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639 lines (564 loc) · 27.1 KB
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library(DT)
library(magrittr)
library(dplyr)
library(parallel)
library(naturalsort)
args = commandArgs(trailingOnly = TRUE)
if (length(args) != 1) {
stop("the mk_html_tables.R script requires exactly one argument: name of run config file ... thank you. goodbye.")
}
source(args[1])
run_name = gsub(".R", "", args[1])
source(file.path("utilities",
"helpers.R"))
dir.create(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"landing"),
recursive = TRUE)
dir.create(file.path(results_base_dir,
run_name,
"dashboard",
"entities"),
recursive = TRUE)
d = read.csv(file.path(data_base_dir,
"flat_w_composites.csv"),
stringsAsFactors = FALSE)
d = d[, which(sapply(names(d), function(v) !all(is.na(d[,v]))))]
d %<>% lapply(function(y) if(is.numeric(y)) round(y, 3) else y) %>%
as.data.frame
d_ = d
names_d_ = names(d_)
d_ = lapply(names(d_), function(j) get_pretty_name_simple(d_[,j])) %>% as.data.frame
names(d_) = names_d_
#d_$entity_label = d$entity_label # here we override pretty names for entity_label -- this is a special case for the defcon dashboard
names(d_) %<>% get_pretty_name_simple %>%
gsub("<sup>", "", .) %>%
gsub("</sup>", "", .)
datatable(d_,
width = "75%",
#fillContainer = TRUE,
#autoHideNavigation = TRUE,
rownames = NULL,
options = list(pageLength=10, autoHeight=TRUE, initComplete = JS(
"function(settidefaultHeightngs, json) {",
"$(this.api().table().header()).css({'color': '#46A2DA'});",
"}"))
) %>%
formatStyle(columns = 1:ncol(d),
color = title_color) %>%
saveWidget(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"landing",
"summary_table.html"),
background = background_color,
selfcontained = FALSE,
libdir = "js_libs")
dir.create(file.path(results_base_dir,
run_name,
"dashboard",
"js_libs"),
recursive = TRUE)
paste0("mv ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"landing",
"js_libs/*"),
" ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"js_libs")) %>%
system
paste0("rm -r ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"landing",
"js_libs")) %>%
system
paste0("sed -i 's|js_libs|../js_libs|g' '",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"landing",
"summary_table.html"),
"'") %>%
system
print(ifelse(background_color == "#FFFFFF",
"include/web/style_white.css",
"include/web/style_dark.css"))
print("THAT")
d_ = NULL
html = readLines(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"landing",
"summary_table.html"))
if(background_color != "#FFFFFF") {
html %<>% gsub('</head>',
'<link rel="stylesheet" href="style.css"></head>',
.)
}
file.copy(ifelse(background_color == "#FFFFFF",
"include/web/style_white.css",
"include/web/style_dark.css"),
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"landing",
"style.css"),
overwrite = TRUE)
file.copy(ifelse(background_color == "#FFFFFF",
"include/web/style_white.css",
"include/web/style_dark.css"),
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"style.css"),
overwrite = TRUE)
cat(html,
file = file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"landing",
"summary_table.html"),
fill = 2)
mclapply(1:nrow(d),
function(j) {
d_ = d[j,]
this_entity = d_$entity_label
d_[, "entity_label"] = NULL
df = data.frame(Attribute = get_pretty_name_simple(names(d_)) %>%
gsub("<sup>", "", .) %>%
gsub("</sup>", "", .),
Value = (get_pretty_name_simple(d_)) %>%
gsub(".value", "", .) %>%
gsub("<sup>", "", .) %>%
gsub("</sup>", "", .) %>% as.character,
stringsAsFactors = FALSE,
check.names = FALSE)
#df = df[naturalorder(df$Attribute), ]
print("df is")
print(df)
datatable(df,
width = "50%",
rownames = NULL,
options = list(initComplete = JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'color': '#46A2DA'});",
"}"))
) %>%
formatStyle(columns =1:ncol(d),
color = title_color) %>%
saveWidget(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"entities",
paste0(this_entity, ".html")),
background = background_color,
selfcontained = FALSE,
libdir = "js_libs")
paste0("mv ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"entities",
"js_libs/*"),
" ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"js_libs")) %>%
system
paste0("rm -r ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"entities",
"js_libs")) %>%
system
paste0("sed -i 's|js_libs|../js_libs|g' '",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"entities",
paste0(this_entity, ".html")),
"'") %>%
system
html = readLines(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"entities",
paste0(this_entity, ".html")))
if (background_color != "#FFFFFF") {
html %<>% gsub('</head>',
'<link rel="stylesheet" href="style.css"></head>',
.)
