diff --git a/articles/metalite-table1.html b/articles/metalite-table1.html index 26eeb8a..6ae3c90 100644 --- a/articles/metalite-table1.html +++ b/articles/metalite-table1.html @@ -129,11 +129,11 @@

Example data = df, # source data id = "USUBJID" # unique subject id ) -
-
-
-
-

The interactive features are illustrated in the GIF below.

+
+
+
+
+

The interactive features are illustrated in the GIF below.

In comparison with the table1 R package, we are able to answer ad-hoc questions from clinicians with interactive features such @@ -186,9 +186,9 @@

Section Title= "USUBJID", type = "Participants" ) -
-
- +
+
+

Total Column @@ -200,9 +200,9 @@

Total Column= "USUBJID", total = FALSE )

-
-
- +
+
+

Download Data @@ -216,9 +216,9 @@

Download Data= "USUBJID", download = "listing" )

-
-
- +
+
+

Rmarkdown Render @@ -255,24 +255,24 @@

Rmarkdown Render

Table 1

-
+
-
+
- +

Table 2

-
+
-
+
- +
diff --git a/pkgdown.yml b/pkgdown.yml index b1d990f..3bec49c 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,5 +4,5 @@ pkgdown_sha: ~ articles: metalite-table1-cran: metalite-table1-cran.html metalite-table1: metalite-table1.html -last_built: 2023-11-15T04:43Z +last_built: 2023-11-15T04:57Z diff --git a/reference/metalite_table1.html b/reference/metalite_table1.html index 8da255a..e5c445f 100644 --- a/reference/metalite_table1.html +++ b/reference/metalite_table1.html @@ -60,6 +60,7 @@

Usage id, var_listing = NULL, total = TRUE, + header = NULL, download = "none", type = NULL, ... @@ -88,6 +89,11 @@

Arguments +
header
+

a logical vector with length 1 or same length of the variables in formula to show the Number of xxx row of each variable. +Default is to show the row for the first variable.

+ +
download

a character value to enable download button. Allowed values include "none", "listing", "table", and 'all'.

