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Merged
tcoroller merged 1 commit into from
Apr 15, 2026
Merged

shiny feedbacks #6

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20 changes: 14 additions & 6 deletions R/server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ app_server <- function(input, output, session) {
div(
class = "event-row-head",
div("Planned look"),
div("Deaths"),
div("Expected deaths"),
div()
),
div(
Expand Down Expand Up @@ -113,11 +113,14 @@ app_server <- function(input, output, session) {
primary_events <- get_primary_events(rows)

validate(
need(length(primary_events) > 0, "Enter at least one interim-analysis event count."),
need(all(!is.na(primary_events)), "Every interim-analysis row needs a numeric death count."),
need(!is.na(input$eventOS), "Final-analysis deaths must be numeric."),
need(all(diff(primary_events) >= 0), "Interim-analysis deaths should increase across planned looks."),
need(input$eventOS >= max(primary_events), "Final-analysis deaths must be greater than or equal to the last interim analysis.")
need(length(primary_events) > 0, "Enter at least one interim-analysis expected death count."),
need(all(!is.na(primary_events)), "Every interim-analysis row needs a numeric expected death count."),
need(!is.na(input$eventOS), "Targeted deaths at final OS analysis must be numeric."),
need(all(diff(primary_events) >= 0), "Interim-analysis expected deaths should increase across planned looks."),
need(
input$eventOS >= max(primary_events),
"Targeted deaths at final OS analysis must be greater than or equal to the last interim analysis."
)
)

primary_rows(Map(function(row, value) {
Expand All @@ -136,7 +139,12 @@ app_server <- function(input, output, session) {
)$summary

ci_col <- "Level of 2-sided CI needed to rule out delta null"
alt_col <- "Probability of meeting positivity threshold under delta alt"
summary[[ci_col]] <- paste0(summary[[ci_col]], "%")
names(summary)[names(summary) == ci_col] <-
"Level of 2-sided CI needed to rule out the unacceptable detriment"
names(summary)[names(summary) == alt_col] <-
"Probability of meeting positivity threshold under the plausible beneficial effect"

summary[, setdiff(seq_along(summary), c(6, 7)), drop = FALSE]
})
Expand Down
87 changes: 60 additions & 27 deletions R/ui.R
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -270,20 +270,36 @@ app_ui <- function(request = NULL) {
position: sticky;
top: 0;
z-index: 5;
padding: 0.95rem 1rem 1rem;
border-top-left-radius: 0;
border-top-right-radius: 0;
}

.results-card .section-kicker {
margin-bottom: 0.35rem;
}

.results-card h2 {
margin-bottom: 0.35rem;
font-size: 1.35rem;
}

.results-card .inline-note {
margin-bottom: 0;
font-size: 0.86rem;
line-height: 1.4;
}

.summary-strip {
display: grid;
grid-template-columns: repeat(2, minmax(0, 1fr));
gap: 0.75rem;
margin-top: 0.9rem;
gap: 0.55rem;
margin-top: 0.65rem;
}

.summary-item {
padding: 0.8rem 0.9rem;
border-radius: 14px;
padding: 0.55rem 0.7rem;
border-radius: 12px;
background: rgba(245, 245, 245, 0.95);
border: 1px solid rgba(22, 22, 22, 0.06);
}
Expand All @@ -300,8 +316,8 @@ app_ui <- function(request = NULL) {

.summary-item-value {
color: var(--monitos-fg);
font-size: 0.96rem;
line-height: 1.45;
font-size: 0.9rem;
line-height: 1.35;
font-weight: 600;
}

Expand All @@ -315,8 +331,9 @@ app_ui <- function(request = NULL) {
}

.results-frame {
margin-top: 1rem;
overflow-x: auto;
margin-top: 0.75rem;
max-height: min(38vh, 18rem);
overflow: auto;
border: 1px solid rgba(22, 22, 22, 0.08);
border-radius: 16px;
background: #fff;
Expand All @@ -325,24 +342,27 @@ app_ui <- function(request = NULL) {
.results-card table {
width: 100%;
margin: 0;
font-size: 0.95rem;
font-size: 0.88rem;
}

