diff --git a/404.html b/404.html index 1ea9fdd..0ac6d55 100644 --- a/404.html +++ b/404.html @@ -24,7 +24,7 @@ metalite.table1 - 0.3.0 + 0.2.0 diff --git a/LICENSE.html b/LICENSE.html index 9be868c..d155b46 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -10,7 +10,7 @@ metalite.table1 - 0.3.0 + 0.2.0 diff --git a/articles/index.html b/articles/index.html index 4adc457..2ad042e 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ metalite.table1 - 0.3.0 + 0.2.0 diff --git a/articles/metalite-table1-cran.html b/articles/metalite-table1-cran.html index 651bfb2..3ed86f7 100644 --- a/articles/metalite-table1-cran.html +++ b/articles/metalite-table1-cran.html @@ -26,7 +26,7 @@ metalite.table1 - 0.3.0 + 0.2.0 diff --git a/articles/metalite-table1.html b/articles/metalite-table1.html index 1b59e16..e5a541c 100644 --- a/articles/metalite-table1.html +++ b/articles/metalite-table1.html @@ -26,7 +26,7 @@ metalite.table1 - 0.3.0 + 0.2.0 @@ -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", record_name = "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 @@ -255,41 +255,26 @@ Rmarkdown Render Table 1 - + - + - + Table 2 - + - + - + - -RTF file - -User can also export a static table to an RTF file by using the -metalite_table1_to_rtf function. - -metalite_table1( - ~ AGE + SEX + RACE + BMIBLGR1 | ARM, - data = df, - id = "USUBJID" -) |> - metalite_table1_to_rtf("tmp1.rtf") -#> [1] "tmp1.rtf" - - diff --git a/authors.html b/authors.html index ae26dce..716d1c8 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ metalite.table1 - 0.3.0 + 0.2.0 @@ -61,13 +61,13 @@ Citation Zhang Y (2023). metalite.table1: Interactive Table of Descriptive Statistics in HTML. -R package version 0.3.0. +R package version 0.2.0. @Manual{, title = {metalite.table1: Interactive Table of Descriptive Statistics in HTML}, author = {Yilong Zhang}, year = {2023}, - note = {R package version 0.3.0}, + note = {R package version 0.2.0}, } -Installation - -You can install the package via CRAN: - -install.packages("metalite.table1") -Or, install from GitHub: - -remotes::install_github("elong0527/metalite.table1") - - Highlighted features -Drill down listings +Drill down into listings Embedded histogram @@ -139,7 +129,6 @@ Dev status - diff --git a/news/index.html b/news/index.html index 05835d3..dcd493d 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ metalite.table1 - 0.3.0 + 0.2.0 diff --git a/pkgdown.yml b/pkgdown.yml index 0270bcd..0dfdd8e 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: 2023-12-03T21:02Z +last_built: 2023-12-03T21:13Z diff --git a/reference/index.html b/reference/index.html index a6c6e59..2e9daa5 100644 --- a/reference/index.html +++ b/reference/index.html @@ -10,7 +10,7 @@ metalite.table1 - 0.3.0 + 0.2.0 @@ -67,16 +67,6 @@ All functionsmetalite_table1_to_html() Convert to html - - - metalite_table1_to_rtf() - - Convert metalite_table1 to an RTF file - - - reactable_to_df() - - Convert reactable to a data frame diff --git a/reference/metalite.table1-package.html b/reference/metalite.table1-package.html index 15cc9c9..470efe7 100644 --- a/reference/metalite.table1-package.html +++ b/reference/metalite.table1-package.html @@ -10,7 +10,7 @@ metalite.table1 - 0.3.0 + 0.2.0 diff --git a/reference/metalite_table1.html b/reference/metalite_table1.html index d2b912d..5fcf2eb 100644 --- a/reference/metalite_table1.html +++ b/reference/metalite_table1.html @@ -10,7 +10,7 @@ metalite.table1 - 0.3.0 + 0.2.0 diff --git a/reference/metalite_table1_to_html.html b/reference/metalite_table1_to_html.html index c3f3b17..15bab07 100644 --- a/reference/metalite_table1_to_html.html +++ b/reference/metalite_table1_to_html.html @@ -10,7 +10,7 @@ metalite.table1 - 0.3.0 + 0.2.0 diff --git a/search.json b/search.json index 93053ab..ad89e15 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"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. 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GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. 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 record_name 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\", record_name = \"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":"/articles/metalite-table1.html","id":"rtf-file","dir":"Articles","previous_headings":"Features","what":"RTF file","title":"Overview","text":"User can also export static table RTF file using metalite_table1_to_rtf function.","code":"metalite_table1( ~ AGE + SEX + RACE + BMIBLGR1 | ARM, data = df, id = \"USUBJID\" ) |> metalite_table1_to_rtf(\"tmp1.rtf\") #> [1] \"tmp1.rtf\""},{"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 0.3.0.","code":"@Manual{, title = {metalite.table1: Interactive Table of Descriptive Statistics in HTML}, author = {Yilong Zhang}, year = {2023}, note = {R package version 0.3.0}, }"},{"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. metalite.table1 provide interactive table1 enhance communication statisticians clinicians. use case clinical trials, Chapter 4 R clinical study reports submission contains details. R packages create table1: table1 Example:","code":"library(metalite.table1) metalite_table1(~ AGE + SEX + RACE + BMIBLGR1 | ARM, data = r2rtf::r2rtf_adsl, id = \"USUBJID\")"},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Interactive Table of Descriptive Statistics in HTML","text":"can install package via CRAN: , install GitHub:","code":"install.packages(\"metalite.table1\") remotes::install_github(\"elong0527/metalite.table1\")"},{"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\", record_name = 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\", ''. record_name 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":"/reference/metalite_table1_to_rtf.