Defaults and Custom Settings for the Web App
Source:vignettes/dev-app-settings.Rmd
dev-app-settings.RmdNOTES ON GLOBAL DEFAULTS, SHINY INPUTS, BOOKMARKS, AND FUNCTION PARAMETERS
This document provides technical notes on how defaults and custom settings are defined for the EJAM web app.
HOW SETTINGS GET PASSED TO THE WEB APP
Many defaults are defined in files like
global_defaults_*.R. They can be changed there, but also
can be passed to ejamapp() aka run_app() as
parameters, to override those global default settings for the duration
of the app. Using ejamapp() parameters allows experienced
analysts to customize how the web app works without having to edit any
files. For example, one can change default settings for the radius, the
type of sites to analyze, name of the analysis, etc., or to override
caps such as limits on file upload size or number of points:
ejamapp(
radius_default=3.1,
default_max_miles=31,
default_max_mb_upload=100
)These custom parameters are “advanced” features for knowledgeable users, and not all the possible changes to these have been tested, so anyone using them should be careful to understand the details of how this work and confirm it is doing what is expected.
For example, the radius is defined like this:
if a user in RStudio launches the app with something like
ejamapp(radius_default=3.1), the settingradius_defaultis defined, and will override what it says inglobal_defaults_shiny.Rthe files
global_defaults_*.Rare where the settings likeradius_defaultare defined and stored as appOptions.that option/setting is checked in the advanced tab UI, to provide the initially selected value of
input$radius_defaultin a bookmarkable input control found in the advanced tab. In this case the option and input used the same exact name, “radius_default” but that is not always the case for other settings.in the advanced tab,
input$radius_defaultcan then be adjusted by a user or just left alone. It provides the initially selected value ofinput$radius_now(which is for the slider UI, but happens to be defined in the server not ui in this case).the radius slider bar will change the value of
input$radius_nowwhen a user moves the radius slider bar in the UI.the value of
input$radius_nowis what the app uses in calculations when the start analysis button is clicked.
A setting can be named differently in three places:
Sometimes there are two or three separate names that affect the same setting. You only need to know about the first one unless you are editing URL-encoded bookmarks or editing source code!
The global default constant that is the initial value of x, and is normally defined in a
global_defaults_*.Rfile installed with the EJAM package, but also can be provided as a parameter toejamapp().for the subset of settings that can be adjusted in the Advanced tab (not all can), there is a second variable: the input$ one can adjust in that tab.
the name of the input$ finally used in the main part of the web app.
The first of these three cannot be saved as a bookmark, but the second or third can be bookmarked since it is a shiny app input$ variable.
Steps in EJAM shiny app launch, and the use of params/ defaults/ advanced tab/ bookmarked inputs/etc.:
app.R and isPublic=T
If the app is on a server or one uses the RStudio button “Run”, app.R is used. app.R is normally how the app is launched if it is a hosted shiny app on a server. app.R mostly just does library(EJAM) and ejamapp(isPublic = TRUE). isPublic is special because it is checked by the global_defaults_shiny_public.R file and some settings depend on isPublic being T or F.
ejamapp() parameters
If the app is launched directly via ejamapp() by a user in RStudio
console, it skips app.R and a user can provide arguments as parameters
in ejamapp(…). See ?ejamapp
global_defaults_*.R files
Many defaults/ settings used by the web app are defined in the
global_defaults_ files (global_defaults_package.R,
global_defaults_shiny.R, global_defaults_shiny_public.R). Some settings
are needed even if the shiny app is never launched, so they are stored
for the package as soon as the package is attached, in a list object
called global_defaults_package in the global environment,
e.g., global_defaults_package$report_title. (When the app
is launched, those and many other global_defaults from the files
global_defaults_*.R, including radius_default, will be
stored in the shiny app). Note the parameter isPublic is special because
it is checked by the global_defaults_shiny_public.R file and some
settings depend on isPublic being T or F.
any ejamapp() parameters will override global_defaults_*.R settings
Just before launching the app, ejamapp() calls
get_global_defaults_or_user_options() which gets the global
defaults and then overrides/replaces them with any user-specified
versions of those options given as arguments in
ejamapp().
app launch
ejamapp() launches the app – it uses a function called
golem::with_golem_options(), which defines the
app object using shiny::shinyApp(), but then
stores all the global defaults and any user-provided parameters as
app$appOptions$golem_options, just before launching the
app. Those options can be retrieved in app or server later, via
EJAM:::global_or_param() which relies on
golem::get_golem_options().
global env?
Then app_ui() and app_server() can check for defaults/params using
EJAM:::global_or_param("radius_default") which uses
golem::get_golem_options() to check for a named option
stored in app$appOptions$golem_options. Usually these are
used as initial/default values for input$ variables in the app. However,
note if an expected setting is not found (ie not set by user in
ejamapp() and not set in any global_defaults_ file)
global_or_param() also looks in global env, as a last
resort!! That might be a problem if ui or server looks for a setting
that we failed to provide in global_defaults files and that variable
name happens to be in the global env !
