diff --git a/R/app_version.R b/R/app_version.R
index ff73a30..b5243e9 100644
--- a/R/app_version.R
+++ b/R/app_version.R
@@ -1 +1 @@
-app_version <- function()'250320_1310'
+app_version <- function()'250324_1432'
diff --git a/R/baseline_table.R b/R/baseline_table.R
index 05af54b..ad90eef 100644
--- a/R/baseline_table.R
+++ b/R/baseline_table.R
@@ -20,3 +20,55 @@ baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary,
return(out)
}
+
+
+#' Create a baseline table
+#'
+#' @param data data
+#' @param ... passed as fun.arg to baseline_table()
+#' @param strat.var grouping/strat variable
+#' @param add.p add comparison/p-value
+#' @param add.overall add overall column
+#'
+#' @returns gtsummary table list object
+#' @export
+#'
+#' @examples
+#' mtcars |> create_baseline(by.var = "gear", add.p="yes"=="yes")
+create_baseline <- function(data,...,by.var,add.p=FALSE,add.overall=FALSE){
+ if (by.var == "none" | !by.var %in% names(data)) {
+ by.var <- NULL
+ }
+
+ ## These steps are to handle logicals/booleans, that messes up the order of columns
+ ## Has been reported
+
+ if (!is.null(by.var)) {
+ if (identical("logical",class(data[[by.var]]))){
+ data[by.var] <- as.character(data[[by.var]])
+ }
+ }
+
+ out <- data |>
+ baseline_table(
+ fun.args =
+ list(
+ by = by.var,
+ ...
+ )
+ )
+
+ if (!is.null(by.var)) {
+ if (isTRUE(add.overall)){
+ out <- out |> gtsummary::add_overall()
+ }
+ if (isTRUE(add.p)) {
+ out <- out |>
+ gtsummary::add_p() |>
+ gtsummary::bold_p()
+ }
+
+ }
+
+ out
+}
diff --git a/R/data_plots.R b/R/data_plots.R
index e9225de..3f40de8 100644
--- a/R/data_plots.R
+++ b/R/data_plots.R
@@ -302,6 +302,7 @@ data_visuals_server <- function(id,
{
tryCatch(
{
+ shiny::withProgress(message = "Drawing the plot. Hold tight for a moment..", {
rv$plot <- create_plot(
data = data(),
type = rv$plot.params()[["fun"]],
@@ -309,6 +310,7 @@ data_visuals_server <- function(id,
y = input$secondary,
z = input$tertiary
)
+ })
},
# warning = function(warn) {
# showNotification(paste0(warn), type = "warning")
diff --git a/R/helpers.R b/R/helpers.R
index 4e24796..9696823 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -29,7 +29,7 @@ getfun <- function(x) {
#' @return output file name
#' @export
#'
-write_quarto <- function(data,...) {
+write_quarto <- function(data, ...) {
# Exports data to temporary location
#
# I assume this is more secure than putting it in the www folder and deleting
@@ -50,7 +50,7 @@ write_quarto <- function(data,...) {
)
}
-write_rmd <- function(data,...) {
+write_rmd <- function(data, ...) {
# Exports data to temporary location
#
# I assume this is more secure than putting it in the www folder and deleting
@@ -210,17 +210,17 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
#' default_parsing() |>
#' str()
default_parsing <- function(data) {
- name_labels <- lapply(data,\(.x) REDCapCAST::get_attr(.x,attr = "label"))
+ name_labels <- lapply(data, \(.x) REDCapCAST::get_attr(.x, attr = "label"))
out <- data |>
REDCapCAST::parse_data() |>
REDCapCAST::as_factor() |>
- REDCapCAST::numchar2fct(numeric.threshold = 8,character.throshold = 10) |>
+ REDCapCAST::numchar2fct(numeric.threshold = 8, character.throshold = 10) |>
REDCapCAST::as_logical() |>
REDCapCAST::fct_drop()
- purrr::map2(out,name_labels,\(.x,.l){
- if (!(is.na(.l) | .l=="")) {
+ purrr::map2(out, name_labels, \(.x, .l){
+ if (!(is.na(.l) | .l == "")) {
REDCapCAST::set_attr(.x, .l, attr = "label")
} else {
attr(x = .x, which = "label") <- NULL
@@ -238,12 +238,14 @@ default_parsing <- function(data) {
#' @export
#'
#' @examples
-#' ds <- mtcars |> lapply(\(.x) REDCapCAST::set_attr(.x,label=NA,attr = "label"))
-#' ds |> remove_na_attr() |> str()
-remove_na_attr <- function(data,attr="label"){
+#' ds <- mtcars |> lapply(\(.x) REDCapCAST::set_attr(.x, label = NA, attr = "label"))
+#' ds |>
+#' remove_na_attr() |>
+#' str()
+remove_na_attr <- function(data, attr = "label") {
out <- data |> lapply(\(.x){
- ls <- REDCapCAST::get_attr(data = .x,attr = attr)
- if (is.na(ls) | ls == ""){
+ ls <- REDCapCAST::get_attr(data = .x, attr = attr)
+ if (is.na(ls) | ls == "") {
attr(x = .x, which = attr) <- NULL
}
.x
@@ -261,10 +263,10 @@ remove_na_attr <- function(data,attr="label"){
#' @export
#'
#' @examples
-#'data.frame(a=1:10,b=NA, c=c(2,NA)) |> remove_empty_cols(cutoff=.5)
-remove_empty_cols <- function(data,cutoff=.7){