}
file.copy(ifelse(background_color == "#FFFFFF",
"include/web/style_white.css",
"include/web/style_dark_zero_margin.css"),
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"entities",
"style.css"),
overwrite = TRUE)
cat(html,
file = file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"entities",
paste0(this_entity, ".html")),
fill = 2)
}, mc.cores = 1)
d$entity_label = NULL
mclapply(names(d),
function(name) {
print(name)
if (exists("grouped_time_cdfs_histos_and_trends_config") &&
name == grouped_time_cdfs_histos_and_trends_config$input_tilda_time_var %>%
gsub(".*~", "", .) %>%
gsub(" ", "", .)) {
for (gbv in grouped_time_cdfs_histos_and_trends_config$group_by_vars) {
print("check a")
print(gbv)
print(gsub(",", "_", gbv) %>% gsub(" ", "", .))
tryCatch({
d_ = read.csv(file.path(results_base_dir,
run_name,
"dashboard",
"attributes",
"grouped_time_cdfs_histos_and_trends",
paste0(name,
"_counts_by_",
gsub(",", "_", gbv) %>% gsub(" ", "", .),
".csv")),
stringsAsFactors = FALSE,
check.names = FALSE)
if(!is.null(d_$diagnostic)) d_$diagnostic %<>% get_pretty_name_simple(pretty_names_file = file.path("include",
"standard_pretty_names.csv"))
names(d_) %<>% get_pretty_name_simple(pretty_names_file = file.path("include",
"standard_pretty_names.csv"))
datatable(d_,
width = "50%",
rownames = NULL,
options = list(initComplete = JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'color': '#46A2DA'});",
"}"))
) %>%
formatStyle(columns = 1:ncol(d_),
color = title_color,
`text-align` = 'right') %>%
formatStyle(columns = 1,
`text-align` = 'left') %>%
saveWidget(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"attributes",
"grouped_time_cdfs_histos_and_trends",
paste0(name,
"_counts_by_",
gsub(",", "_", gbv) %>% gsub(" ", "", .),
".html")),
background = background_color,
selfcontained = FALSE,
libdir = "js_libs")
paste0("mv ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"attributes",
"grouped_time_cdfs_histos_and_trends",
"js_libs/*"),
" ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"js_libs")) %>%
system
paste0("rm -r ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"attributes",
"grouped_time_cdfs_histos_and_trends",
"js_libs")) %>%
system
paste0("sed -i 's|js_libs|../../js_libs|g' '",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"attributes",
"grouped_time_cdfs_histos_and_trends",
paste0(name,
"_counts_by_",
gsub(",", "_", gbv) %>% gsub(" ", "", .),
".html")),
"'") %>%
system
html = readLines(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"attributes",
"grouped_time_cdfs_histos_and_trends",
paste0(name,
"_counts_by_",
gsub(",", "_", gbv) %>% gsub(" ", "", .),
".html")))
if (background_color != "#FFFFFF") {
html %<>% gsub('</head>',
'<link rel="stylesheet" href="style.css"></head>',
.)