Advanced Tab
Then, SOME BUT NOT ALL global_defaults_ settings are in the Advanced Tab (in app_ui) where they typically provide the default for an input$ but that default can be overridden there by someone using the app’s Advanced Tab, so what ui or server ends up using could be an input$ that is adjustable in the Advanced Tab and therefore can be bookmarked (since inputs can be bookmarked unless specifically excluded from that).
web app reactives and interactive inputs
The shiny app uses some settings as initial values for parameters that can get changed by the user via sliders, radio buttons, text boxes, dropdowns, etc. and some selections/inputs can get changed by reactive observers, etc.
Bookmarks (URL or server-based) for saved input$ state
If the app is launched by a bookmark (e.g.URL-encoded bookmark), any inputs encoded in the URL will override the above and the app will change to a state where the inputs are as specified by the bookmark.
Bookmarks have limitations though: Notably, uploaded files can only
be bookmarked if enableBookmarking=“server” not enableBookmarking=“url”.
Also, bookmarks normally just save the state of UI inputs, not other
reactive values (unless the server code specifies otherwise by using the
shiny::onBookmark() and shiny::onRestore()
functions to make bookmarks store other information, beyond just
inputs). Some important global defaults affect the app but not by
providing initial values for inputs in the shiny app, so some useful
information including some that is controlled by global defaults or user
parameters in ejamapp() cannot be bookmarked because it is stored in
reactives but not as shiny app inputs.
EXAMPLES OF USING CUSTOM SETTINGS
Launch local app (the R user’s computer) with custom settings
# Type out the custom settings each time you use ejamapp()
ejamapp(
default_standard_analysis_title="Custom NAICS Analysis",
default_upload_dropdown="dropdown",
default_selected_type_of_site_category="NAICS",
default_naics_digits_shown="detailed",
default_naics="562211",
radius_default=3.1,
default_ui_show_advanced_settings=1
)Launch hosted app (online, URL) with custom settings
If the web app is running locally or hosted on a server, launching it via URL-encoded bookmark can provide it any of the input$ variables as a starting state.
This approach cannot provide settings that are not input$ reactives, like some of the defaults in global_defaults_ that are not turned into inputs in the app, such as “app_logo_aboutpage” set in global_defaults_package.R and used in app_ui.R as the src parameter for img().
Also note that url-encoded bookmarked inputs can launch the app and
pass various input$ settings to the app, which would override the
default values of those input$ settings provided by the
global_defaults_*.R and/or ejamapp() parameters handled by
the utility function get_global_defaults_or_user_options().
Example that will launch app with a custom title and radius
Note this tries to specify the NAICS method, but at least initially the draft code handling this could not specify the NAICS code itself or start analysis via URL bookmark:
Here is an example using the URL of one copy of the hosted app:
*** THIS EXAMPLE WILL WORK only with VERSION 2.32.6 or later:
Locally hosted app example
# In 1 R session, launch locally with advanced tab disabled
myport <- 5432
ejamapp(isPublic=TRUE, options = list(port=myport))
# Then you can open a second R session and in that new R session
# paste/use the code below to relaunch the app
# with a parameter that enables the advanced tab:
params <- c('ui_show_advanced_settings=1')
urlbase <- paste0("http://127.0.0.1:", myport, "/?_inputs_&")
urlx <- URLencode(paste0(urlbase, paste0(params, collapse = "&")))
browseURL(urlx)Using a custom URL to go to a web app with custom settings
urlbase <- "https://ejam.policyinnovation.info/?_inputs_&"
myparams <- c(
standard_analysis_title="Custom NAICS Analysis",
default_ss_choose_method="dropdown",
ss_choose_method_drop="NAICS",
naics_digits_shown="detailed",
# ss_select_naics=313,
radius_default=3.1,
ui_show_advanced_settings=1
)
params <- c('standard_analysis_title="Custom NAICS Analysis"',
'ss_choose_method="dropdown"', # like ejamapp( default_upload_dropdown="dropdown" )
'ss_choose_method_drop="NAICS"', # see ?ejamapp()
'naics_digits_shown="detailed"', # like ejamapp( default_naics_digits_shown = "detailed")
# 'ss_select_naics=313', # like ejamapp(default_naics=313)
'radius_default=3.1', # like ejamapp(radius_default = 3.1)
'ui_show_advanced_settings=1')
urlx <- URLencode(paste0(urlbase, paste0(params, collapse = "&")))
browseURL(urlx)
# URL tried, with fips picked
# http://127.0.0.1:4200/?_inputs_&standard_analysis_title=%22Custom%20COUNTIES%20Analysis%22&pickermoduleid-all_regions_button=%22TRUE%22&pickermoduleid-all_states_button=%22TRUE%22&ui_show_advanced_settings=1&ss_choose_method=%22dropdown%22&fipspicker_done_button=2&ss_choose_method_drop=%22FIPS_PLACE%22&pickermoduleid-fips_type2pick=%22Counties%22&pickermoduleid-counties_picked=%2202110%22COMPILED LISTS OF ALL SETTINGS (FUNCTION PARAMETERS, GLOBAL_DEFAULTS_, AND SHINY INPUT$ VARS)
> global_defaults_xyz - compiled full list
gdefs = EJAM:::get_global_defaults_or_user_options()
#> Checking for index of Census blocks called 'localtree' ...localtree already exists.