- filter <- apply(X = data,MARGIN = 2,FUN = \(.x){
- sum(as.numeric(!is.na(.x)))/length(.x)
+#' data.frame(a = 1:10, b = NA, c = c(2, NA)) |> remove_empty_cols(cutoff = .5)
+remove_empty_cols <- function(data, cutoff = .7) {
+ filter <- apply(X = data, MARGIN = 2, FUN = \(.x){
+ sum(as.numeric(!is.na(.x))) / length(.x)
}) >= cutoff
data[filter]
}
@@ -280,18 +282,18 @@ remove_empty_cols <- function(data,cutoff=.7){
#' @export
#'
#' @examples
-#' ls_d <- list(test=c(1:20))
+#' ls_d <- list(test = c(1:20))
#' ls_d <- list()
-#' data.frame(letters[1:20],1:20) |> append_list(ls_d,"letters")
-#' letters[1:20]|> append_list(ls_d,"letters")
-append_list <- function(data,list,index){
+#' data.frame(letters[1:20], 1:20) |> append_list(ls_d, "letters")
+#' letters[1:20] |> append_list(ls_d, "letters")
+append_list <- function(data, list, index) {
## This will overwrite and not warn
## Not very safe, but convenient to append code to list
- if (index %in% names(list)){
+ if (index %in% names(list)) {
list[[index]] <- data
out <- list
} else {
- out <- setNames(c(list,list(data)),c(names(list),index))
+ out <- setNames(c(list, list(data)), c(names(list), index))
}
out
}
@@ -305,7 +307,33 @@ append_list <- function(data,list,index){
#' @export
#'
#' @examples
-#' c(NA,1:10,rep(NA,3)) |> missing_fraction()
-missing_fraction <- function(data){
- NROW(data[is.na(data)])/NROW(data)
+#' c(NA, 1:10, rep(NA, 3)) |> missing_fraction()
+missing_fraction <- function(data) {
+ NROW(data[is.na(data)]) / NROW(data)
+}
+
+
+
+#' Ultra short data dascription
+#'
+#' @param data
+#'
+#' @returns character vector
+#' @export
+#'
+#' @examples
+#' data.frame(
+#' sample(1:8, 20, TRUE),
+#' sample(c(1:8, NA), 20, TRUE)
+#' ) |> data_description()
+data_description <- function(data) {
+ data <- if (shiny::is.reactive(data)) data() else data
+
+ sprintf(
+ i18n("Data has %s observations and %s variables, with %s (%s%%) complete cases"),
+ nrow(data),
+ ncol(data),
+ sum(complete.cases(data)),
+ signif(100 * (1 - missing_fraction(data)), 3)
+ )
}
diff --git a/R/regression_plot.R b/R/regression_plot.R
index adb0a47..252e1ec 100644
--- a/R/regression_plot.R
+++ b/R/regression_plot.R
@@ -43,15 +43,16 @@ plot.tbl_regression <- function(x,
# Removes redundant label
df_coefs$label[df_coefs$row_type == "label"] <- ""
-
+ # browser()
# Add estimate value to reference level
- if (plot_ref == TRUE){
- df_coefs[df_coefs$var_type == "categorical" & is.na(df_coefs$reference_row),"estimate"] <- if (x$inputs$exponentiate) 1 else 0}
+ if (plot_ref == TRUE) {
+ df_coefs[df_coefs$var_type %in% c("categorical", "dichotomous") & df_coefs$reference_row & !is.na(df_coefs$reference_row), "estimate"] <- if (x$inputs$exponentiate) 1 else 0
+ }
p <- df_coefs |>
ggstats::ggcoef_plot(exponentiate = x$inputs$exponentiate, ...)
- if (x$inputs$exponentiate){
+ if (x$inputs$exponentiate) {
p <- symmetrical_scale_x_log10(p)
}
p
@@ -89,7 +90,8 @@ merge_long <- function(list, model.names) {
)
setNames(d, gsub("_[0-9]{,}$", "", names(d)))
}) |>
- dplyr::bind_rows() |> dplyr::mutate(model=as_factor(model))
+ dplyr::bind_rows() |>
+ dplyr::mutate(model = as_factor(model))
l_merged$table_body <- df_body_long
@@ -109,12 +111,25 @@ merge_long <- function(list, model.names) {
#' @export
#'
#' @examples
-#' limit_log(-.1,floor)
-#' limit_log(.1,ceiling)
-#' limit_log(-2.1,ceiling)
-#' limit_log(2.1,ceiling)
-limit_log <- function(data,fun,...){
- fun(10^-floor(data)*10^data)/10^-floor(data)
+#' limit_log(-.1, floor)
+#' limit_log(.1, ceiling)
+#' limit_log(-2.1, ceiling)
+#' limit_log(2.1, ceiling)
+limit_log <- function(data, fun, ...) {
+ fun(10^-floor(data) * 10^data) / 10^-floor(data)
+}
+
+#' Create summetric log ticks
+#'
+#' @param data numeric vector
+#'
+#' @returns
+#' @export
+#'
+#' @examples
+#' c(sample(seq(.1, 1, .1), 3), sample(1:10, 3)) |> create_log_tics()
+create_log_tics <- function(data) {
+ sort(round(unique(c(1 / data, data, 1)), 2))
}
#' Ensure symmetrical plot around 1 on a logarithmic x scale for ratio plots
@@ -126,18 +141,18 @@ limit_log <- function(data,fun,...){
#' @returns ggplot2 object
#' @export
#'
-symmetrical_scale_x_log10 <- function(plot,breaks=c(1,2,3,5,10),...){
+symmetrical_scale_x_log10 <- function(plot, breaks = c(1, 2, 3, 5, 10), ...) {
rx <- ggplot2::layer_scales(plot)$x$get_limits()