.results-card thead th {
position: sticky;
top: 0;
z-index: 1;
padding: 0.85rem 0.85rem;
padding: 0.6rem 0.65rem;
border: 0;
background: rgba(245, 245, 245, 0.98);
color: var(--monitos-fg);
font-size: 0.78rem;
font-weight: 700;
line-height: 1.3;
}

.results-card tbody td {
padding: 0.85rem;
padding: 0.6rem 0.65rem;
vertical-align: top;
border-color: rgba(22, 22, 22, 0.08);
line-height: 1.4;
}

.results-card tbody tr:nth-child(odd) td {
Expand Down Expand Up @@ -440,6 +460,10 @@ app_ui <- function(request = NULL) {
.results-card {
position: static;
}

.results-frame {
max-height: none;
}
}
"))
),
Expand Down Expand Up @@ -495,7 +519,7 @@ app_ui <- function(request = NULL) {
h2("Set assumptions, then review the threshold"),
p(
class = "inline-note",
"1. Set effect sizes. 2. Add interim event counts. 3. Review the final-analysis threshold and interim operating characteristics."
"1. Set effect sizes. 2. Add interim expected death counts. 3. Review the final-analysis threshold and interim operating characteristics."
),
p(class = "helper-copy", "HR below 1 indicates benefit.")
),
Expand All @@ -521,7 +545,7 @@ app_ui <- function(request = NULL) {
class = "field-note",
tags$strong("Use for: "),
"choose the OS hazard ratio that would already be too harmful to accept. ",
tags$em("Example: set delta null to 1.33 if any HR at or above 1.33 would be unacceptable.")
tags$em("Example: set this to 1.33 if any HR at or above 1.33 would be unacceptable.")
)
),
div(
Expand All @@ -540,7 +564,7 @@ app_ui <- function(request = NULL) {
class = "field-note",
tags$strong("Use for: "),
"reflect the benefit you could reasonably expect from prior evidence or mechanism of action. ",
tags$em("Example: use 0.90 if a 10% OS hazard reduction would still be clinically meaningful.")
tags$em("Example: use 0.90 if a 10% OS hazard reduction would still be a plausible beneficial effect.")
)
)
)
Expand All @@ -556,24 +580,24 @@ app_ui <- function(request = NULL) {
div(
numericInput(
"eventOS",
"Deaths at final analysis",
"Targeted deaths at final OS analysis",
value = 70,
min = 1
),
p(
class = "helper-copy",
"Use the longest feasible follow-up window for the final analysis."
"Use the longest feasible follow-up window when setting the targeted deaths for the final OS analysis."
)
),
div(
tags$label(
`for` = "primary_events_ui",
"Interim analysis schedule"
"Interim OS analysis schedule"
),
uiOutput("primary_events_ui"),
p(
class = "helper-copy",
"Add one row per planned look, ordered by increasing deaths."
"Add one row per planned look, ordered by increasing expected deaths."
)
)
)
Expand Down Expand Up @@ -601,8 +625,9 @@ app_ui <- function(request = NULL) {
class = "field-note",
tags$strong("Interpretation: "),
paste(
"this controls the final-analysis reassurance threshold when the true OS HR",
"is equal to your unacceptable detriment."
"this controls the final-analysis threshold for positivity.",
"It is the risk of being wrongly reassured when the true OS HR",
"is in fact equal to your unacceptable detriment."
)
)
),
Expand All @@ -611,7 +636,7 @@ app_ui <- function(request = NULL) {
div(
sliderInput(
"power_int",
"Required power at interim analyses under delta alt",
"Required power at interim analyses under the plausible beneficial effect",
min = 0.7,
max = 1,
value = 0.9,
Expand All @@ -620,8 +645,16 @@ app_ui <- function(request = NULL) {
),
div(
class = "field-note",
tags$strong("Typical choice: "),
"0.80 or 0.90, depending on how strict the primary-analysis reassurance should be."
tags$strong("Interpretation: "),
paste(
"this controls the interim analysis threshold for positivity.",
"It is the chance of being correctly reassured when the true OS HR",
"is in fact equal to your plausible beneficial effect."
),
tags$br(),
tags$em(
"Typical choices include 0.80 or 0.90, depending on the possible impact on the program of wrongly flagging a potential detriment at the interim OS analysis."
)
)
)
)
Expand All @@ -647,7 +680,7 @@ app_ui <- function(request = NULL) {
div(
class = "field-note",
tags$strong("When to use: "),
"use this when the drug may still be valuable under a smaller OS benefit than delta alt."
"use this when the drug may still be valuable under a smaller OS benefit than your plausible beneficial effect."
)
),
div(
Expand Down Expand Up @@ -681,9 +714,9 @@ app_ui <- function(request = NULL) {
tags$ul(
class = "list-tight",
tags$li("OS HR threshold for positivity: the observed HR must be at or below this value."),
tags$li("One-sided false positive error rate: the tolerated risk of passing when the true effect equals delta null."),
tags$li("Level of 2-sided CI needed to rule out delta null: the confidence level required to exclude the unacceptable detriment."),
tags$li("Probability of meeting positivity threshold under delta alt: the chance of passing when the treatment effect equals your plausible benefit.")
tags$li("One-sided false positive error rate: the tolerated risk of passing when the true effect equals your unacceptable detriment."),
tags$li("Level of 2-sided CI needed to rule out the unacceptable detriment: the confidence level required to exclude that detriment."),
tags$li("Probability of meeting positivity threshold under the plausible beneficial effect: the chance of passing when the treatment effect equals your plausible beneficial effect.")
)
)
),
Expand Down
2 changes: 1 addition & 1 deletion docs/shinylive-app/app.json
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20 changes: 14 additions & 6 deletions inst/shinylive-app/R/server.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ app_server <- function(input, output, session) {
div(
class = "event-row-head",
div("Planned look"),
div("Deaths"),
div("Expected deaths"),
div()
),
div(
Expand Down Expand Up @@ -113,11 +113,14 @@ app_server <- function(input, output, session) {
primary_events <- get_primary_events(rows)