#> isPublic = FALSE
gdefnames = sort(unique(names(gdefs)))
cbind(global_defaults = gdefnames)
#> global_defaults
#> [1,] "aboutpage_text"
#> [2,] "app_logo"
#> [3,] "app_logo_aboutpage"
#> [4,] "app_logo_html"
#> [5,] "app_title"
#> [6,] "app_version"
#> [7,] "app_version_header_text"
#> [8,] "app_version_short"
#> [9,] "bookmarking_allowed"
#> [10,] "default_add_naics_subcategories"
#> [11,] "default_allow_median_in_barplot_indicators"
#> [12,] "default_avoidorphans"
#> [13,] "default_bysite_webtable_colnames"
#> [14,] "default_calculate_ratios"
#> [15,] "default_can_show_advanced_settings"
#> [16,] "default_choices_for_type_of_site_category"
#> [17,] "default_choices_for_type_of_site_upload"
#> [18,] "default_circleweight"
#> [19,] "default_cities_picked"
#> [20,] "default_counties_picked"
#> [21,] "default_download_city_fips_bounds"
#> [22,] "default_download_noncity_fips_bounds"
#> [23,] "default_epa_program_selected"
#> [24,] "default_extra_demog"
#> [25,] "default_extratable_hide_missing_rows_for"
#> [26,] "default_extratable_list_of_sections"
#> [27,] "default_extratable_show_ratios_in_report"
#> [28,] "default_extratable_title"
#> [29,] "default_extratable_title_top_row"
#> [30,] "default_hide_about_tab"
#> [31,] "default_hide_ejscreenapi_tab"
#> [32,] "default_hide_plot_barplot_tab"
#> [33,] "default_hide_plot_histo_tab"
#> [34,] "default_hide_written_report"
#> [35,] "default_hyperlink_colnames"
#> [36,] "default_include_averages"
#> [37,] "default_include_ejindexes"
#> [38,] "default_include_extraindicators"
#> [39,] "default_max_mb_upload"
#> [40,] "default_max_miles"
#> [41,] "default_max_pts_map"
#> [42,] "default_max_pts_run"
#> [43,] "default_max_pts_select"
#> [44,] "default_max_pts_showtable"
#> [45,] "default_max_pts_upload"
#> [46,] "default_max_shapes_map"
#> [47,] "default_maxradius"
#> [48,] "default_naics"
#> [49,] "default_naics_digits_shown"
#> [50,] "default_need_proximityscore"
#> [51,] "default_ok2plot"
#> [52,] "default_plotkind_1pager"
#> [53,] "default_print_uploaded_points_to_log"
#> [54,] "default_reports"
#> [55,] "default_shiny.testmode"
#> [56,] "default_show_advanced_settings"
#> [57,] "default_show_full_header_footer"
#> [58,] "default_show_ratios_in_report"
#> [59,] "default_shp_oktypes_1"
#> [60,] "default_standard_analysis_title"
#> [61,] "default_states_picked"
#> [62,] "default_subgroups_type"
#> [63,] "default_testing"
#> [64,] "default_upload_dropdown"
#> [65,] "default.an_thresh_comp1"
#> [66,] "default.an_thresh_comp2"
#> [67,] "default.an_threshgroup1"
#> [68,] "default.an_threshgroup2"
#> [69,] "default.an_threshnames1"
#> [70,] "default.an_threshnames2"
#> [71,] "ejamapi_is_down"
#> [72,] "ejscreen_is_down"
#> [73,] "epa_program_help_msg"
#> [74,] "escape_html"
#> [75,] "fips_help_msg"
#> [76,] "fipspicker_all_counties_button_defaultchecked"
#> [77,] "fipspicker_all_counties_button_defaultshow"
#> [78,] "fipspicker_all_regions_button_defaultchecked"
#> [79,] "fipspicker_all_regions_button_defaultshow"
#> [80,] "fipspicker_all_states_button_defaultchecked"
#> [81,] "fipspicker_all_states_button_defaultshow"
#> [82,] "fipspicker_fips_type2pick_choices_default"
#> [83,] "fipspicker_fips_type2pick_default"
#> [84,] "fipspicker_maxOptions_default_cities_picked"
#> [85,] "fipspicker_maxOptions_default_counties_picked"
#> [86,] "fipspicker_maxOptions_default_states_picked"
#> [87,] "frs_help_msg"
#> [88,] "html_footer_fmt"
#> [89,] "html_header_fmt"
#> [90,] "latlon_help_msg"
#> [91,] "marker_cluster_cutoff"
#> [92,] "max_radius_default"
#> [93,] "maxmax_mb_upload"
#> [94,] "maxmax_miles"
#> [95,] "maxmax_pts_map"
#> [96,] "maxmax_pts_run"
#> [97,] "maxmax_pts_select"
#> [98,] "maxmax_pts_showtable"
#> [99,] "maxmax_pts_upload"
#> [100,] "maxmax_shapes_map"
#> [101,] "minmax_mb_upload"
#> [102,] "minradius"
#> [103,] "minradius_shapefile"
#> [104,] "radius_default"
#> [105,] "radius_default_shapefile"
#> [106,] "report_logo"
#> [107,] "report_logo_dir"
#> [108,] "report_logo_file"
#> [109,] "report_title"
#> [110,] "sanitize_numeric"
#> [111,] "sanitize_text"
#> [112,] "shp_help_msg"
#> [113,] "sitereport_download_buttons_colname"
#> [114,] "sitereport_download_buttons_show"
#> [115,] "stepradius"
#> [116,] "tabshown_default"
#> [117,] "use_shapefile_from_any"> function params - compiled full list
params = formals(ejamit)
# params = c(formals(getblocksnearby), formals(getblocksnearbyviaQuadTree), formals(get_blockpoints_in_shape), formals(getblocksnearby_from_fips), formals(ejamit), formals(doaggregate))
paramnames = sort(unique(names(params)))
cbind(params = paramnames)
#> params
#> [1,] "..."
