MNG01
Mean Plot
Output
This option is not supported.
Code
library(dplyr)
library(tern)
library(nestcolor)
adsl <- random.cdisc.data::cadsl
adlb <- random.cdisc.data::cadlb
advs <- random.cdisc.data::cadvs
adsl_f <- adsl %>%
filter(SAFFL == "Y") %>%
df_explicit_na()
adlb_f <- adlb %>%
mutate(AVISIT = forcats::fct_reorder(AVISIT, AVISITN, min)) %>%
dplyr::filter(
SAFFL == "Y",
ANL01FL == "Y",
ONTRTFL == "Y",
PARAMCD == "ALT",
AVISIT != "SCREENING"
) %>%
droplevels() %>%
df_explicit_na()
advs_f <- advs %>%
mutate(AVISIT = forcats::fct_reorder(AVISIT, AVISITN, min)) %>%
dplyr::filter(
SAFFL == "Y",
ONTRTFL == "Y",
PARAMCD == "DIABP",
AVISIT != "SCREENING"
) %>%
droplevels() %>%
df_explicit_na()
teal
App
Code
library(teal.modules.clinical)
## Data reproducible code
data <- teal_data()
data <- within(data, {
library(dplyr)
library(forcats)
ADSL <- random.cdisc.data::cadsl
ADLB <- random.cdisc.data::cadlb %>%
mutate(AVISIT = fct_reorder(AVISIT, AVISITN, min))
})
datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
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]
## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]
## Setup App
app <- init(
data = data,
modules = modules(
tm_g_lineplot(
label = "LINE PLOT",
dataname = "ADLB",
strata = choices_selected(
variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
"ARM"
),
y = choices_selected(
variable_choices(ADLB, c("AVAL", "BASE", "CHG", "PCHG")),
"AVAL"
),
param = choices_selected(
value_choices(ADLB, "PARAMCD", "PARAM"),
"ALT"
)
)
)
)
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, {
library(dplyr)
library(forcats)
ADSL <- random.cdisc.data::cadsl
ADLB <- random.cdisc.data::cadlb %>%
mutate(AVISIT = fct_reorder(AVISIT, AVISITN, min))
})
datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]
## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]
## Setup App
app <- init(
data = data,
modules = modules(
tm_g_lineplot(
label = "LINE PLOT",
dataname = "ADLB",
strata = choices_selected(
variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
"ARM"
),
y = choices_selected(
variable_choices(ADLB, c("AVAL", "BASE", "CHG", "PCHG")),
"AVAL"
),
param = choices_selected(
value_choices(ADLB, "PARAMCD", "PARAM"),
"ALT"
)
)
)
)
shinyApp(app$ui, app$server)
Reproducibility
Timestamp
[1] "2024-11-21 14:58:59 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 2024-11-21
pandoc 3.4 @ /usr/bin/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
backports 1.5.0 2024-05-23 [1] RSPM
brio 1.1.5 2024-04-24 [1] RSPM
broom 1.0.7 2024-09-26 [1] RSPM
bslib 0.8.0 2024-07-29 [1] RSPM
cachem 1.1.0 2024-05-16 [1] RSPM
callr 3.7.6 2024-03-25 [1] RSPM
checkmate 2.3.2 2024-07-29 [1] RSPM
chromote 0.3.1 2024-08-30 [1] RSPM
cli 3.6.3 2024-06-21 [1] RSPM
coda 0.19-4.1 2024-01-31 [1] CRAN (R 4.4.1)
codetools 0.2-20 2024-03-31 [2] CRAN (R 4.4.1)
colorspace 2.1-1 2024-07-26 [1] RSPM
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evaluate 1.0.1 2024-10-10 [1] RSPM
fansi 1.0.6 2023-12-08 [1] RSPM
farver 2.1.2 2024-05-13 [1] RSPM
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fontawesome 0.5.3 2024-11-16 [1] RSPM
forcats * 1.0.0 2023-01-29 [1] RSPM
formatR 1.14 2023-01-17 [1] CRAN (R 4.4.1)
