP) at the Centers for Disease and Control has a large Community of Practice (CoP) | ||
| #' 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. | ||
| #' | ||
| #' @section Rnssp functions: | ||
| #' The Rnssp functions include: | ||
| #' \itemize{ | ||
| #' \item API functions to pull data from the ESSENCE system | ||
| #' \item Various utility functions to securely set user credentials, add or remove R Markdown templates, or set new dates in API urls. | ||
| #' \item Anomaly detection and Time Series Trend classification algorithms | ||
| #' } | ||
| #' | ||
| #' @section Rnssp vignettes: | ||
| #' The vignettes serve as instructive tutorials demonstrating practical uses of the | ||
| #' Rnssp package. Please run the \code{\link[Rnnsp]{Rnssp_vignettes()}} function to browse all available vignettes. | ||
| #' | ||
| #' @section Rnssp Rmarkdown templates: | ||
| #' By default, the Rnssp package comes with one R Markdown template. We leave it up | ||
| #' to users to decide which template to extend the package with post-installation. | ||
| #' To list all available template, run the \code{\link[Rnnsp]{list_templates()}} function. Please, check | ||
| #' the Rnssp R markdown template Github repository at | ||
| #' \href{https://github.com/cdcgov/rnssp-rmd-templates}{https://github.com/cdcgov/rnssp-rmd-templates}. | ||
| #' | ||
| #' @docType package | ||
| #' @name Rnssp | ||
| #' @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 | ||
| NULL | ||
| # > NULL |
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|---|---|---|
| @@ -1,23 +1,23 @@ | ||
| #' US Core-Based Statistical Area Shapefile | ||
| #' | ||
| #' Useful `sf`` object shapefile for US Core-Based Statistical Area. | ||
| #' | ||
| #' \preformatted{ | ||
| #' Rows: 933 | ||
| #' Columns: 9 | ||
| #' $ CSAFP <fct> NA, NA, NA, NA, 220, 184, NA, NA, 440, 104, 172, NA, 290, 106, 142, NA, NA, 204, 408, 394, NA, NA, NA, 108, NA, 218, 104, NA, 258, 2... | ||
| #' $ CBSAFP <fct> 10100, 10140, 10180, 10220, 10300, 10420, 10460, 10500, 10540, 10580, 10620, 10660, 10700, 10740, 10760, 10780, 10820, 10860, 10900,... | ||
| #' $ AFFGEOID <fct> 310M400US10100, 310M400US10140, 310M400US10180, 310M400US10220, 310M400US10300, 310M400US10420, 310M400US10460, 310M400US10500, 310M... | ||
| #' $ GEOID <fct> 10100, 10140, 10180, 10220, 10300, 10420, 10460, 10500, 10540, 10580, 10620, 10660, 10700, 10740, 10760, 10780, 10820, 10860, 10900,... | ||
| #' $ NAME <fct> "Aberdeen, SD", "Aberdeen, WA", "Abilene, TX", "Ada, OK", "Adrian, MI", "Akron, OH", "Alamogordo, NM", "Albany, GA", "Albany, OR", "... | ||
| #' $ LSAD <fct> M2, M2, M1, M2, M2, M1, M2, M1, M1, M1, M2, M2, M2, M1, M2, M1, M2, M2, M1, M2, M2, M1, M2, M1, M2, M1, M2, M2, M2, M1, M1, M1, M2, ... | ||
| #' $ ALAND <fct> 7353004578, 4924421612, 7105577213, 1865885645, 1941541486, 2331552026, 17126456771, 5006277239, 5923636964, 7282214082, 1023370459,... | ||
| #' $ AWATER <fct> 111384297, 834689898, 36847511, 12421414, 30482189, 62086003, 36943378, 64821308, 50354267, 172506034, 25242751, 39237837, 148495464... | ||
| #' $ geometry <MULTIPOLYGON [m]> MULTIPOLYGON (((22796.3 369..., MULTIPOLYGON (((-1733803 53..., MULTIPOLYGON (((-13821.28 -..., MULTIPOLYGON (((280928.... | ||
| #' } | ||
| #' @examples | ||
| #' library(Rnssp) | ||
| #' data("cbsa_sf") | ||
| #' | ||
| #' plot(cbsa_sf$geometry) | ||
| "cbsa_sf" | ||
| #' US Core-Based Statistical Area Shapefile | ||
| #' | ||
| #' Useful \code{sf} object shapefile for US Core-Based Statistical Area. | ||
| #' | ||
| #' \preformatted{ | ||