- x_min <- floor(10*rx[1])/10
- x_max <- ceiling(10*rx[2])/10
+ x_min <- floor(10 * rx[1]) / 10
+ x_max <- ceiling(10 * rx[2]) / 10
- rx_min <- limit_log(rx[1],floor)
- rx_max <- limit_log(rx[2],ceiling)
+ rx_min <- limit_log(rx[1], floor)
+ rx_max <- limit_log(rx[2], ceiling)
- max_abs_x <- max(abs(c(x_min,x_max)))
+ max_abs_x <- max(abs(c(x_min, x_max)))
- ticks <- log10(breaks)+(ceiling(max_abs_x)-1)
+ ticks <- log10(breaks) + (ceiling(max_abs_x) - 1)
- plot + ggplot2::scale_x_log10(limits=c(rx_min,rx_max),breaks=create_log_tics(10^ticks[ticks<=max_abs_x]))
+ plot + ggplot2::scale_x_log10(limits = c(rx_min, rx_max), breaks = create_log_tics(10^ticks[ticks <= max_abs_x]))
}
diff --git a/R/regression_table.R b/R/regression_table.R
index c9fa513..5e90a27 100644
--- a/R/regression_table.R
+++ b/R/regression_table.R
@@ -119,8 +119,8 @@ regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::
}
out <- do.call(getfun(fun), c(list(x = x), args.list))
- out |>
- gtsummary::add_glance_source_note() # |>
+ out #|>
+ # gtsummary::add_glance_source_note() # |>
# gtsummary::bold_p()
}
diff --git a/inst/apps/FreesearchR/app.R b/inst/apps/FreesearchR/app.R
index 683b6f2..1dbfff5 100644
--- a/inst/apps/FreesearchR/app.R
+++ b/inst/apps/FreesearchR/app.R
@@ -10,7 +10,7 @@
#### Current file: R//app_version.R
########
-app_version <- function()'250320_1310'
+app_version <- function()'250324_1432'
########
@@ -41,6 +41,58 @@ baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary,
+#' Create a baseline table
+#'
+#' @param data data
+#' @param ... passed as fun.arg to baseline_table()
+#' @param strat.var grouping/strat variable
+#' @param add.p add comparison/p-value
+#' @param add.overall add overall column
+#'
+#' @returns gtsummary table list object
+#' @export
+#'
+#' @examples
+#' mtcars |> create_baseline(by.var = "gear", add.p="yes"=="yes")
+create_baseline <- function(data,...,by.var,add.p=FALSE,add.overall=FALSE){
+ if (by.var == "none" | !by.var %in% names(data)) {
+ by.var <- NULL
+ }
+
+ ## These steps are to handle logicals/booleans, that messes up the order of columns
+ ## Has been reported
+
+ if (!is.null(by.var)) {
+ if (identical("logical",class(data[[by.var]]))){
+ data[by.var] <- as.character(data[[by.var]])
+ }
+ }
+
+ out <- data |>
+ baseline_table(
+ fun.args =
+ list(
+ by = by.var,
+ ...
+ )
+ )
+
+ if (!is.null(by.var)) {
+ if (isTRUE(add.overall)){
+ out <- out |> gtsummary::add_overall()
+ }
+ if (isTRUE(add.p)) {
+ out <- out |>
+ gtsummary::add_p() |>
+ gtsummary::bold_p()
+ }
+
+ }
+
+ out
+}
+
+
########
#### Current file: R//contrast_text.R
########
@@ -356,76 +408,6 @@ columnSelectInput <- function(inputId, label, data, selected = "", ...,
)
}
-columnSelectInputStat <- function(inputId, label, data, selected = "", ...,
- col_subset = NULL, placeholder = "", onInitialize, none_label="No variable selected",maxItems=NULL) {
- data <- if (is.reactive(data)) data() else data
- col_subsetr <- if (is.reactive(col_subset)) col_subset else reactive(col_subset)
-
- labels <- Map(function(col) {
- json <- sprintf(
- IDEAFilter:::strip_leading_ws('
- {
- "name": "%s",
- "label": "%s",
- "dataclass": "%s",
- "datatype": "%s"
- }'),
- col,
- attr(data[[col]], "label") %||% "",
- IDEAFilter:::get_dataFilter_class(data[[col]]),
- data_type(data[[col]])
- )
- }, col = names(data))
-
- if (!"none" %in% names(data)){
- labels <- c("none"=list(sprintf('\n {\n \"name\": \"none\",\n \"label\": \"%s\",\n \"dataclass\": \"\",\n \"datatype\": \"\"\n }',none_label)),labels)
- choices <- setNames(names(labels), labels)
- choices <- choices[match(if (length(col_subsetr()) == 0 || isTRUE(col_subsetr() == "")) names(data) else col_subsetr(), choices)]
- } else {
- choices <- setNames(names(data), labels)
- choices <- choices[match(if (length(col_subsetr()) == 0 || isTRUE(col_subsetr() == "")) choices else col_subsetr(), choices)]
- }
-
- shiny::selectizeInput(
- inputId = inputId,
- label = label,
- choices = choices,
- selected = selected,
- ...,
- options = c(
- list(render = I("{
- // format the way that options are rendered
- option: function(item, escape) {
- item.data = JSON.parse(item.label);
- return '
' +
- '
' +
- escape(item.data.name) + ' ' +
- '' +
- (item.data.dataclass != '' ?
- ' ' +
- item.data.dataclass +
- '
' : '' ) + ' ' +
- (item.data.datatype != '' ?