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This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"/articles/metalite-table1.html","id":"motivation","dir":"Articles","previous_headings":"","what":"Motivation","title":"Overview","text":"table descriptive statistics widely used medical research typically first table (.e. table1) manuscript. R packages examples create table1: table1 use case clinical trials, Chapter 4 R clinical study reports submission contains details. metalite.table1 provide interactive table1 enhance communication statisticians clinicians.","code":""},{"path":"/articles/metalite-table1.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Overview","text":"use subject level dataset r2rtf::r2rtf_adsl create example interactive table1. First, modify dataset adding missing values. order group variables. keep relevent variables. interactive table1 can created metalite_table1 function. interactive features illustrated GIF . comparison table1 R package, able answer ad-hoc questions clinicians interactive features subjects missing value. outliers. ’s distribution variable treatment group. common questions ongoing clinical trials.","code":"# Prepare analysis ready data df <- r2rtf_adsl df$AGE[1:3] <- NA # Create missing value for illustration purpose. df$ARM <- factor( df$ARM, c(\"Placebo\", \"Xanomeline Low Dose\", \"Xanomeline High Dose\"), c(\"Placebo\", \"Low Dose\", \"High Dose\") ) df <- df[, c(\"USUBJID\", \"ARM\", \"AGE\", \"SEX\", \"RACE\", \"BMIBLGR1\")] head(df) #> USUBJID ARM AGE SEX RACE BMIBLGR1 #> 1 01-701-1015 Placebo NA F WHITE 25-<30 #> 2 01-701-1023 Placebo NA M WHITE >=30 #> 3 01-701-1028 High Dose NA M WHITE >=30 #> 4 01-701-1033 Low Dose 74 M WHITE 25-<30 #> 5 01-701-1034 High Dose 77 F WHITE 25-<30 #> 6 01-701-1047 Placebo 85 F WHITE >=30 metalite_table1( ~ AGE + SEX + RACE + BMIBLGR1 | ARM, # formula data = df, # source data id = \"USUBJID\" # unique subject id )"},{"path":[]},{"path":"/articles/metalite-table1.html","id":"section-title","dir":"Articles","previous_headings":"Features","what":"Section Title","title":"Overview","text":"section title defined column labels. metalite::get_labels allows quickly check label. metalite::assign_labels can modify labels type argument can modify term first row, example, “Number Participants”.","code":"metalite::get_label(df) #> USUBJID ARM #> \"Unique Subject Identifier\" \"ARM\" #> AGE SEX #> \"Age\" \"Sex\" #> RACE BMIBLGR1 #> \"Race\" \"Pooled Baseline BMI Group 1\" df <- metalite::assign_label( df, var = c(\"AGE\", \"BMIBLGR1\"), label = c(\"Age (Year)\", \"BMI Group (kg/m2)\") ) metalite::get_label(df) #> USUBJID ARM #> \"Unique Subject Identifier\" \"ARM\" #> AGE SEX #> \"Age (Year)\" \"Sex\" #> RACE BMIBLGR1 #> \"Race\" \"BMI Group (kg/m2)\" metalite_table1(~ AGE + SEX | ARM, data = df, id = \"USUBJID\", type = \"Participants\" )"},{"path":"/articles/metalite-table1.html","id":"total-column","dir":"Articles","previous_headings":"Features","what":"Total Column","title":"Overview","text":"Total column can hided.","code":"metalite_table1(~ AGE + SEX | ARM, data = df, id = \"USUBJID\", total = FALSE )"},{"path":"/articles/metalite-table1.html","id":"download-data","dir":"Articles","previous_headings":"Features","what":"Download Data","title":"Overview","text":"can allow user download raw data, example can set download=\"listing\" enable user download drill listing.","code":"metalite_table1(~ AGE + SEX | ARM, data = df, id = \"USUBJID\", download = \"listing\" )"},{"path":"/articles/metalite-table1.html","id":"rmarkdown-render","dir":"Articles","previous_headings":"Features","what":"Rmarkdown Render","title":"Overview","text":"Sometimes want create multiple tables loop, need clearly call metalite_table1_to_html function output text raw content using resutls=\"asis\" (e.g., {r, results=\"asis\"}) Rmarkdown code chunk. Create dummy reactable object outside loop necessary include required javascript library. full Rmarkdown example .","code":"```{r} library(metalite.table1) ``` ```{r, include = FALSE} reactable::reactable(data.frame(x = 1)) ``` ```{r, results=\"asis\"} type <- c(\"Subjects\", \"Records\") for (i in 1:2) { cat(\"### Table \", i, \"\\n\") tbl <- metalite_table1(~ AGE + SEX | ARM, data = r2rtf::r2rtf_adsl, id = \"USUBJID\", type = type[i] ) metalite_table1_to_html(tbl) } ```"},{"path":[]},{"path":[]},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Yilong Zhang. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhang Y (2023). metalite.table1: Interactive Table Descriptive Statistics HTML. R package version 0.1.0.","code":"@Manual{, title = {metalite.table1: Interactive Table of Descriptive Statistics in HTML}, author = {Yilong Zhang}, year = {2023}, note = {R package version 0.1.0}, }"},{"path":[]},{"path":"/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Interactive Table of Descriptive Statistics in HTML","text":"table descriptive statistics widely used medical research typically first table (.e. table1) manuscript. R packages examples create table1: table1 use case clinical trials, Chapter 4 R clinical study reports submission contains details. metalite.table1 provide interactive table1 enhance communication statisticians clinicians. Example:","code":"library(metalite.table1) metalite_table1(~ AGE + SEX + RACE + BMIBLGR1 | ARM, data = r2rtf::r2rtf_adsl, id = \"USUBJID\")"},{"path":"/index.html","id":"highlighted-features","dir":"","previous_headings":"","what":"Highlighted features","title":"Interactive Table of Descriptive Statistics in HTML","text":"Drill listings Embedded histogram","code":""},{"path":"/reference/metalite.table1-package.html","id":null,"dir":"Reference","previous_headings":"","what":"metalite.table1: Interactive Table of Descriptive Statistics in HTML — metalite.table1-package","title":"metalite.table1: Interactive Table of Descriptive Statistics in HTML — metalite.table1-package","text":"Create interactive table descriptive statistics HTML. table typically used exploratory analysis clinical study (referred 'Table 1').","code":""},{"path":"/reference/metalite.table1-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"metalite.table1: Interactive Table of Descriptive Statistics in HTML — metalite.table1-package","text":"Maintainer: Yilong Zhang elong0527@gmail.com","code":""},{"path":"/reference/metalite_table1.html","id":null,"dir":"Reference","previous_headings":"","what":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","title":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","text":"Interactive Table Descriptive Statistics HTML","code":""},{"path":"/reference/metalite_table1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","text":"","code":"metalite_table1( formula, data, id, var_listing = NULL, total = TRUE, download = \"none\", type = NULL, ... )"},{"path":"/reference/metalite_table1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","text":"formula object class \"formula\". data data frame contain variables described formula. id character value indicate subject/record id variable name data. var_listing character vector additional variables included drill listing. total logical value display hide \"Total\" column. download character value enable download button. Allowed values include \"none\", \"listing\", \"table\", ''. type character value control section title (e.g. \"Subjects\", \"Records\"). ... additional arguments passed reactable. details refer https://glin.github.io/reactable/reference/reactable.html","code":""},{"path":"/reference/metalite_table1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","text":"shiny.tag.list object contain reactable HTML widget interactive table describptive statistics.","code":""},{"path":"/reference/metalite_table1.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","text":"","code":"if (interactive()) { metalite_table1(~ AGE + SEX | TRT01A, data = r2rtf::r2rtf_adsl, id = \"SUBJID\") }"},{"path":"/reference/metalite_table1_to_html.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert to html — metalite_table1_to_html","title":"Convert to html — metalite_table1_to_html","text":"Convert html","code":""},{"path":"/reference/metalite_table1_to_html.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert to html — metalite_table1_to_html","text":"","code":"metalite_table1_to_html(x)"},{"path":"/reference/metalite_table1_to_html.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert to html — metalite_table1_to_html","text":"x output metalite_table1.","code":""},{"path":"/reference/metalite_table1_to_html.