| #' Rows: 933 | ||
| #' Columns: 9 | ||
| #' $ CSAFP <fct> NA, NA, NA, NA, 220, 184, NA, NA, 440, 104, 172, NA, 290, 106, 142, NA, NA, 204, 408, 394, NA, NA, NA, 108, NA, 218, 104, NA, 258, 2... | ||
| #' $ CBSAFP <fct> 10100, 10140, 10180, 10220, 10300, 10420, 10460, 10500, 10540, 10580, 10620, 10660, 10700, 10740, 10760, 10780, 10820, 10860, 10900,... | ||
| #' $ AFFGEOID <fct> 310M400US10100, 310M400US10140, 310M400US10180, 310M400US10220, 310M400US10300, 310M400US10420, 310M400US10460, 310M400US10500, 310M... | ||
| #' $ GEOID <fct> 10100, 10140, 10180, 10220, 10300, 10420, 10460, 10500, 10540, 10580, 10620, 10660, 10700, 10740, 10760, 10780, 10820, 10860, 10900,... | ||
| #' $ NAME <fct> "Aberdeen, SD", "Aberdeen, WA", "Abilene, TX", "Ada, OK", "Adrian, MI", "Akron, OH", "Alamogordo, NM", "Albany, GA", "Albany, OR", "... | ||
| #' $ LSAD <fct> M2, M2, M1, M2, M2, M1, M2, M1, M1, M1, M2, M2, M2, M1, M2, M1, M2, M2, M1, M2, M2, M1, M2, M1, M2, M1, M2, M2, M2, M1, M1, M1, M2, ... | ||
| #' $ ALAND <fct> 7353004578, 4924421612, 7105577213, 1865885645, 1941541486, 2331552026, 17126456771, 5006277239, 5923636964, 7282214082, 1023370459,... | ||
| #' $ AWATER <fct> 111384297, 834689898, 36847511, 12421414, 30482189, 62086003, 36943378, 64821308, 50354267, 172506034, 25242751, 39237837, 148495464... | ||
| #' $ geometry <MULTIPOLYGON [m]> MULTIPOLYGON (((22796.3 369..., MULTIPOLYGON (((-1733803 53..., MULTIPOLYGON (((-13821.28 -..., MULTIPOLYGON (((280928.... | ||
| #' } | ||
| #' @examples | ||
| #' library(Rnssp) | ||
| #' data("cbsa_sf") | ||
| #' | ||
| #' plot(cbsa_sf$geometry) | ||
| "cbsa_sf" |
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|---|---|---|
| @@ -1,32 +1,32 @@ | ||
| #' A `NSSPContainer` Class to store a value in a container object | ||
| #' | ||
| #' @description | ||
| #' A `NSSPContainer` object stores a value | ||
| #' | ||
| #' @details | ||
| #' A `NSSPContainer` object can be used to retrieve a value | ||
| NSSPContainer <- R6::R6Class( | ||
| "NSSPContainer", | ||
| private = list( | ||
| ..value = NULL | ||
| ), | ||
| active = list( | ||
| value = function() { | ||
| private$..value | ||
| } | ||
| ), | ||
| public = list( | ||
|
|
||
| #' @description | ||
| #' Initializes a new NSSPContainer object. | ||
| #' @param entry an object or value to be stored | ||
| #' @return A new `NSSPContainer` object | ||
| initialize = function(entry) { | ||
| if (missing(entry)) { | ||
| private$..value | ||
| } else { | ||
| private$..value <- entry | ||
| } | ||
| } | ||
| ) | ||
| ) | ||
| #' A \code{NSSPCredentials} Class to store a value in a container object | ||
| #' | ||
| #' @description | ||
| #' A \code{NSSPCredentials} object stores a value | ||
| #' | ||
| #' @details | ||
| #' A \code{NSSPCredentials} object can be used to retrieve a value | ||
| NSSPContainer <- R6::R6Class( | ||
| "NSSPContainer", | ||
| private = list( | ||
| ..value = NULL | ||
| ), | ||
| active = list( | ||
| value = function() { | ||
| private$..value | ||
| } | ||
| ), | ||
| public = list( | ||
|
|
||
| #' @description | ||
| #' Initializes a new NSSPContainer object. | ||
| #' @param entry an object or value to be stored | ||
| #' @return A new \code{NSSPCredentials} object | ||
| initialize = function(entry) { | ||
| if (missing(entry)) { | ||
| private$..value | ||
| } else { | ||
| private$..value <- entry | ||
| } | ||
| } | ||
| ) | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,24 +1,24 @@ | ||
| #' US Counties Shapefile | ||
| #' | ||
| #' Useful `sf`` object shapefile for US Counties. | ||