- ' ' +
- item.data.datatype +
- '
' : '' ) +
- '
' +
- (item.data.label != '' ? '
' + escape(item.data.label) + '
' : '') +
- '
';
- },
-
- // avoid data vomit splashing on screen when an option is selected
- item: function(item, escape) {
- item.data = JSON.parse(item.label);
- return '' +
- escape(item.data.name) +
- '
';
- }
- }")),
- if (!is.null(maxItems)) list(maxItems=maxItems)
- )
- )
-}
#' A selectizeInput customized for named vectors
#'
@@ -1476,6 +1458,7 @@ data_visuals_server <- function(id,
{
tryCatch(
{
+ shiny::withProgress(message = "Drawing the plot. Hold tight for a moment..", {
rv$plot <- create_plot(
data = data(),
type = rv$plot.params()[["fun"]],
@@ -1483,6 +1466,7 @@ data_visuals_server <- function(id,
y = input$secondary,
z = input$tertiary
)
+ })
},
# warning = function(warn) {
# showNotification(paste0(warn), type = "warning")
@@ -2533,7 +2517,7 @@ getfun <- function(x) {
#' @return output file name
#' @export
#'
-write_quarto <- function(data,...) {
+write_quarto <- function(data, ...) {
# Exports data to temporary location
#
# I assume this is more secure than putting it in the www folder and deleting
@@ -2554,7 +2538,7 @@ write_quarto <- function(data,...) {
)
}
-write_rmd <- function(data,...) {
+write_rmd <- function(data, ...) {
# Exports data to temporary location
#
# I assume this is more secure than putting it in the www folder and deleting
@@ -2714,17 +2698,17 @@ file_export <- function(data, output.format = c("df", "teal", "list"), filename,
#' default_parsing() |>
#' str()
default_parsing <- function(data) {
- name_labels <- lapply(data,\(.x) REDCapCAST::get_attr(.x,attr = "label"))
+ name_labels <- lapply(data, \(.x) REDCapCAST::get_attr(.x, attr = "label"))
out <- data |>
REDCapCAST::parse_data() |>
REDCapCAST::as_factor() |>
- REDCapCAST::numchar2fct(numeric.threshold = 8,character.throshold = 10) |>
+ REDCapCAST::numchar2fct(numeric.threshold = 8, character.throshold = 10) |>
REDCapCAST::as_logical() |>
REDCapCAST::fct_drop()
- purrr::map2(out,name_labels,\(.x,.l){
- if (!(is.na(.l) | .l=="")) {
+ purrr::map2(out, name_labels, \(.x, .l){
+ if (!(is.na(.l) | .l == "")) {
REDCapCAST::set_attr(.x, .l, attr = "label")
} else {
attr(x = .x, which = "label") <- NULL
@@ -2742,12 +2726,14 @@ default_parsing <- function(data) {
#' @export
#'
#' @examples
-#' ds <- mtcars |> lapply(\(.x) REDCapCAST::set_attr(.x,label=NA,attr = "label"))
-#' ds |> remove_na_attr() |> str()
-remove_na_attr <- function(data,attr="label"){
+#' ds <- mtcars |> lapply(\(.x) REDCapCAST::set_attr(.x, label = NA, attr = "label"))
+#' ds |>
+#' remove_na_attr() |>
+#' str()
+remove_na_attr <- function(data, attr = "label") {
out <- data |> lapply(\(.x){
- ls <- REDCapCAST::get_attr(data = .x,attr = attr)
- if (is.na(ls) | ls == ""){
+ ls <- REDCapCAST::get_attr(data = .x, attr = attr)
+ if (is.na(ls) | ls == "") {
attr(x = .x, which = attr) <- NULL
}
.x
@@ -2765,10 +2751,10 @@ remove_na_attr <- function(data,attr="label"){
#' @export
#'
#' @examples
-#'data.frame(a=1:10,b=NA, c=c(2,NA)) |> remove_empty_cols(cutoff=.5)
-remove_empty_cols <- function(data,cutoff=.7){
- filter <- apply(X = data,MARGIN = 2,FUN = \(.x){
- sum(as.numeric(!is.na(.x)))/length(.x)
+#' data.frame(a = 1:10, b = NA, c = c(2, NA)) |> remove_empty_cols(cutoff = .5)
+remove_empty_cols <- function(data, cutoff = .7) {
+ filter <- apply(X = data, MARGIN = 2, FUN = \(.x){
+ sum(as.numeric(!is.na(.x))) / length(.x)
}) >= cutoff
data[filter]
}
@@ -2784,18 +2770,18 @@ remove_empty_cols <- function(data,cutoff=.7){
#' @export
#'
#' @examples
-#' ls_d <- list(test=c(1:20))
+#' ls_d <- list(test = c(1:20))
#' ls_d <- list()
-#' data.frame(letters[1:20],1:20) |> append_list(ls_d,"letters")
-#' letters[1:20]|> append_list(ls_d,"letters")
-append_list <- function(data,list,index){
+#' data.frame(letters[1:20], 1:20) |> append_list(ls_d, "letters")
+#' letters[1:20] |> append_list(ls_d, "letters")
+append_list <- function(data, list, index) {
## This will overwrite and not warn
## Not very safe, but convenient to append code to list
- if (index %in% names(list)){
+ if (index %in% names(list)) {
list[[index]] <- data
out <- list
} else {
- out <- setNames(c(list,list(data)),c(names(list),index))
+ out <- setNames(c(list, list(data)), c(names(list), index))
}
out
}
@@ -2809,9 +2795,35 @@ append_list <- function(data,list,index){
#' @export
#'
#' @examples
-#' c(NA,1:10,rep(NA,3)) |> missing_fraction()
-missing_fraction <- function(data){
- NROW(data[is.na(data)])/NROW(data)
+#' c(NA, 1:10, rep(NA, 3)) |> missing_fraction()
+missing_fraction <- function(data) {
+ NROW(data[is.na(data)]) / NROW(data)
+}
+
+
+
+#' Ultra short data dascription
+#'
+#' @param data
+#'
+#' @returns character vector
+#' @export
+#'
+#' @examples
+#' data.frame(
+#' sample(1:8, 20, TRUE),
+#' sample(c(1:8, NA), 20, TRUE)
+#' ) |> data_description()
+data_description <- function(data) {
+ data <- if (shiny::is.reactive(data)) data() else data
+
+ sprintf(
+ i18n("Data has %s observations and %s variables, with %s (%s%%) complete cases"),
+ nrow(data),
+ ncol(data),
+ sum(complete.cases(data)),
+ signif(100 * (1 - missing_fraction(data)), 3)
+ )
}
@@ -5352,15 +5364,16 @@ plot.tbl_regression <- function(x,
# Removes redundant label
df_coefs$label[df_coefs$row_type == "label"] <- ""
-
+ # browser()
# Add estimate value to reference level
- if (plot_ref == TRUE){
- df_coefs[df_coefs$var_type == "categorical" & is.na(df_coefs$reference_row),"estimate"] <- if (x$inputs$exponentiate) 1 else 0}
+ if (plot_ref == TRUE) {
+ df_coefs[df_coefs$var_type %in% c("categorical", "dichotomous") & df_coefs$reference_row & !is.na(df_coefs$reference_row), "estimate"] <- if (x$inputs$exponentiate) 1 else 0
+ }
p <- df_coefs |>
ggstats::ggcoef_plot(exponentiate = x$inputs$exponentiate, ...)