validate(
need(length(primary_events) > 0, "Enter at least one interim-analysis event count."),
need(all(!is.na(primary_events)), "Every interim-analysis row needs a numeric death count."),
need(!is.na(input$eventOS), "Final-analysis deaths must be numeric."),
need(all(diff(primary_events) >= 0), "Interim-analysis deaths should increase across planned looks."),
need(input$eventOS >= max(primary_events), "Final-analysis deaths must be greater than or equal to the last interim analysis.")
need(length(primary_events) > 0, "Enter at least one interim-analysis expected death count."),
need(all(!is.na(primary_events)), "Every interim-analysis row needs a numeric expected death count."),
need(!is.na(input$eventOS), "Targeted deaths at final OS analysis must be numeric."),
need(all(diff(primary_events) >= 0), "Interim-analysis expected deaths should increase across planned looks."),
need(
input$eventOS >= max(primary_events),
"Targeted deaths at final OS analysis must be greater than or equal to the last interim analysis."
)
)

primary_rows(Map(function(row, value) {
Expand All @@ -136,7 +139,12 @@ app_server <- function(input, output, session) {
)$summary

ci_col <- "Level of 2-sided CI needed to rule out delta null"
alt_col <- "Probability of meeting positivity threshold under delta alt"
summary[[ci_col]] <- paste0(summary[[ci_col]], "%")
names(summary)[names(summary) == ci_col] <-
"Level of 2-sided CI needed to rule out the unacceptable detriment"
names(summary)[names(summary) == alt_col] <-
"Probability of meeting positivity threshold under the plausible beneficial effect"

summary[, setdiff(seq_along(summary), c(6, 7)), drop = FALSE]
})
Expand Down
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