| #' | ||
| #' \preformatted{ | ||
| #' Rows: 3,142 | ||
| #' Columns: 10 | ||
| #' $ STATEFP <fct> 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, ... | ||
| #' $ COUNTYFP <fct> 001, 003, 005, 007, 009, 011, 013, 015, 017, 019, 021, 023, 025, 027, 029, 031, 033, 035, 037, 039, 041, 043, 045, 047, 049, 051, 05... | ||
| #' $ COUNTYNS <fct> 00161526, 00161527, 00161528, 00161529, 00161530, 00161531, 00161532, 00161533, 00161534, 00161535, 00161536, 00161537, 00161538, 00... | ||
| #' $ AFFGEOID <fct> 0500000US01001, 0500000US01003, 0500000US01005, 0500000US01007, 0500000US01009, 0500000US01011, 0500000US01013, 0500000US01015, 0500... | ||
| #' $ GEOID <fct> 01001, 01003, 01005, 01007, 01009, 01011, 01013, 01015, 01017, 01019, 01021, 01023, 01025, 01027, 01029, 01031, 01033, 01035, 01037,... | ||
| #' $ NAME <fct> Autauga, Baldwin, Barbour, Bibb, Blount, Bullock, Butler, Calhoun, Chambers, Cherokee, Chilton, Choctaw, Clarke, Clay, Cleburne, Cof... | ||
| #' $ LSAD <fct> 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, ... | ||
| #' $ ALAND <fct> 1539602123, 4117546676, 2292144655, 1612167481, 1670103911, 1613059160, 2012002530, 1569189622, 1545085607, 1433623321, 1794477075, ... | ||
| #' $ AWATER <fct> 25706961, 1133055836, 50538698, 9602089, 15015423, 6054988, 2701198, 16627597, 16971701, 120308339, 20592144, 19144469, 36657891, 52... | ||
| #' $ geometry <MULTIPOLYGON [m]> MULTIPOLYGON (((1225889 -12..., MULTIPOLYGON (((1151155 -15..., MULTIPOLYGON (((1355398 -13..., MULTIPOLYGON (((1174172.. | ||
| #' } | ||
| #' @examples | ||
| #' library(Rnssp) | ||
| #' data("county_sf") | ||
| #' | ||
| #' plot(county_sf$geometry) | ||
| "county_sf" | ||
| #' US Counties Shapefile | ||
| #' | ||
| #' Useful \code{sf} object shapefile for US Counties. | ||
| #' | ||
| #' \preformatted{ | ||
| #' Rows: 3,142 | ||
| #' Columns: 10 | ||
| #' $ STATEFP <fct> 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, 01, ... | ||
| #' $ COUNTYFP <fct> 001, 003, 005, 007, 009, 011, 013, 015, 017, 019, 021, 023, 025, 027, 029, 031, 033, 035, 037, 039, 041, 043, 045, 047, 049, 051, 05... | ||
| #' $ COUNTYNS <fct> 00161526, 00161527, 00161528, 00161529, 00161530, 00161531, 00161532, 00161533, 00161534, 00161535, 00161536, 00161537, 00161538, 00... | ||
| #' $ AFFGEOID <fct> 0500000US01001, 0500000US01003, 0500000US01005, 0500000US01007, 0500000US01009, 0500000US01011, 0500000US01013, 0500000US01015, 0500... | ||
| #' $ GEOID <fct> 01001, 01003, 01005, 01007, 01009, 01011, 01013, 01015, 01017, 01019, 01021, 01023, 01025, 01027, 01029, 01031, 01033, 01035, 01037,... | ||
| #' $ NAME <fct> Autauga, Baldwin, Barbour, Bibb, Blount, Bullock, Butler, Calhoun, Chambers, Cherokee, Chilton, Choctaw, Clarke, Clay, Cleburne, Cof... | ||
| #' $ LSAD <fct> 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, 06, ... | ||
| #' $ ALAND <fct> 1539602123, 4117546676, 2292144655, 1612167481, 1670103911, 1613059160, 2012002530, 1569189622, 1545085607, 1433623321, 1794477075, ... | ||
| #' $ AWATER <fct> 25706961, 1133055836, 50538698, 9602089, 15015423, 6054988, 2701198, 16627597, 16971701, 120308339, 20592144, 19144469, 36657891, 52... | ||
| #' $ geometry <MULTIPOLYGON [m]> MULTIPOLYGON (((1225889 -12..., MULTIPOLYGON (((1151155 -15..., MULTIPOLYGON (((1355398 -13..., MULTIPOLYGON (((1174172.. | ||
| #' } | ||
| #' @examples | ||
| #' library(Rnssp) | ||
| #' data("county_sf") | ||
| #' | ||
| #' plot(county_sf$geometry) | ||
| "county_sf" |
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