#> [2,] "avoidorphans"
#> [3,] "calctype_maxbg"
#> [4,] "calctype_minbg"
#> [5,] "calculate_ratios"
#> [6,] "calculatedcols"
#> [7,] "called_by_ejamit"
#> [8,] "countcols"
#> [9,] "download_city_fips_bounds"
#> [10,] "download_noncity_fips_bounds"
#> [11,] "extra_demog"
#> [12,] "fips"
#> [13,] "in_shiny"
#> [14,] "include_ejindexes"
#> [15,] "infer_sitepoints"
#> [16,] "maxradius"
#> [17,] "need_blockwt"
#> [18,] "need_proximityscore"
#> [19,] "progress_all"
#> [20,] "quadtree"
#> [21,] "quiet"
#> [22,] "radius"
#> [23,] "radius_donut_lower_edge"
#> [24,] "reports"
#> [25,] "shapefile"
#> [26,] "showdrinkingwater"
#> [27,] "showpctowned"
#> [28,] "silentinteractive"
#> [29,] "sitepoints"
#> [30,] "subgroups_type"
#> [31,] "testing"
#> [32,] "threshgroups"
#> [33,] "threshnames"
#> [34,] "thresholds"
#> [35,] "updateProgress"
#> [36,] "updateProgress_getblocks"
#> [37,] "wtdmeancols"> shiny inputs - compiled full list
Compilation of input$ variables used in the shiny app
# getwd() must be the source pkg root folder
getwd()
lines_with_inputnames = trimws(grep("input\\$", gsub("^(.*)(input\\$.*\\))(.*)", "\\2", readLines("./R/app_server.R") ), value=T))
x = gsub("^(.*)(input\\$.*)", "\\2", lines_with_inputnames)
x = gsub("]|)|,|}", " ", x)
x = gsub("(input\\$)([^ ]*)(.*)", "\\1\\2", x)
# cbind(x, lines_with_inputnames)
inputnames = sort(unique(x)); rm(x,lines_with_inputnames)
inputnames = grep("\\.$|\\$$", inputnames, value = TRUE, invert = TRUE)
# cbind(inputnames)
# cbind(part_of_a_named_list = inputnames[grepl("\\$.*\\$", inputnames)])
inputnames = inputnames[!grepl("\\$.*\\$", inputnames)] # they all also showed up without the extra $xyz part
# What names are used in the shiny app input$ reactives?
cbind(shiny_inputs = inputnames)
inputnames = gsub("^input\\$", "", inputnames)
dput(inputnames)
inputnames = c("add_naics_subcategories", "all_tabs", "allow_median_in_barplot_indicators",
"an_map_clusters",
"an_thresh_comp2", "an_threshgroup1", "an_threshgroup2", "an_threshnames2",
"analysis_title",
"avoidorphans",
"back_to_site_sel", "back_to_site_sel2", "bt_get_results",
"calculate_ratios", "checkbox1",
"coauthor_emails", "coauthor_names", "conclusion1", "conclusion2", "conclusion3",
"Custom_title_for_bar_plot_of_indicators",
"default_ss_choose_method",
"demog_high_at_what_share_of_sites", "demog_how_elevated",
"envt_high_at_what_share_of_sites", "envt_how_elevated",
"epa_program_help",
"extra_demog", "extratable_hide_missing_rows_for",
"extratable_show_ratios_in_report", "extratable_title", "extratable_title_top_row",
"facilities_studied", "facilities_studied_enter", "fips_help",
"fipspicker_done_button",
"format1pager", "frs_help", "fundingsource",
"go", "in_areas_where_enter", "in_the_x_zone", "in_the_x_zone_enter",
"include_ejindexes", "latlon_help", "latlontypedin_submit_button",
"max_mb_upload", "max_miles", "maxradius",
"max_pts_map", "max_pts_run", "max_pts_select", "max_pts_upload", "max_shapes_map",
"naics_digits_shown",
"need_proximityscore", "ok2plot", "plotkind_1pager",
"radius_default", "radius_default_shapefile", "radius_now", "radius_units",
"results_tabs", "return_to_results",
"rg_author_email", "rg_author_name",
"rg_enter_miles", "rg_enter_sites", "rg_zonetype", "risks_are_x",
"shiny.testmode",
"show_data_preview", "show_ratios_in_report", "shp_help", "source_of_latlons",
"ss_choose_method", "ss_choose_method_drop", "ss_choose_method_upload",
"ss_select_mact", "ss_select_naics", "ss_select_program", "ss_select_sic",
"ss_upload_fips", "ss_upload_frs", "ss_upload_latlon", "ss_upload_program",
"ss_upload_shp",
"standard_analysis_title",
"subgroups_type",
"summ_bar_data", "summ_bar_ind", "summ_bar_stat", "summ_hist_bins",
"summ_hist_data", "summ_hist_distn", "summ_hist_ind",
"testing",
"ui_hide_advanced_settings", "ui_show_advanced_settings", "y"
)> ALL OVERLAPS/ DIFFS (compiled func params, global defaults, shiny inputs)
gdefnames_noprefix = gsub("default_", "", gdefnames)
cat("How many are named the same way in shiny inputs, global_defaults_, and function parameters?\n\n")
length(
intersect(inputnames, gdefnames_noprefix) # about 28
)
length(
