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Save EJAM results in a spreadsheet

Source: R/ejam2excel.R
ejam2excel.Rd

ejam2excel() takes the output of something like ejamit() and creates a spreadsheet with an overall summary tab, a site by site table tab, as well as other tabs such as map, plot, notes, etc.

Usage

ejam2excel(
  ejamitout,
  fname = NULL,
  save_now = TRUE,
  overwrite = TRUE,
  launchexcel = FALSE,
  interactive_console = TRUE,
  in.testing = FALSE,
  updateProgress = NULL,
  analysis_title = "EJAM analysis",
  site_method = NULL,
  radius_or_buffer_in_miles = NULL,
  radius_or_buffer_description = NULL,
  buffer_desc = "Selected Locations",
  reports = EJAM:::global_or_param("default_reports"),
  ok2plot = TRUE,
  report_plot = NULL,
  plot_distance_by_group = FALSE,
  plotlatest = FALSE,
  plotfilename = NULL,
  mapadd = FALSE,
  report_map = NULL,
  shp = NULL,
  community_reportadd = TRUE,
  community_html = NULL,
  heatmap_colnames = NULL,
  heatmap_cuts = c(80, 90, 95),
  heatmap_colors = c("yellow", "orange", "red"),
  heatmap2_colnames = NULL,
  heatmap2_cuts = c(1.009, 2, 3),
  heatmap2_colors = c("yellow", "orange", "red"),
  graycolnames = NULL,
  graycolor = "gray",
  narrowcolnames = NULL,
  narrow6 = 6,
  notes = NULL,
  custom_tab = ejamitout$results_summarized$cols,
  custom_tab_name = "thresholds",
  ejscreen_ejam_caveat = NULL,
  ...
)

Arguments

ejamitout

output of ejamit()

fname

optional name or full path and name of file to save locally, like "out.xlsx"

save_now

optional logical, whether to save as a .xlsx file locally or just return workbook object that can later be written to .xlsx file using openxlsx::saveWorkbook()

overwrite

optional logical, passed to openxlsx::saveWorkbook()

launchexcel

optional logical, passed to table_xls_format(), whether to launch browser to see spreadsheet immediately

interactive_console

optional - should set to FALSE when used in code or server. If TRUE, prompts RStudio user interactively asking where to save the downloaded file

in.testing

optional logical

updateProgress

optional function used by shiny app to track progress of slow operation

analysis_title

optional title as character string, used only in 'Notes' sheet (and to create a default filename if fname not specified). Not used in the copy of the report.

site_method

optional word or phrase about the sites or how they were selected.

The site_method parameter can be used as-is by create_filename() to be part of the saved file name. It can also be used by the shiny app to add informational text in the header of a report, via ejam2report() and related helper functions like report_residents_within_xyz() or via ejam2excel() and related helper functions.

The site_method parameter provides more detailed info about how sites were specified in the web app, beyond what sitetype provides (e.g., from ejamit()$sitetype or ejamitout$sitetype):

  • sitetype can be "latlon", "fips", or "shp"

  • site_method can be one of these: "latlon", "SHP", "FIPS", "FIPS_PLACE", "FRS", "NAICS", "SIC", "EPA_PROGRAM", "MACT"

The shiny app server provides site_method from the reactive called submitted_upload_method() which is much like the one called current_upload_method().

radius_or_buffer_in_miles

optional radius in miles

radius_or_buffer_description

optional text phrase describing places analyzed, like in report headers

buffer_desc

description of location to use in labels, like "Selected Locations"

reports

info about which columns to treat as URLs that should be hyperlinks - see url_columns_bysite()

ok2plot

optional logical, passed to table_xls_format(), whether safe to try and plot or set FALSE if debugging plot problems

report_plot

optional - a plot object

plot_distance_by_group

optional logical, whether to try to add a plot of mean distance by group. This requires that bybg be provided as a parameter input to this function.

plotlatest

optional logical. If TRUE, the most recently displayed plot (prior to this function being called) will be inserted into a tab called plot2

plotfilename

optional the full path including name of a .png file to insert

mapadd

optional logical, whether to add a tab with a map of the sites. If report tab is added, though, standalone static map in excel tab is redundant.

report_map

the leaflet map to display in 'Map' sheet if mapadd is TRUE (re-created if this is omitted/NULL but mapadd is TRUE)

shp

optional shapefile used to create map if not providing it via report_map or community_html parameters

community_reportadd

Logical, whether to add a tab with a static copy of the summary report (tables, map, barplot).

community_html

the HTML file of the summary/community report if available (re-created if this is omitted/NULL but community_reportadd is TRUE)

heatmap_colnames

optional vector of colnames to apply heatmap colors, defaults to percentiles

heatmap_cuts

vector of values to separate heatmap colors, between 0-100 for percentiles

heatmap_colors

vector of color names for heatmap bins, same length as heatmap_cuts, where first color is for those >= 1st cutpoint, but <2d, second color is for those >=2d cutpoint but <3d, etc.

heatmap2_colnames

like heatmap_colnames but for ratios by default

heatmap2_cuts

like heatmap_cuts but for ratios by default

heatmap2_colors

like heatmap_colors but for ratios

graycolnames

which columns to de-emphasize

graycolor

color used to de-emphasize some columns

narrowcolnames

which column numbers to make narrow

narrow6

how narrow

notes

Text of additional notes to put in the notes tab, optional vector of character elements pasted in as one line each.

custom_tab

optional table to put in an extra tab

custom_tab_name

optional name of optional custom_tab

ejscreen_ejam_caveat

optional text if you want to change this in the notes tab

...

optional additional parameters passed to table_xls_format(), currently unused

Value

returns a workbook object for use by openxlsx::saveWorkbook(wb_out, pathname) or returns just the full path/file name of where it was saved if save_now = TRUE

Examples

# \donttest{
# Add purple to flag indicators at 99th percentile
ejam2excel(testoutput_ejamit_10pts_1miles,
  # View spreadsheet 1st without saving it as a file
  launchexcel = T, save_now = F,
  heatmap_cuts = c(80, 90, 95, 99),
  heatmap_colors  = c("yellow", "orange", "red", "purple"),
  # Apply heatmap to only a few of the ratio columns
  heatmap2_colnames = names_d_ratio_to_state_avg)
# }