Package 'RtD3'

default_data_ref

Description

Create a default reference for a input datasets. Also useful as a template when defining your own.

Usage

default_data_ref()

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default_map_legend_ref

Description

Create a default reference for a map legend. Also useful as a template when defining your own.

Usage

default_map_legend_ref()

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default_ts_color_ref

Description

Create a default reference for time series colors. Also useful as a template when defining your own.

Usage

default_ts_color_ref()

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default_ts_colors

Description

Define default colors for time series plots

Can be overridden with a list of the same format

Usage

default_ts_colors()

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Get Subregional Estimate Urls

Description

Get Subregional Estimate Urls

Usage

getSubregionalUrls(path, areas)

Arguments

path	A character string container the overall path to subnational estimates
areas	A character vector listing the subregional estimates (assuming that listed in the geoData with capitalisation and without capitalisation in the path).

Value

A named list of subnational urls.

Examples

getSubregionalUrls(path = "https://epiforecasts.io/covid/posts/national/",
                  areas = c('Afghanistan', 'Brazil', 'Colombia', 'United States'))

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Join RtData

Description

Joins two nested lists in the format required by summaryWidget. This may be useful for merging estimates from disparate data sources or linking national level estimates with subnational estimates

Usage

joinRtData(rtData, rtData2)

Arguments

rtData	A nested list as required by summaryWidget
rtData2	A nested list as required by summaryWidget

Value

A nested list as required by summaryWidget

Examples

base_url <- "https://raw.githubusercontent.com/epiforecasts/covid-rt-estimates/master/"
subnational <-   national <- list("Cases" = readInEpiNow2(
path = paste0(base_url, "subnational/italy/cases/summary"),
region_var = "region"))


national <- list("Cases" = readInEpiNow2(
path = paste0(base_url, "national/cases/summary"),
region_var = "country"),
regions = "Italy")

out <- list()
out$Cases <- joinRtData(subnational$Cases, national$Cases)

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legend_qualitative

Description

Create a qualitative legend.

Usage

legend_qualitative(variable_name, legend_values)

Arguments

variable_name	string, name of the variable of this legend.
legend_values	list, reference for legend colors in the format: 'value':'color', ....

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legend_sequential

Description

Create a qualitative legend. 'legend_scale“ accepts scales listed in d3-scale.

Usage

legend_sequential(
  variable_name,
  legend_scale = "scaleLinear",
  color_low = "white",
  color_high = "green",
  color_no_data = "lightgrey"
)

Arguments

variable_name	string, name of the variable of this legend.
legend_scale	string, type of legend scale, must be the name of a d3 scale. Default: "scaleLinear".
color_low	string, color for the lowest value of the legend.
color_high	string, color for the highest value of the legend.
color_no_data	string, color for no data entries.

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Read in Results from EpiNow2

Description

Reads in results from EpiNow2 and converts them into the RtD3 format. Supports either input via a list object or from a file path/url.

Usage

readInEpiNow2(input_list, path, region_var = "region", regions)

Arguments

input_list	A list of results as returned by EpiNow2::regional_summary
path	A character string indicating the path (either file or URL) to the summary results
region_var	A character string that identifies the region name used.
regions	A character string indicating the regions of interest to returns. Defaults to all regions.

Value

A named list in the format required by summaryWidget along with a summary table.

Examples

# Read in each summary folder

base_path <- "https://raw.githubusercontent.com/epiforecasts/covid-rt-estimates/"
rtData <- readInEpiNow2(
  path = paste0(base_path, "master/national/cases/summary"),
  region_var = "country")

rtData



france <- readInEpiNow2(
  path = paste0(base_path, "master/national/cases/summary"),
  region_var = "country",
  regions = "France")

france

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summaryWidget

Description

Create an Rt visualisation using D3. Need convenience functions to define defaults

Usage

summaryWidget(
  geoData = NULL,
  rtData = NULL,
  data_ref = NULL,
  subregional_ref = NULL,
  ts_color_ref = NULL,
  ts_bar_color = "lightgrey",
  projection = "geoEquirectangular",
  map_legend_ref = NULL,
  credible_threshold = 10,
  width = NULL,
  activeArea = "United Kingdom",
  downloadUrl = NULL,
  dryRun = FALSE
)

Arguments

geoData	sf object, map data
rtData	data.frame, rt estimates in the format 'Source':'rtData':x, 'casesInfectionData':x, 'casesReportData':x, 'obsCasesData':x, ...
data_ref	list, reference for input data column names. Specify the column holding geometry to be symbolized 'rtData':'geometry_name':'region', ...
subregional_ref	list, reference to subnational estimates in the format 'country_name':'url', ....
ts_color_ref	list, reference for colors for time series plots.
ts_bar_color	string, color of observed cases bars in time series plots.
projection	string, map projection, must be named in d3-geo-projection.
map_legend_ref	list, reference for map legend variables
credible_threshold	integer, Threshold for credible intervals, maximum observed cases * this value will be removed.
width	integer, Width of widget in pixels.
activeArea	string, Area to symbolize first.
downloadUrl	string, URL to download data.
dryRun	Logical, defaults to FALSE. Should the function be tested without the widget being created. Useful for checking the integrity of input data.

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Shiny bindings for summaryWidget

Description

Output and render functions for using summaryWidget within Shiny applications and interactive Rmd documents.

Usage

summaryWidgetOutput(outputId, width = "100%", height = "400px")

rendersummaryWidget(expr, env = parent.frame(), quoted = FALSE)

Arguments

outputId	output variable to read from
width, height	Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.
expr	An expression that generates a RtD3
env	The environment in which to evaluate expr.
quoted	Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

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