intersect(paramnames, gdefnames_noprefix)
)
length(
intersect(paramnames, inputnames)
)
# in all 3 lists
print(
intersect(paramnames, intersect(inputnames, gdefnames_noprefix))
)
cat("Unique names in shiny inputs, as named \n")
length(
setdiff(inputnames, c(paramnames, gdefnames_noprefix))
)
cat("Unique names in global_defaults_ (not function parameters or inputs, as named) \n")
length(
setdiff(gdefnames_noprefix, c(paramnames, inputnames))
)
cat("Unique names in function parameters \n")
length(
setdiff(paramnames, c(gdefnames_noprefix, inputnames))
)ANNOTATED LISTS OF SOME SETTINGS
> function params - grouped by function
Function parameters whose defaults are or could be included in
advanced tab, and allowed by ejamapp().
EJAM:::args2(getblocksnearby)
#>
#>
#> An attempt to print a view of function defaults with one per row of text:
#>
#> getblocksnearby(
#> sitepoints,
#> radius = 3,
#> maxradius = 31.07,
#> radius_donut_lower_edge = 0,
#> avoidorphans = FALSE,
#> quadtree = NULL,
#> quaddatatable = NULL,
#> quiet = FALSE,
#> parallel = FALSE,
#> use_unadjusted_distance = TRUE,
#> ...
#> )
#>
#>
#> What str() shows (minus the attributes)
#>
#> function (sitepoints, radius = 3, maxradius = 31.07, radius_donut_lower_edge = 0,
#> avoidorphans = FALSE, quadtree = NULL, quaddatatable = NULL, quiet = FALSE,
#> parallel = FALSE, use_unadjusted_distance = TRUE, ...)
#> NULL
EJAM:::args2(getblocksnearbyviaQuadTree)
#>
#>
#> An attempt to print a view of function defaults with one per row of text:
#>
#> getblocksnearbyviaQuadTree(
#> sitepoints,
#> radius = 3,
#> radius_donut_lower_edge = 0,
#> maxradius = 31.07,
#> avoidorphans = FALSE,
#> report_progress_every_n = 500,
#> quiet = FALSE,
#> use_unadjusted_distance = FALSE,
#> retain_unadjusted_distance = TRUE,
#> quadtree,
#> updateProgress = NULL
#> )
#>
#>
#> What str() shows (minus the attributes)
#>
#> function (sitepoints, radius = 3, radius_donut_lower_edge = 0, maxradius = 31.07,
#> avoidorphans = FALSE, report_progress_every_n = 500, quiet = FALSE,
#> use_unadjusted_distance = FALSE, retain_unadjusted_distance = TRUE,
#> quadtree, updateProgress = NULL)
#> NULL
EJAM:::args2(get_blockpoints_in_shape)
#>
#>
#> An attempt to print a view of function defaults with one per row of text:
#>
#> get_blockpoints_in_shape(
#> polys,
#> addedbuffermiles = 0,
#> blocksnearby = NULL,
#> dissolved = FALSE,
#> safety_margin_ratio = 1.1,
#> crs = 4269,
#> updateProgress = NULL
#> )
#>
#>
#> What str() shows (minus the attributes)
#>
#> function (polys, addedbuffermiles = 0, blocksnearby = NULL, dissolved = FALSE,
#> safety_margin_ratio = 1.1, crs = 4269, updateProgress = NULL)
#> NULL
EJAM:::args2(getblocksnearby_from_fips)
#>
#>
#> An attempt to print a view of function defaults with one per row of text:
#>
#> getblocksnearby_from_fips(
#> fips,
#> in_shiny = FALSE,
#> need_blockwt = TRUE,
#> return_shp = FALSE,
#> allow_multiple_fips_types = TRUE,
#> radius = 0
#> )
#>
#>
#> What str() shows (minus the attributes)
#>
#> function (fips, in_shiny = FALSE, need_blockwt = TRUE, return_shp = FALSE,
#> allow_multiple_fips_types = TRUE, radius = 0)
#> NULL
# sitepoints can be a param in ejamapp()
# shapefile can be a param in ejamapp()
# fips
# radius_donut_lower_edge
# quiet = FALSE> function params - annotated list of most
# > cbind(formals(ejamit))
EJAM:::args2(ejamit)
#>
#>
#> An attempt to print a view of function defaults with one per row of text:
#>
#> ejamit(
#> sitepoints = NULL,
#> radius = 3,
#> radius_donut_lower_edge = 0,
#> maxradius = 31.07,
#> avoidorphans = FALSE,
#> quadtree = NULL,
#> fips = NULL,
#> shapefile = NULL,
#> countcols = NULL,
#> wtdmeancols = NULL,
#> calculatedcols = NULL,
#> calctype_maxbg = NULL,
#> calctype_minbg = NULL,
#> subgroups_type = "nh",
#> include_ejindexes = TRUE,
#> calculate_ratios = TRUE,
#> extra_demog = TRUE,
#> need_proximityscore = FALSE,
#> infer_sitepoints = FALSE,
#> need_blockwt = TRUE,
#> thresholds = list(80, 80),
#> threshnames = list(c(names_ej_pctile, names_ej_state_pctile), c(names_ej_supp_pctile, names_ej_supp_state_pctile)),
#> threshgroups = list("EJ-US-or-ST", "Supp-US-or-ST"),