- if (x$inputs$exponentiate){
+ if (x$inputs$exponentiate) {
p <- symmetrical_scale_x_log10(p)
}
p
@@ -5398,7 +5411,8 @@ merge_long <- function(list, model.names) {
)
setNames(d, gsub("_[0-9]{,}$", "", names(d)))
}) |>
- dplyr::bind_rows() |> dplyr::mutate(model=as_factor(model))
+ dplyr::bind_rows() |>
+ dplyr::mutate(model = as_factor(model))
l_merged$table_body <- df_body_long
@@ -5418,12 +5432,25 @@ merge_long <- function(list, model.names) {
#' @export
#'
#' @examples
-#' limit_log(-.1,floor)
-#' limit_log(.1,ceiling)
-#' limit_log(-2.1,ceiling)
-#' limit_log(2.1,ceiling)
-limit_log <- function(data,fun,...){
- fun(10^-floor(data)*10^data)/10^-floor(data)
+#' limit_log(-.1, floor)
+#' limit_log(.1, ceiling)
+#' limit_log(-2.1, ceiling)
+#' limit_log(2.1, ceiling)
+limit_log <- function(data, fun, ...) {
+ fun(10^-floor(data) * 10^data) / 10^-floor(data)
+}
+
+#' Create summetric log ticks
+#'
+#' @param data numeric vector
+#'
+#' @returns
+#' @export
+#'
+#' @examples
+#' c(sample(seq(.1, 1, .1), 3), sample(1:10, 3)) |> create_log_tics()
+create_log_tics <- function(data) {
+ sort(round(unique(c(1 / data, data, 1)), 2))
}
#' Ensure symmetrical plot around 1 on a logarithmic x scale for ratio plots
@@ -5435,20 +5462,20 @@ limit_log <- function(data,fun,...){
#' @returns ggplot2 object
#' @export
#'
-symmetrical_scale_x_log10 <- function(plot,breaks=c(1,2,3,5,10),...){
+symmetrical_scale_x_log10 <- function(plot, breaks = c(1, 2, 3, 5, 10), ...) {
rx <- ggplot2::layer_scales(plot)$x$get_limits()
- x_min <- floor(10*rx[1])/10
- x_max <- ceiling(10*rx[2])/10
+ x_min <- floor(10 * rx[1]) / 10
+ x_max <- ceiling(10 * rx[2]) / 10
- rx_min <- limit_log(rx[1],floor)
- rx_max <- limit_log(rx[2],ceiling)
+ rx_min <- limit_log(rx[1], floor)
+ rx_max <- limit_log(rx[2], ceiling)
- max_abs_x <- max(abs(c(x_min,x_max)))
+ max_abs_x <- max(abs(c(x_min, x_max)))
- ticks <- log10(breaks)+(ceiling(max_abs_x)-1)
+ ticks <- log10(breaks) + (ceiling(max_abs_x) - 1)
- plot + ggplot2::scale_x_log10(limits=c(rx_min,rx_max),breaks=create_log_tics(10^ticks[ticks<=max_abs_x]))
+ plot + ggplot2::scale_x_log10(limits = c(rx_min, rx_max), breaks = create_log_tics(10^ticks[ticks <= max_abs_x]))
}
@@ -5577,8 +5604,8 @@ regression_table_create <- function(x, ..., args.list = NULL, fun = "gtsummary::
}
out <- do.call(getfun(fun), c(list(x = x), args.list))
- out |>
- gtsummary::add_glance_source_note() # |>
+ out #|>
+ # gtsummary::add_glance_source_note() # |>
# gtsummary::bold_p()
}
@@ -7101,6 +7128,7 @@ ui_elements <- list(
shinyWidgets::noUiSliderInput(
inputId = "complete_cutoff",
label = NULL,
+ update_on = "change",
min = 0,
max = 100,
step = 5,
@@ -7111,7 +7139,8 @@ ui_elements <- list(
shiny::helpText("Filter variables with completeness above the specified percentage."),
shiny::br(),
shiny::br(),
- shiny::uiOutput(outputId = "import_var")
+ shiny::uiOutput(outputId = "import_var"),
+ shiny::uiOutput(outputId = "data_info_import", inline = TRUE)
)
),
shiny::br(),
@@ -7148,10 +7177,9 @@ ui_elements <- list(
fluidRow(
shiny::column(
width = 9,
+ shiny::uiOutput(outputId = "data_info", inline = TRUE),
shiny::tags$p(
- "Below is a short summary table of the provided data.
