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Dynamically generate mantis output for an rmd chunk

Source: R/construct.R
bespoke_rmd_output.Rd

Add mantis tabs and visualisations to an existing rmarkdown report. The function writes directly to the chunk using side-effects, so chunk options must contain results = 'asis'. Make sure you read the vignette: vignette("bespoke-reports", package = "mantis") as it contains further important information.

Usage

bespoke_rmd_output(
  df,
  inputspec,
  outputspec,
  alertspec = NULL,
  timepoint_limits = c(NA, NA),
  fill_with_zero = FALSE,
  tab_name = NULL,
  tab_level = 1
)

Arguments

df

A data frame containing multiple time series in long format. See Details.

inputspec

inputspec() object specifying which columns in the supplied df represent the "timepoint", "item", and "value" for the time series. A separate tab will be created for each distinct value in the "tab" column.

outputspec

outputspec object specifying the desired format of the html table(s)/plot(s). If not supplied, default values will be used.

alertspec

alertspec() object specifying conditions to test and display

timepoint_limits

Set start and end dates for time period to include. Defaults to min/max of timepoint_col

fill_with_zero

Logical. Replace any missing or NA values with 0? Useful when value_col is a record count

tab_name

Character string to appear on the tab label. If omitted or NULL, only the content/child tabs (and not the parent tab) will be created.

tab_level

integer specifying the nesting level of the tab. If tab_name is specified, a value of 1 generates a tab at rmd level "##", and any tab_col tabs at a level down. If tab_name is not specified, any tab_col tabs will be created at rmd level "##".

Value

(invisibly) the supplied df

Details

You can:

  • add a single visualisation, with or without creating the container tab, or

  • add a set of tabs, each based on the same output specification, with or without creating the parent tab.

The supplied data frame should contain multiple time series in long format, i.e.:

  • one "timepoint" (date/posixt) column which will be used for the x-axes. Values should follow a regular pattern, e.g. daily or monthly, but do not have to be consecutive.

  • one or more "item" (character) columns containing categorical values identifying distinct time series.

  • one "value" (numeric) column containing the time series values which will be used for the y-axes.

The inputspec parameter maps the data frame columns to the above. Optionally, if there are multiple columns specified in item_cols, one of them can be used to group the time series into different child tabs, by using the tab_col parameter.

See also

bespoke_rmd_initialise_widgets()

Examples

if (FALSE) { # \dontrun{

# put this inside a chunk in the rmd file,
# with chunk option `results = 'asis'`
mantis::bespoke_rmd_output(
  df = mantis::example_prescription_numbers,
  inputspec = mantis::inputspec(
    timepoint_col = "PrescriptionDate",
    item_cols = c("Location", "Antibiotic"),
    value_col = "NumberOfPrescriptions",
    tab_col = "Location"
  ),
  outputspec = mantis::outputspec_interactive(
    plot_value_type = "value",
    plot_type = "bar",
    item_labels = c("Antibiotic" = "Antibiotic name"),
    plot_label = "Prescriptions over time",
    sync_axis_range = FALSE,
    item_order = list("Location" = c("SITE3", "SITE2", "SITE1"))
  ),
  timepoint_limits = c(NA, Sys.Date()),
  fill_with_zero = FALSE,
  tab_name = "Group of child tabs",
  tab_level = 1
)
} # }