#> reports = EJAM:::global_or_param("default_reports"),
#> updateProgress = NULL,
#> updateProgress_getblocks = NULL,
#> progress_all = NULL,
#> in_shiny = FALSE,
#> quiet = TRUE,
#> silentinteractive = FALSE,
#> called_by_ejamit = TRUE,
#> testing = FALSE,
#> showdrinkingwater = TRUE,
#> showpctowned = TRUE,
#> download_city_fips_bounds = TRUE,
#> download_noncity_fips_bounds = FALSE,
#> ...
#> )
#>
#>
#> What str() shows (minus the attributes)
#>
#> function (sitepoints = NULL, radius = 3, radius_donut_lower_edge = 0, maxradius = 31.07,
#> avoidorphans = FALSE, quadtree = NULL, fips = NULL, shapefile = NULL,
#> countcols = NULL, wtdmeancols = NULL, calculatedcols = NULL, calctype_maxbg = NULL,
#> calctype_minbg = NULL, subgroups_type = "nh", include_ejindexes = TRUE,
#> calculate_ratios = TRUE, extra_demog = TRUE, need_proximityscore = FALSE,
#> infer_sitepoints = FALSE, need_blockwt = TRUE, thresholds = list(80,
#> 80), threshnames = list(c(names_ej_pctile, names_ej_state_pctile),
#> c(names_ej_supp_pctile, names_ej_supp_state_pctile)), threshgroups = list("EJ-US-or-ST",
#> "Supp-US-or-ST"), reports = EJAM:::global_or_param("default_reports"),
#> updateProgress = NULL, updateProgress_getblocks = NULL, progress_all = NULL,
#> in_shiny = FALSE, quiet = TRUE, silentinteractive = FALSE, called_by_ejamit = TRUE,
#> testing = FALSE, showdrinkingwater = TRUE, showpctowned = TRUE, download_city_fips_bounds = TRUE,
#> download_noncity_fips_bounds = FALSE, ...)
#> NULL
# sitepoints NULL -- Now can be passed to ejamapp()
# shapefile NULL ---- shapefile now can be passed to ejamapp()
# fips NULL ---- fips will be enabled as param
# radius 3 for getblocksnearby(), shiny radius_default is in global_defaults_
# radius_donut_lower_edge 0 na
# maxradius 31.07 for getblocksnearby(), shiny default is set in global
# avoidorphans FALSE for getblocksnearby(), shiny default is set in global
# quadtree NULL na
# countcols NULL for doaggregate() ** shiny default NOT specified here
# popmeancols NULL for doaggregate() ** shiny default NOT specified here
# calculatedcols NULL for doaggregate() ** shiny default NOT specified here
# calctype_maxbg NULL for doaggregate() ** shiny default NOT specified here
# calctype_minbg NULL for doaggregate() ** shiny default NOT specified here
# subgroups_type "nh" for doaggregate(), shiny default is set in global
# include_ejindexes TRUE for doaggregate(), shiny default is set in global
# calculate_ratios TRUE for doaggregate(), shiny default is set in global
# extra_demog TRUE for doaggregate(), shiny default is set in global
# need_proximityscore FALSE for doaggregate(), shiny default is set in global
# infer_sitepoints FALSE for doaggregate() ** shiny default NOT specified here
# need_blockwt TRUE for getblocksnearby_from_fips(), shiny default not specified here, but by function defaults
# thresholds expression for batch.summarize() - set in global_ but named differently
# threshnames expression for batch.summarize() - set in global_ but named differently
# threshgroups expression for batch.summarize() - set in global_ but named differently
# updateProgress NULL ** shiny default NOT specified here
# updateProgress_getblocks NULL ** shiny default NOT specified here
# in_shiny FALSE for ejamit(), build_community_report(), and related functions
# quiet TRUE for getblocksnearby() and batch.summarize(), na
# testing FALSE for doaggregate(), shiny default is set in global
# silentinteractive FALSE for doaggregate() etc. na
# called_by_ejamit TRUE for doaggregate(), na
# showdrinkingwater TRUE for doaggregate(), na
# showpctowned TRUE for doaggregate(), na
# download_fips_bounds_to_calc_areas FALSE
# ... ? for getblocksnearby(), like use_unadjusted_distance ** shiny default NOT specified here> shiny inputs - categorized (partial)
EJAM shiny app inputs that can be URL-encoded in a bookmark to reopen the app with those settings Note the URL cuts off at about 4096 characters
inputs: tabs and nav and help buttons
all_tabs="See Results" # or # all_tabs="Advanced Settings"
results_tabs="Community Report"
details_subtabs="Site-by-Site Table"
show_advanced_settings="TRUE" # ??