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert metalite_table1 to an RTF file — metalite_table1_to_rtf","title":"Convert metalite_table1 to an RTF file — metalite_table1_to_rtf","text":"Convert metalite_table1 RTF file","code":""},{"path":"/reference/metalite_table1_to_rtf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert metalite_table1 to an RTF file — metalite_table1_to_rtf","text":"","code":"metalite_table1_to_rtf( x, file, title = \"Baseline Characteristics\", col_rel_width = NULL )"},{"path":"/reference/metalite_table1_to_rtf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert metalite_table1 to an RTF file — metalite_table1_to_rtf","text":"x Output metalite_table1. file character string naming file save rtf file. title Title character string. col_rel_width Column relative width vector e.g. c(2,1,1) refers 2:1:1. Default NULL equal column width.","code":""},{"path":"/reference/metalite_table1_to_rtf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert metalite_table1 to an RTF file — metalite_table1_to_rtf","text":"string RTF file path","code":""},{"path":"/reference/reactable_to_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert reactable to a data frame — reactable_to_df","title":"Convert reactable to a data frame — reactable_to_df","text":"Convert reactable data frame","code":""},{"path":"/reference/reactable_to_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert reactable to a data frame — reactable_to_df","text":"","code":"reactable_to_df(x)"},{"path":"/reference/reactable_to_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert reactable to a data frame — reactable_to_df","text":"x reactable HTML widget","code":""},{"path":"/reference/reactable_to_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert reactable to a data frame — reactable_to_df","text":"data frame","code":""},{"path":"/news/index.html","id":"metalitetable1-020","dir":"Changelog","previous_headings":"","what":"metalite.table1 0.2.0","title":"metalite.table1 0.2.0","text":"CRAN release: 2023-11-17 metalite_table1: add ... header argument (#10, #11), rename type record_name. allow user specify first column width (#9). error message formula one group.","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. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. 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 record_name 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\", record_name = \"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 0.2.0.","code":"@Manual{, title = {metalite.table1: Interactive Table of Descriptive Statistics in HTML}, author = {Yilong Zhang}, year = {2023}, note = {R package version 0.2.0}, }"},{"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\", record_name = 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\", ''. record_name 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":"metalitetable1-020","dir":"Changelog","previous_headings":"","what":"metalite.table1 0.2.0","title":"metalite.table1 0.2.0","text":"CRAN release: 2023-11-17 metalite_table1: add ... header argument (#10, #11), rename type record_name. allow user specify first column width (#9). error message formula one group.","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":""}] diff --git a/sitemap.xml b/sitemap.xml index ed7483f..300b3ee 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -36,10 +36,4 @@ /reference/metalite_table1_to_html.html - - /reference/metalite_table1_to_rtf.html - - - /reference/reactable_to_df.html -
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 @@
table1
User can also export a static table to an RTF file by using the -metalite_table1_to_rtf function.
metalite_table1_to_rtf
-metalite_table1( - ~ AGE + SEX + RACE + BMIBLGR1 | ARM, - data = df, - id = "USUBJID" -) |> - metalite_table1_to_rtf("tmp1.rtf") -#> [1] "tmp1.rtf"
metalite_table1( - ~ AGE + SEX + RACE + BMIBLGR1 | ARM, - data = df, - id = "USUBJID" -) |> - metalite_table1_to_rtf("tmp1.rtf") -#> [1] "tmp1.rtf"
Zhang Y (2023). metalite.table1: Interactive Table of Descriptive Statistics in HTML. -R package version 0.3.0. +R package version 0.2.0.
@Manual{, title = {metalite.table1: Interactive Table of Descriptive Statistics in HTML}, author = {Yilong Zhang}, year = {2023}, - note = {R package version 0.3.0}, + note = {R package version 0.2.0}, }
You can install the package via CRAN:
-install.packages("metalite.table1")
install.packages("metalite.table1")
Or, install from GitHub:
-remotes::install_github("elong0527/metalite.table1")
remotes::install_github("elong0527/metalite.table1")
metalite_table1_to_rtf()
metalite_table1
reactable_to_df()