- On the right hand side you have the option to create filters.
- At the bottom you'll find a raw overview of the original vs the modified data."
+ "Below is a short summary table, on the right you can create data filters."
)
)
),
@@ -7406,6 +7434,7 @@ ui_elements <- list(
# bslib::layout_sidebar(
# fillable = TRUE,
sidebar = bslib::sidebar(
+ shiny::uiOutput(outputId = "data_info_regression", inline = TRUE),
bslib::accordion(
open = "acc_reg",
multiple = FALSE,
@@ -7467,7 +7496,7 @@ ui_elements <- list(
),
shiny::conditionalPanel(
condition = "input.all==1",
- shiny::uiOutput("include_vars")
+ shiny::uiOutput("regression_vars")
)
)
),
@@ -7823,11 +7852,12 @@ server <- function(input, output, session) {
shiny::observeEvent(
eventExpr = list(
- input$import_var
+ input$import_var,
+ input$complete_cutoff
),
handlerExpr = {
shiny::req(rv$data_temp)
-
+# browser()
rv$data_original <- rv$data_temp |>
dplyr::select(input$import_var) |>
default_parsing()
@@ -7847,6 +7877,11 @@ server <- function(input, output, session) {
}
)
+ output$data_info_import <- shiny::renderUI({
+ shiny::req(rv$data_original)
+ data_description(rv$data_original)
+ })
+
shiny::observeEvent(rv$data_original, {
if (is.null(rv$data_original) | NROW(rv$data_original) == 0) {
@@ -7911,6 +7946,17 @@ server <- function(input, output, session) {
modal_update_variables("modal_variables", title = "Update and select variables")
)
+ output$data_info <- shiny::renderUI({
+ shiny::req(data_filter())
+ data_description(data_filter())
+ })
+
+ output$data_info_regression <- shiny::renderUI({
+ shiny::req(regression_vars())
+ shiny::req(rv$list$data)
+ data_description(rv$list$data[regression_vars()])
+ })
+
######### Create factor
@@ -8131,40 +8177,25 @@ server <- function(input, output, session) {
## Keep these "old" selection options as a simple alternative to the modification pane
- output$include_vars <- shiny::renderUI({
- columnSelectInputStat(
- inputId = "include_vars",
+
+ output$regression_vars <- shiny::renderUI({
+ columnSelectInput(
+ inputId = "regression_vars",
selected = NULL,
label = "Covariables to include",
data = rv$data_filtered,
- multiple = TRUE
+ multiple = TRUE,
)
-
- # shiny::selectizeInput(
- # inputId = "include_vars",
- # selected = NULL,
- # label = "Covariables to include",
- # choices = colnames(rv$data_filtered),
- # multiple = TRUE
- # )
})
output$outcome_var <- shiny::renderUI({
- columnSelectInputStat(
+ columnSelectInput(
inputId = "outcome_var",
selected = NULL,
label = "Select outcome variable",
data = rv$data_filtered,
multiple = FALSE
)
-
- # shiny::selectInput(
- # inputId = "outcome_var",
- # selected = NULL,
- # label = "Select outcome variable",
- # choices = colnames(rv$data_filtered),
- # multiple = FALSE
- # )
})
output$regression_type <- shiny::renderUI({
@@ -8198,16 +8229,16 @@ server <- function(input, output, session) {
## Collected regression variables
regression_vars <- shiny::reactive({
- if (is.null(input$include_vars)) {
+ if (is.null(input$regression_vars)) {
out <- colnames(rv$data_filtered)
} else {
- out <- unique(c(input$include_vars, input$outcome_var))
+ out <- unique(c(input$regression_vars, input$outcome_var))
}
return(out)
})
output$strat_var <- shiny::renderUI({
- columnSelectInputStat(
+ columnSelectInput(
inputId = "strat_var",
selected = "none",
label = "Select variable to stratify baseline",
@@ -8217,27 +8248,6 @@ server <- function(input, output, session) {
names(rv$data_filtered)[unlist(lapply(rv$data_filtered, data_type)) %in% c("dichotomous", "categorical", "ordinal")]
)
)
-
- # shiny::selectInput(
- # inputId = "strat_var",
- # selected = "none",
- # label = "Select variable to stratify baseline",
- # choices = c(
- # "none",
- # names(rv$list$data)[unlist(lapply(rv$list$data,data_type)) %in% c("dichotomous","categorical","ordinal")]
- # # rv$data_filtered |>
- # # (\(.x){
- # # lapply(.x, \(.c){
- # # if (identical("factor", class(.c))) {
- # # .c
- # # }
- # # }) |>
- # # dplyr::bind_cols()
- # # })() |>
- # # colnames()
- # ),
- # multiple = FALSE
- # )
})
@@ -8267,7 +8277,7 @@ server <- function(input, output, session) {
# shiny::reactive(rv$data_original),
# data_filter(),
# input$strat_var,
- # input$include_vars,
+ # input$regression_vars,
# input$complete_cutoff,
# input$add_p
input$act_eval
@@ -8276,48 +8286,16 @@ server <- function(input, output, session) {
shiny::req(input$strat_var)
shiny::req(rv$list$data)
- data_tbl1 <- rv$list$data
+ # data_tbl1 <- rv$list$data
- if (input$strat_var == "none" | !input$strat_var %in% names(data_tbl1)) {
- by.var <- NULL
- } else {
- by.var <- input$strat_var
- }
-
- ## These steps are to handle logicals/booleans, that messes up the order of columns
- ## Has been reported
-