can_show_advanced_settings="TRUE"
# buttons:
ui_show_advanced_settings=1 #button
ui_hide_advanced_settings=0 #button
show_data_preview=0
back_to_site_sel2=0
return_to_results=0
latlon_help=0
shp_help=0
fips_help=0
frs_help=0
epa_program_help=0inputs: site selection (buttons/dropdowns)
default_ss_choose_method="upload" # or "dropdown"
ss_choose_method="upload" # or "dropdown"
ss_choose_method_upload="latlon" # see global_defaults_*.R for options
ss_choose_method_drop="FIPS_PLACE" # see global_defaults_*.R for options
ss_upload_shp=null
ss_upload_fips=null
ss_upload_frs=null
ss_upload_program=null
ss_select_program="CAMDBS"
ss_select_naics=null
ss_select_sic=null
ss_select_mact="AA"
naics_digits_shown="basic"
add_naics_subcategories="TRUE"
shinyjs-resettable-ss_upload_latlon={}
shinyjs-resettable-ss_upload_shp={}
shinyjs-resettable-ss_upload_frs={}
shinyjs-resettable-ss_upload_program={}
shinyjs-resettable-ss_upload_fips={}
pickermoduleid-fips_type2pick="Counties"
pickermoduleid-states_picked=null
pickermoduleid-counties_picked=null
pickermoduleid-cities_picked=null
pickermoduleid-regions_picked=["1","2","3","4","5","6","7","8","9","10"]
pickermoduleid-all_regions_button=true
pickermoduleid-all_states_button=true
pickermoduleid-all_counties_button=false
pickermoduleid-all_cities_button=false
pickermoduleid-reset_button=0
fipspicker_done_button=0inputs: radius and caps
radius_now=3.1 # input from slider but not the way to bookmark /url-encode the radius
radius_default=3.1 # works as parameter to ejamapp() or as bookmarked input$
radius_default_shapefile=0
max_miles=10
maxradius=31.06856
max_pts_upload=5000
max_pts_select=5000
max_pts_map=5000
max_pts_showtable=1000
max_pts_run=10000
max_shapes_map=159
max_mb_upload=50inputs: more ejamit() parameters, summary report and excel output settings, etc.
standard_analysis_title="CUSTOM Analysis" # shown on webpage of app and on reports
analysis_title="testname"
Custom_title_for_bar_plot_of_indicators=""
include_ejindexes="TRUE"
calculate_ratios=true
include_averages=true
show_ratios_in_report="TRUE"
extratable_show_ratios_in_report="TRUE"
more3="a"
avoidorphans="FALSE"
need_proximityscore="FALSE"
plotkind_1pager="bar"
format1pager="html"
ok2plot=true
allow_median_in_barplot_indicators="FALSE"
summ_hist_distn="People" # histograms
summ_hist_data="pctile"
summ_hist_bins=10
extra_demog="TRUE"
include_extraindicators=true
extratable_title=""
extratable_title_top_row="ADDITIONAL INFORMATION"
extratable_list_of_sections="pctpoor"
# extratable_hide_missing_rows_for=["pcthisp","pctnhba","pctnhaa","pctnhaiana","pctnhnhpia","pctnhotheralone","pctnhmulti","pctnhwa","pctlan_ie","pctlan_api","pctlan_other","pctlan_english","pctlan_spanish","pctlan_french",
# "pctlan_rus_pol_slav","p_chinese","p_korean","pctlan_other_ie","pctlan_vietnamese","pctlan_other_asian","pctlan_arabic","pctlan_nonenglish",
# "pctspanish_li","pctie_li","pctapi_li","pctother_li","pctmale","pctfemale","pctdisability","lowlifex","rateheartdisease","rateasthma","ratecancer","pctunder5","pctunder18","pctover64","occupiedunits","lifexyears",
# "percapincome","pctownedunits","pctpoor","sitecount_avg","sitecount_unique","sitecount_max","distance_min_avgperson","distance_min","count.NPL","count.TSDF","num_waterdis","num_airpoll","num_brownfield","num_tri","num_school",
# "num_hospital","num_church","yesno_tribal","yesno_airnonatt","yesno_impwaters","yesno_cejstdis","yesno_iradis","pctflood","pctfire","pctfire30","pctflood30","yesno_houseburden","yesno_transdis","yesno_fooddesert","pctnobroadband",
# "pctnohealthinsurance","pop","nonmins","age25up","hhlds","unemployedbase","pre1960","builtunits","povknownratio"]
# thresholds - counting how many of a certain indicator type are at/above some threshold
# see help docs on ejamapp() for examples of using these (but they are named a bit differently as parameters there)
an_thresh_comp1=80