formatters * 0.5.9.9003 2024-11-21 [1] https://p~
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generics 0.1.3 2022-07-05 [1] RSPM
ggplot2 3.5.1 2024-04-23 [1] RSPM
glue 1.8.0 2024-09-30 [1] RSPM
gtable 0.3.6 2024-10-25 [1] RSPM
htmltools 0.5.8.1 2024-04-04 [1] RSPM
htmlwidgets 1.6.4 2023-12-06 [1] RSPM
httpuv 1.6.15 2024-03-26 [1] RSPM
jquerylib 0.1.4 2021-04-26 [1] RSPM
jsonlite 1.8.9 2024-09-20 [1] RSPM
knitr 1.49 2024-11-08 [1] RSPM
labeling 0.4.3 2023-08-29 [1] RSPM
later 1.3.2 2023-12-06 [1] RSPM
lattice 0.22-6 2024-03-20 [2] CRAN (R 4.4.1)
lifecycle 1.0.4 2023-11-07 [1] RSPM
logger 0.4.0 2024-10-22 [1] RSPM
magrittr * 2.0.3 2022-03-30 [1] RSPM
MASS 7.3-61 2024-06-13 [2] CRAN (R 4.4.1)
Matrix 1.7-1 2024-10-18 [1] RSPM
memoise 2.0.1 2021-11-26 [1] RSPM
mime 0.12 2021-09-28 [1] RSPM
multcomp 1.4-26 2024-07-18 [1] CRAN (R 4.4.1)
munsell 0.5.1 2024-04-01 [1] RSPM
mvtnorm 1.3-2 2024-11-04 [1] RSPM
nestcolor * 0.1.2.9017 2024-11-21 [1] https://p~
nlme 3.1-166 2024-08-14 [2] CRAN (R 4.4.1)
pillar 1.9.0 2023-03-22 [1] RSPM
pkgcache 2.2.3 2024-09-12 [1] RSPM
pkgconfig 2.0.3 2019-09-22 [1] RSPM
processx 3.8.4 2024-03-16 [1] RSPM
promises 1.3.0 2024-04-05 [1] RSPM
ps 1.8.1 2024-10-28 [1] RSPM
purrr 1.0.2 2023-08-10 [1] RSPM
R6 2.5.1 2021-08-19 [1] RSPM
ragg 1.3.3 2024-09-11 [1] RSPM
random.cdisc.data 0.3.16.9001 2024-11-21 [1] https://p~
rbibutils 2.3 2024-10-04 [1] RSPM
Rcpp 1.0.13-1 2024-11-02 [1] RSPM
Rdpack 2.6.2 2024-11-15 [1] RSPM
rlang 1.1.4 2024-06-04 [1] RSPM
rmarkdown 2.29 2024-11-04 [1] RSPM
rtables * 0.6.10.9005 2024-11-21 [1] https://p~
sandwich 3.1-1 2024-09-15 [1] CRAN (R 4.4.1)
sass 0.4.9 2024-03-15 [1] RSPM
scales 1.3.0 2023-11-28 [1] RSPM
sessioninfo 1.2.2 2021-12-06 [1] any (@1.2.2)
shiny * 1.9.1 2024-08-01 [1] RSPM
shinycssloaders 1.1.0 2024-07-30 [1] RSPM
shinyjs 2.1.0 2021-12-23 [1] RSPM
shinyvalidate 0.1.3 2023-10-04 [1] RSPM
shinyWidgets 0.8.7 2024-09-23 [1] RSPM
stringi 1.8.4 2024-05-06 [1] RSPM
stringr 1.5.1 2023-11-14 [1] RSPM
survival 3.7-0 2024-06-05 [2] CRAN (R 4.4.1)
systemfonts 1.1.0 2024-05-15 [1] RSPM
teal * 0.15.2.9089 2024-11-21 [1] https://p~
teal.code * 0.5.0.9018 2024-11-21 [1] https://p~
teal.data * 0.6.0.9021 2024-11-21 [1] https://p~
teal.logger 0.3.0.9002 2024-11-21 [1] https://p~
teal.modules.clinical * 0.9.1.9031 2024-11-21 [1] https://p~
teal.reporter 0.3.1.9016 2024-11-21 [1] https://p~
teal.slice * 0.5.1.9016 2024-11-21 [1] https://p~
teal.transform * 0.5.0.9016 2024-11-21 [1] https://p~
teal.widgets 0.4.2.9022 2024-11-21 [1] https://p~
tern * 0.9.6.9016 2024-11-21 [1] https://p~
tern.gee 0.1.5.9004 2024-11-21 [1] https://p~
testthat 3.2.1.1 2024-04-14 [1] RSPM
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tidyselect 1.2.1 2024-03-11 [1] RSPM
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webshot2 0.1.1 2023-08-11 [1] RSPM
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withr 3.0.2 2024-10-28 [1] RSPM
xfun 0.49 2024-10-31 [1] RSPM
xtable 1.8-4 2019-04-21 [1] RSPM
yaml 2.3.10 2024-07-26 [1] RSPM
zoo 1.8-12 2023-04-13 [1] CRAN (R 4.4.1)
[1] /usr/local/lib/R/site-library
[2] /usr/local/lib/R/library
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