- if (!is.null(by.var) & identical("logical",class(data_tbl1[[by.var]]))) {
- data_tbl1[by.var] <- as.character(data_tbl1[[by.var]])
- }
-
- rv$list$table1 <-
- data_tbl1 |>
- baseline_table(
- fun.args =
- list(
- by = by.var
- )
- ) |>
- (\(.x){
- if (!is.null(by.var)) {
- .x |> gtsummary::add_overall()
- } else {
- .x
- }
- })() |>
- (\(.x){
- if (input$add_p == "yes" & !is.null(by.var)) {
- .x |>
- gtsummary::add_p() |>
- gtsummary::bold_p()
- } else {
- .x
- }
- })()
-
- # gtsummary::as_kable(rv$list$table1) |>
- # readr::write_lines(file="./www/_table1.md")
+ shiny::withProgress(message = "Creating the table. Hold on for a moment..", {
+ rv$list$table1 <- create_baseline(
+ rv$list$data,
+ by.var = input$strat_var,
+ add.p = input$add_p == "yes",
+ add.overall = TRUE
+ )
+ })
}
)
@@ -8416,9 +8394,9 @@ server <- function(input, output, session) {
# .x$model
# })
},
- warning = function(warn) {
- showNotification(paste0(warn), type = "warning")
- },
+ # warning = function(warn) {
+ # showNotification(paste0(warn), type = "warning")
+ # },
error = function(err) {
showNotification(paste0("Creating regression models failed with the following error: ", err), type = "err")
}
@@ -8441,9 +8419,9 @@ server <- function(input, output, session) {
purrr::pluck("Multivariable") |>
performance::check_model()
},
- warning = function(warn) {
- showNotification(paste0(warn), type = "warning")
- },
+ # warning = function(warn) {
+ # showNotification(paste0(warn), type = "warning")
+ # },
error = function(err) {
showNotification(paste0("Running model assumptions checks failed with the following error: ", err), type = "err")
}
diff --git a/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf b/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
index 8d5d512..ce7c605 100644
--- a/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
+++ b/inst/apps/FreesearchR/rsconnect/shinyapps.io/agdamsbo/freesearcheR.dcf
@@ -5,6 +5,6 @@ account: agdamsbo
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 13611288
-bundleId: 9974967
+bundleId: 9994253
url: https://agdamsbo.shinyapps.io/freesearcheR/
version: 1
diff --git a/inst/apps/FreesearchR/server.R b/inst/apps/FreesearchR/server.R
index 30ee43e..790d2dd 100644
--- a/inst/apps/FreesearchR/server.R
+++ b/inst/apps/FreesearchR/server.R
@@ -160,11 +160,12 @@ server <- function(input, output, session) {
shiny::observeEvent(
eventExpr = list(
- input$import_var
+ input$import_var,
+ input$complete_cutoff
),
handlerExpr = {
shiny::req(rv$data_temp)
-
+# browser()
rv$data_original <- rv$data_temp |>
dplyr::select(input$import_var) |>
default_parsing()
@@ -184,6 +185,11 @@ server <- function(input, output, session) {
}
)
+ output$data_info_import <- shiny::renderUI({
+ shiny::req(rv$data_original)
+ data_description(rv$data_original)
+ })
+
shiny::observeEvent(rv$data_original, {
if (is.null(rv$data_original) | NROW(rv$data_original) == 0) {
@@ -248,6 +254,17 @@ server <- function(input, output, session) {
modal_update_variables("modal_variables", title = "Update and select variables")
)
+ output$data_info <- shiny::renderUI({
+ shiny::req(data_filter())
+ data_description(data_filter())
+ })
+
+ output$data_info_regression <- shiny::renderUI({
+ shiny::req(regression_vars())
+ shiny::req(rv$list$data)
+ data_description(rv$list$data[regression_vars()])
+ })
+
######### Create factor
@@ -468,40 +485,25 @@ server <- function(input, output, session) {
## Keep these "old" selection options as a simple alternative to the modification pane
- output$include_vars <- shiny::renderUI({
- columnSelectInputStat(
- inputId = "include_vars",
+
+ output$regression_vars <- shiny::renderUI({
+ columnSelectInput(
+ inputId = "regression_vars",
selected = NULL,
label = "Covariables to include",
data = rv$data_filtered,
- multiple = TRUE
+ multiple = TRUE,
)
-
- # shiny::selectizeInput(
- # inputId = "include_vars",
- # selected = NULL,
- # label = "Covariables to include",
- # choices = colnames(rv$data_filtered),
- # multiple = TRUE
- # )
})
output$outcome_var <- shiny::renderUI({
- columnSelectInputStat(
+ columnSelectInput(
inputId = "outcome_var",
selected = NULL,
label = "Select outcome variable",
data = rv$data_filtered,
multiple = FALSE
)
-
- # shiny::selectInput(
- # inputId = "outcome_var",
- # selected = NULL,
- # label = "Select outcome variable",
- # choices = colnames(rv$data_filtered),
- # multiple = FALSE
- # )
})
output$regression_type <- shiny::renderUI({
@@ -535,16 +537,16 @@ server <- function(input, output, session) {
## Collected regression variables
regression_vars <- shiny::reactive({
- if (is.null(input$include_vars)) {
+ if (is.null(input$regression_vars)) {
out <- colnames(rv$data_filtered)
} else {
- out <- unique(c(input$include_vars, input$outcome_var))