an_thresh_comp2=80
an_threshgroup1="EJ-US-or-ST"
an_threshgroup2="Supp-US-or-ST"
an_threshnames1=["pctile.EJ.DISPARITY.dpm.eo","pctile.EJ.DISPARITY.drinking.eo","pctile.EJ.DISPARITY.no2.eo","pctile.EJ.DISPARITY.o3.eo","pctile.EJ.DISPARITY.pctpre1960.eo","pctile.EJ.DISPARITY.pm.eo","pctile.EJ.DISPARITY.proximity.npdes.eo",
"pctile.EJ.DISPARITY.proximity.npl.eo","pctile.EJ.DISPARITY.proximity.rmp.eo","pctile.EJ.DISPARITY.proximity.tsdf.eo","pctile.EJ.DISPARITY.rsei.eo","pctile.EJ.DISPARITY.traffic.score.eo","pctile.EJ.DISPARITY.ust.eo",
"state.pctile.EJ.DISPARITY.dpm.eo","state.pctile.EJ.DISPARITY.drinking.eo","state.pctile.EJ.DISPARITY.no2.eo","state.pctile.EJ.DISPARITY.o3.eo","state.pctile.EJ.DISPARITY.pctpre1960.eo","state.pctile.EJ.DISPARITY.pm.eo","state.pctile.EJ.DISPARITY.proximity.npdes.eo",
"state.pctile.EJ.DISPARITY.proximity.npl.eo","state.pctile.EJ.DISPARITY.proximity.rmp.eo","state.pctile.EJ.DISPARITY.proximity.tsdf.eo","state.pctile.EJ.DISPARITY.rsei.eo","state.pctile.EJ.DISPARITY.traffic.score.eo","state.pctile.EJ.DISPARITY.ust.eo"]
an_threshnames2=["pctile.EJ.DISPARITY.dpm.supp","pctile.EJ.DISPARITY.drinking.supp","pctile.EJ.DISPARITY.no2.supp","pctile.EJ.DISPARITY.o3.supp","pctile.EJ.DISPARITY.pctpre1960.supp","pctile.EJ.DISPARITY.pm.supp","pctile.EJ.DISPARITY.proximity.npdes.supp",
"pctile.EJ.DISPARITY.proximity.npl.supp","pctile.EJ.DISPARITY.proximity.rmp.supp","pctile.EJ.DISPARITY.proximity.tsdf.supp","pctile.EJ.DISPARITY.rsei.supp","pctile.EJ.DISPARITY.traffic.score.supp","pctile.EJ.DISPARITY.ust.supp","state.pctile.EJ.DISPARITY.dpm.supp",
"state.pctile.EJ.DISPARITY.drinking.supp","state.pctile.EJ.DISPARITY.no2.supp","state.pctile.EJ.DISPARITY.o3.supp","state.pctile.EJ.DISPARITY.pctpre1960.supp","state.pctile.EJ.DISPARITY.pm.supp","state.pctile.EJ.DISPARITY.proximity.npdes.supp",
"state.pctile.EJ.DISPARITY.proximity.npl.supp","state.pctile.EJ.DISPARITY.proximity.rmp.supp","state.pctile.EJ.DISPARITY.proximity.tsdf.supp","state.pctile.EJ.DISPARITY.rsei.supp","state.pctile.EJ.DISPARITY.traffic.score.supp","state.pctile.EJ.DISPARITY.ust.supp"]inputs: draft / reserved for a long word/pdf report
# authors
rg_author_name="FirstName LastName"
rg_author_email="author@email.org"
rg_add_coauthors=false
coauthor_names=""
coauthor_emails=""
fundingsource=""
# methods & data
acs_version=""
ejscreen_version=""
subgroups_type="nh"
## sites selected for analysis
prefix_filenames=""
in_the_x_zone="area"
facilities_studied="rule"
facilities_studied_enter=""
rg_enter_sites="facilities in the _____ source category"
source_of_latlons=""
in_areas_where_enter=""
in_the_x_zone_enter="in "
rg_zonetype="zone_is_named_x"
within_x_miles_of="near the"
in_areas_where="in areas with"
risks_are_x="risk is at or above 1 per million (lifetime individual cancer risk due to inhalation of air toxics from this source category)"
# results
demog_how_elevated=""
envt_how_elevated=""
demog_high_at_what_share_of_sites="some of these sites, just as it varies nationwide"
envt_high_at_what_share_of_sites="some of these sites, just as it varies nationwide"
conclusion1=""
conclusion2=""
conclusion3=""