KMG01
Kaplan-Meier Plot
Output
Code
variables$strata <- c("STRATA1", "STRATA2")
plot <- g_km(
df = anl,
variables = variables,
control_surv = control_surv_timepoint(conf_level = 0.8),
xlab = "Time (Days)",
ylim = c(0, 1),
annot_coxph = TRUE,
control_coxph_pw = control_coxph(
pval_method = "wald",
ties = "breslow",
conf_level = 0.8
)
)
plot
teal
App
Code
Warning: `datanames<-()` was deprecated in teal.data 0.6.1.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
`teal_data`. See ?names.teal_data
Code
join_keys(data) <- default_cdisc_join_keys[datanames]
arm_ref_comp <- list(
ACTARMCD = list(
ref = "ARM B",
comp = c("ARM A", "ARM C")
),
ARM = list(
ref = "B: Placebo",
comp = c("A: Drug X", "C: Combination")
)
)
## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]
ADTTE <- data[["ADTTE"]]
## Setup App
app <- init(
data = data,
modules = modules(
tm_g_km(
label = "KM PLOT",
plot_height = c(600, 100, 2000),
dataname = "ADTTE",
arm_var = choices_selected(
variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
"ARM"
),
paramcd = choices_selected(
value_choices(ADTTE, "PARAMCD", "PARAM"),
"OS"
),
arm_ref_comp = arm_ref_comp,
strata_var = choices_selected(
variable_choices(ADSL, c("SEX", "BMRKR2")),
"SEX"
),
facet_var = choices_selected(
variable_choices(ADSL, c("SEX", "BMRKR2")),
NULL
)
)
)
)
shinyApp(app$ui, app$server)
Experimental use!
shinylive
allow you to modify to run shiny
application entirely in the web browser. Modify the code below and click re-run the app to see the results. The performance is slighly worse and some of the features (e.g. downloading) might not work at all.
#| '!! shinylive warning !!': |
#| shinylive does not work in self-contained HTML documents.
#| Please set `embed-resources: false` in your metadata.
#| standalone: true
#| viewerHeight: 800
#| editorHeight: 200
#| components: [viewer, editor]
#| layout: vertical
# -- WEBR HELPERS --
options(webr_pkg_repos = c("r-universe" = "https://pharmaverse.r-universe.dev", getOption("webr_pkg_repos")))
# -- APP CODE --
library(teal.modules.clinical)
## Data reproducible code
data <- teal_data()
data <- within(data, {
ADSL <- random.cdisc.data::cadsl
ADTTE <- random.cdisc.data::cadtte
})
datanames <- c("ADSL", "ADTTE")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]
arm_ref_comp <- list(
ACTARMCD = list(
ref = "ARM B",
comp = c("ARM A", "ARM C")
),
ARM = list(
ref = "B: Placebo",
comp = c("A: Drug X", "C: Combination")
)
)
## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]
ADTTE <- data[["ADTTE"]]
## Setup App
app <- init(
data = data,
modules = modules(
tm_g_km(
label = "KM PLOT",
plot_height = c(600, 100, 2000),
dataname = "ADTTE",
arm_var = choices_selected(
variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
"ARM"
),
paramcd = choices_selected(
value_choices(ADTTE, "PARAMCD", "PARAM"),
"OS"
),
arm_ref_comp = arm_ref_comp,
strata_var = choices_selected(
variable_choices(ADSL, c("SEX", "BMRKR2")),
"SEX"
),
facet_var = choices_selected(
variable_choices(ADSL, c("SEX", "BMRKR2")),
NULL
)
)
)
)
shinyApp(app$ui, app$server)
Reproducibility
Timestamp
[1] "2024-11-20 17:39:22 UTC"
Session Info
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.4.1 (2024-06-14)
os Ubuntu 22.04.5 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2024-11-20
pandoc 3.4 @ /usr/bin/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
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Matrix 1.7-1 2024-10-18 [1] RSPM
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[2] /usr/local/lib/R/library
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