+ out <- unique(c(input$regression_vars, input$outcome_var))
}
return(out)
})
output$strat_var <- shiny::renderUI({
- columnSelectInputStat(
+ columnSelectInput(
inputId = "strat_var",
selected = "none",
label = "Select variable to stratify baseline",
@@ -554,27 +556,6 @@ server <- function(input, output, session) {
names(rv$data_filtered)[unlist(lapply(rv$data_filtered, data_type)) %in% c("dichotomous", "categorical", "ordinal")]
)
)
-
- # shiny::selectInput(
- # inputId = "strat_var",
- # selected = "none",
- # label = "Select variable to stratify baseline",
- # choices = c(
- # "none",
- # names(rv$list$data)[unlist(lapply(rv$list$data,data_type)) %in% c("dichotomous","categorical","ordinal")]
- # # rv$data_filtered |>
- # # (\(.x){
- # # lapply(.x, \(.c){
- # # if (identical("factor", class(.c))) {
- # # .c
- # # }
- # # }) |>
- # # dplyr::bind_cols()
- # # })() |>
- # # colnames()
- # ),
- # multiple = FALSE
- # )
})
@@ -604,7 +585,7 @@ server <- function(input, output, session) {
# shiny::reactive(rv$data_original),
# data_filter(),
# input$strat_var,
- # input$include_vars,
+ # input$regression_vars,
# input$complete_cutoff,
# input$add_p
input$act_eval
@@ -613,48 +594,16 @@ server <- function(input, output, session) {
shiny::req(input$strat_var)
shiny::req(rv$list$data)
- data_tbl1 <- rv$list$data
+ # data_tbl1 <- rv$list$data
- if (input$strat_var == "none" | !input$strat_var %in% names(data_tbl1)) {
- by.var <- NULL
- } else {
- by.var <- input$strat_var
- }
-
- ## These steps are to handle logicals/booleans, that messes up the order of columns
- ## Has been reported
-
- if (!is.null(by.var) & identical("logical",class(data_tbl1[[by.var]]))) {
- data_tbl1[by.var] <- as.character(data_tbl1[[by.var]])
- }
-
- rv$list$table1 <-
- data_tbl1 |>
- baseline_table(
- fun.args =
- list(
- by = by.var
- )
- ) |>
- (\(.x){
- if (!is.null(by.var)) {
- .x |> gtsummary::add_overall()
- } else {
- .x
- }
- })() |>
- (\(.x){
- if (input$add_p == "yes" & !is.null(by.var)) {
- .x |>
- gtsummary::add_p() |>
- gtsummary::bold_p()
- } else {
- .x
- }
- })()
-
- # gtsummary::as_kable(rv$list$table1) |>
- # readr::write_lines(file="./www/_table1.md")
+ shiny::withProgress(message = "Creating the table. Hold on for a moment..", {
+ rv$list$table1 <- create_baseline(
+ rv$list$data,
+ by.var = input$strat_var,
+ add.p = input$add_p == "yes",
+ add.overall = TRUE
+ )
+ })
}
)
@@ -753,9 +702,9 @@ server <- function(input, output, session) {
# .x$model
# })
},
- warning = function(warn) {
- showNotification(paste0(warn), type = "warning")
- },
+ # warning = function(warn) {
+ # showNotification(paste0(warn), type = "warning")
+ # },
error = function(err) {
showNotification(paste0("Creating regression models failed with the following error: ", err), type = "err")
}
@@ -778,9 +727,9 @@ server <- function(input, output, session) {
purrr::pluck("Multivariable") |>
performance::check_model()
},
- warning = function(warn) {
- showNotification(paste0(warn), type = "warning")
- },
+ # warning = function(warn) {
+ # showNotification(paste0(warn), type = "warning")
+ # },
error = function(err) {
showNotification(paste0("Running model assumptions checks failed with the following error: ", err), type = "err")
}
diff --git a/inst/apps/FreesearchR/ui.R b/inst/apps/FreesearchR/ui.R
index ea40eb8..1683c79 100644
--- a/inst/apps/FreesearchR/ui.R
+++ b/inst/apps/FreesearchR/ui.R
@@ -84,6 +84,7 @@ ui_elements <- list(
shinyWidgets::noUiSliderInput(
inputId = "complete_cutoff",
label = NULL,
+ update_on = "change",
min = 0,
max = 100,
step = 5,
@@ -94,7 +95,8 @@ ui_elements <- list(
shiny::helpText("Filter variables with completeness above the specified percentage."),
shiny::br(),
shiny::br(),
- shiny::uiOutput(outputId = "import_var")
+ shiny::uiOutput(outputId = "import_var"),
+ shiny::uiOutput(outputId = "data_info_import", inline = TRUE)
)
),
shiny::br(),
@@ -131,10 +133,9 @@ ui_elements <- list(
fluidRow(
shiny::column(
width = 9,
+ shiny::uiOutput(outputId = "data_info", inline = TRUE),
shiny::tags$p(
- "Below is a short summary table of the provided data.
- On the right hand side you have the option to create filters.
- At the bottom you'll find a raw overview of the original vs the modified data."
+ "Below is a short summary table, on the right you can create data filters."
)
)
),
@@ -389,6 +390,7 @@ ui_elements <- list(
# bslib::layout_sidebar(
# fillable = TRUE,
sidebar = bslib::sidebar(
+ shiny::uiOutput(outputId = "data_info_regression", inline = TRUE),
bslib::accordion(
open = "acc_reg",
multiple = FALSE,
@@ -450,7 +452,7 @@ ui_elements <- list(
),
shiny::conditionalPanel(
condition = "input.all==1",
- shiny::uiOutput("include_vars")
+ shiny::uiOutput("regression_vars")
)
)
),