}
file.copy(ifelse(background_color == "#FFFFFF",
"include/web/style_white.css",
"include/web/style_dark_zero_margin.css"),
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"attributes",
"grouped_time_cdfs_histos_and_trends",
"style.css"),
overwrite = TRUE)
cat(html,
file = file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"attributes",
"grouped_time_cdfs_histos_and_trends",
paste0(name,
"_counts_by_",
gsub(",", "_", gbv) %>% gsub(" ", "", .),
".html")),
fill = 2)
}, error = function(e) {})
}}
tryCatch({
d_ = read.csv(file.path(results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_summary.csv")),
stringsAsFactors = FALSE)
if(!is.null(d_$diagnostic)) d_$diagnostic %<>% get_pretty_name_simple(pretty_names_file = file.path("include",
"standard_pretty_names.csv"))
names(d_) %<>% get_pretty_name_simple(pretty_names_file = file.path("include",
"standard_pretty_names.csv"))
datatable(d_,
width = "40%",
rownames = NULL,
options = list(initComplete = JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'color': '#46A2DA'});",
"}"))
) %>%
formatStyle(columns =1:ncol(d_),
`text-align` = 'right',
color = title_color) %>%
formatStyle(columns =1,
`text-align` = 'left',
color = title_color) %>%
saveWidget(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_summary.html")),
background = background_color,
selfcontained = FALSE,
libdir = "js_libs")
html = readLines(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_summary.html")))
if (background_color != "#FFFFFF") {
html %<>% gsub('</head>',
'<link rel="stylesheet" href="style.css"></head>',
.)
}
file.copy(ifelse(background_color == "#FFFFFF",
"include/web/style_white.css",
"include/web/style_dark_zero_margin.css"),
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
"style.css"),
overwrite = TRUE)
cat(html,
file = file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_summary.html")),
fill = 2)
d_ = read.csv(file.path(results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_standardized_coeffs.csv")),
stringsAsFactors = FALSE,
check.names = FALSE)
print(d_)
d_$predictor = ifelse(d_$predictor != "(Intercept)", d_$predictor, "Intercept")
if(!is.null(d_$coeff_std)) d_ = d_[order(abs(d_$coeff_std), decreasing = TRUE),]
if(!is.null(d_$predictor)) d_$predictor %<>%
get_pretty_name_simple %>%
strip_units
names(d_) %<>% get_pretty_name_simple(pretty_names_file = file.path("include",
"standard_pretty_names.csv")) %>%
get_pretty_name_simple
print(d_)
datatable(d_,
width = "50%",
rownames = NULL,
options = list(initComplete = JS(
"function(settings, json) {",
"$(this.api().table().header()).css({'color': '#46A2DA'});",
"}"))
) %>%
formatStyle(columns =1:ncol(d),
color = title_color) %>%
saveWidget(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_standardized_coeffs.html")),
background = background_color,
selfcontained = FALSE,
libdir = "js_libs")
paste0("mv ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
"js_libs/*"),
" ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"js_libs")) %>%
system
paste0("rm -r ",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
"js_libs")) %>%
system
paste0("sed -i 's|js_libs|../js_libs|g' '",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_summary.html")),
"'") %>%
system
paste0("sed -i 's|js_libs|../js_libs|g' '",
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_standardized_coeffs.html")),
"'") %>%
system
html = readLines(file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_standardized_coeffs.html")))
if (background_color != "#FFFFFF") {
html %<>% gsub('</head>',
'<link rel="stylesheet" href="style.css"></head>',
.)
}
file.copy(ifelse(background_color == "#FFFFFF",
"include/web/style_white.css",
"include/web/style_dark_zero_margin.css"),
file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
"style.css"),
overwrite = TRUE)
cat(html,
file = file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_standardized_coeffs.html")),
fill = 2)
}, error = function(e) {
print(paste0("WARNING: Model tables failed for attribute ",
name,
" ...this is probably because model fitting failed for this variable."))
cat("<link rel='stylesheet' type='text/css' href='css?family=Nunito'>
<style>
body {
overflow: hidden;
}
</style>
<div id='contentframe' style='position:relative; left: 10px; font:sans-serif'>
<h3 href='css?family=Nunito' style='color:#cccccc; font-family:sans-serif'>We were unable to fit a model of this variable.
This frequently occurs when attempting<br>to fit a multinomial model to a categorical response with a high number of
levels but an insufficient<br>amount of data. Contact info is at the bottom of the page if you need modeling assistance.</h3></div>",
file = file.path(getwd(),
results_base_dir,
run_name,
"dashboard",
"models",
paste0(name, "_model_standardized_coeffs.html")),
fill = 2)
#cat("<br>",
# file = file.path(getwd(),
# results_base_dir,
# run_name,
# "dashboard",
# "models",
# paste0(name, "_model_summary.html")),
# fill = 2)
})}, mc.cores = 1)