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert to html — metalite_table1_to_html","text":"HTML string reactable HTML widget interactive table describptive statistics.","code":""},{"path":"/news/index.html","id":"metalitetable1-010","dir":"Changelog","previous_headings":"","what":"metalite.table1 0.1.0","title":"metalite.table1 0.1.0","text":"CRAN release: 2023-10-27 Initial CRAN submission.","code":""}] +[{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"/articles/metalite-table1.html","id":"motivation","dir":"Articles","previous_headings":"","what":"Motivation","title":"Overview","text":"table descriptive statistics widely used medical research typically first table (.e. table1) manuscript. R packages examples create table1: table1 use case clinical trials, Chapter 4 R clinical study reports submission contains details. metalite.table1 provide interactive table1 enhance communication statisticians clinicians.","code":""},{"path":"/articles/metalite-table1.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Overview","text":"use subject level dataset r2rtf::r2rtf_adsl create example interactive table1. First, modify dataset adding missing values. order group variables. keep relevent variables. interactive table1 can created metalite_table1 function. interactive features illustrated GIF . comparison table1 R package, able answer ad-hoc questions clinicians interactive features subjects missing value. outliers. ’s distribution variable treatment group. common questions ongoing clinical trials.","code":"# Prepare analysis ready data df <- r2rtf_adsl df$AGE[1:3] <- NA # Create missing value for illustration purpose. df$ARM <- factor( df$ARM, c(\"Placebo\", \"Xanomeline Low Dose\", \"Xanomeline High Dose\"), c(\"Placebo\", \"Low Dose\", \"High Dose\") ) df <- df[, c(\"USUBJID\", \"ARM\", \"AGE\", \"SEX\", \"RACE\", \"BMIBLGR1\")] head(df) #> USUBJID ARM AGE SEX RACE BMIBLGR1 #> 1 01-701-1015 Placebo NA F WHITE 25-<30 #> 2 01-701-1023 Placebo NA M WHITE >=30 #> 3 01-701-1028 High Dose NA M WHITE >=30 #> 4 01-701-1033 Low Dose 74 M WHITE 25-<30 #> 5 01-701-1034 High Dose 77 F WHITE 25-<30 #> 6 01-701-1047 Placebo 85 F WHITE >=30 metalite_table1( ~ AGE + SEX + RACE + BMIBLGR1 | ARM, # formula data = df, # source data id = \"USUBJID\" # unique subject id )"},{"path":[]},{"path":"/articles/metalite-table1.html","id":"section-title","dir":"Articles","previous_headings":"Features","what":"Section Title","title":"Overview","text":"section title defined column labels. metalite::get_labels allows quickly check label. metalite::assign_labels can modify labels type argument can modify term first row, example, “Number Participants”.","code":"metalite::get_label(df) #> USUBJID ARM #> \"Unique Subject Identifier\" \"ARM\" #> AGE SEX #> \"Age\" \"Sex\" #> RACE BMIBLGR1 #> \"Race\" \"Pooled Baseline BMI Group 1\" df <- metalite::assign_label( df, var = c(\"AGE\", \"BMIBLGR1\"), label = c(\"Age (Year)\", \"BMI Group (kg/m2)\") ) metalite::get_label(df) #> USUBJID ARM #> \"Unique Subject Identifier\" \"ARM\" #> AGE SEX #> \"Age (Year)\" \"Sex\" #> RACE BMIBLGR1 #> \"Race\" \"BMI Group (kg/m2)\" metalite_table1(~ AGE + SEX | ARM, data = df, id = \"USUBJID\", type = \"Participants\" )"},{"path":"/articles/metalite-table1.html","id":"total-column","dir":"Articles","previous_headings":"Features","what":"Total Column","title":"Overview","text":"Total column can hided.","code":"metalite_table1(~ AGE + SEX | ARM, data = df, id = \"USUBJID\", total = FALSE )"},{"path":"/articles/metalite-table1.html","id":"download-data","dir":"Articles","previous_headings":"Features","what":"Download Data","title":"Overview","text":"can allow user download raw data, example can set download=\"listing\" enable user download drill listing.","code":"metalite_table1(~ AGE + SEX | ARM, data = df, id = \"USUBJID\", download = \"listing\" )"},{"path":"/articles/metalite-table1.html","id":"rmarkdown-render","dir":"Articles","previous_headings":"Features","what":"Rmarkdown Render","title":"Overview","text":"Sometimes want create multiple tables loop, need clearly call metalite_table1_to_html function output text raw content using resutls=\"asis\" (e.g., {r, results=\"asis\"}) Rmarkdown code chunk. Create dummy reactable object outside loop necessary include required javascript library. full Rmarkdown example .","code":"```{r} library(metalite.table1) ``` ```{r, include = FALSE} reactable::reactable(data.frame(x = 1)) ``` ```{r, results=\"asis\"} type <- c(\"Subjects\", \"Records\") for (i in 1:2) { cat(\"### Table \", i, \"\\n\") tbl <- metalite_table1(~ AGE + SEX | ARM, data = r2rtf::r2rtf_adsl, id = \"USUBJID\", type = type[i] ) metalite_table1_to_html(tbl) } ```"},{"path":[]},{"path":[]},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Yilong Zhang. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhang Y (2023). metalite.table1: Interactive Table Descriptive Statistics HTML. R package version 0.1.0.","code":"@Manual{, title = {metalite.table1: Interactive Table of Descriptive Statistics in HTML}, author = {Yilong Zhang}, year = {2023}, note = {R package version 0.1.0}, }"},{"path":[]},{"path":"/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Interactive Table of Descriptive Statistics in HTML","text":"table descriptive statistics widely used medical research typically first table (.e. table1) manuscript. R packages examples create table1: table1 use case clinical trials, Chapter 4 R clinical study reports submission contains details. metalite.table1 provide interactive table1 enhance communication statisticians clinicians. Example:","code":"library(metalite.table1) metalite_table1(~ AGE + SEX + RACE + BMIBLGR1 | ARM, data = r2rtf::r2rtf_adsl, id = \"USUBJID\")"},{"path":"/index.html","id":"highlighted-features","dir":"","previous_headings":"","what":"Highlighted features","title":"Interactive Table of Descriptive Statistics in HTML","text":"Drill listings Embedded histogram","code":""},{"path":"/reference/metalite.table1-package.html","id":null,"dir":"Reference","previous_headings":"","what":"metalite.table1: Interactive Table of Descriptive Statistics in HTML — metalite.table1-package","title":"metalite.table1: Interactive Table of Descriptive Statistics in HTML — metalite.table1-package","text":"Create interactive table descriptive statistics HTML. table typically used exploratory analysis clinical study (referred 'Table 1').","code":""},{"path":"/reference/metalite.table1-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"metalite.table1: Interactive Table of Descriptive Statistics in HTML — metalite.table1-package","text":"Maintainer: Yilong Zhang elong0527@gmail.com","code":""},{"path":"/reference/metalite_table1.html","id":null,"dir":"Reference","previous_headings":"","what":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","title":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","text":"Interactive Table Descriptive Statistics HTML","code":""},{"path":"/reference/metalite_table1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","text":"","code":"metalite_table1( formula, data, id, var_listing = NULL, total = TRUE, header = NULL, download = \"none\", type = NULL, ... )"},{"path":"/reference/metalite_table1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","text":"formula object class \"formula\". data data frame contain variables described formula. id character value indicate subject/record id variable name data. var_listing character vector additional variables included drill listing. total logical value display hide \"Total\" column. header logical vector length 1 length variables formula show Number xxx row variable. Default show row first variable. download character value enable download button. Allowed values include \"none\", \"listing\", \"table\", ''. type character value control section title (e.g. \"Subjects\", \"Records\"). ... additional arguments passed reactable. details refer https://glin.github.io/reactable/reference/reactable.html","code":""},{"path":"/reference/metalite_table1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","text":"shiny.tag.list object contain reactable HTML widget interactive table describptive statistics.","code":""},{"path":"/reference/metalite_table1.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Interactive Table of Descriptive Statistics in HTML — metalite_table1","text":"","code":"if (interactive()) { metalite_table1(~ AGE + SEX | TRT01A, data = r2rtf::r2rtf_adsl, id = \"SUBJID\") }"},{"path":"/reference/metalite_table1_to_html.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert to html — metalite_table1_to_html","title":"Convert to html — metalite_table1_to_html","text":"Convert html","code":""},{"path":"/reference/metalite_table1_to_html.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert to html — metalite_table1_to_html","text":"","code":"metalite_table1_to_html(x)"},{"path":"/reference/metalite_table1_to_html.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert to html — metalite_table1_to_html","text":"x output metalite_table1.","code":""},{"path":"/reference/metalite_table1_to_html.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert to html — metalite_table1_to_html","text":"HTML string reactable HTML widget interactive table describptive statistics.","code":""},{"path":"/news/index.html","id":"metalitetable1-010","dir":"Changelog","previous_headings":"","what":"metalite.table1 0.1.0","title":"metalite.table1 0.1.0","text":"CRAN release: 2023-10-27 Initial CRAN submission.","code":""}]