From ccab72aa0f1cae5430f3ceec0388d4c41b4d724f Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Fri, 8 Nov 2024 15:13:33 +0100 Subject: [PATCH] Initial commit --- .Rbuildignore | 6 + .Rprofile | 1 + .gitignore | 7 + DESCRIPTION | 26 + LICENSE.md | 659 +++++++ NAMESPACE | 10 + R/baseline_table.R | 22 + R/helpers.R | 110 ++ R/regression_model.R | 99 + R/regression_table.R | 40 + README.md | 20 + analyses.qmd | 53 + app/functions.R | 282 +++ .../shinyapps.io/agdamsbo/webResearch.dcf | 10 + app/server.R | 116 ++ app/ui.R | 124 ++ data.Rds | Bin 0 -> 1681 bytes man/baseline_table.Rd | 32 + man/file_extension.Rd | 21 + man/getfun.Rd | 20 + man/read_input.Rd | 22 + man/regression_model.Rd | 54 + man/regression_table.Rd | 45 + man/write_quarto.Rd | 31 + publish_shiny.R | 15 + renv.lock | 1730 +++++++++++++++++ renv/.gitignore | 7 + renv/activate.R | 1305 +++++++++++++ toPdfViaTempFile14132-0.html | 1658 ++++++++++++++++ toPdfViaTempFile14132-1.pdf | 0 webResearch.Rproj | 22 + 31 files changed, 6547 insertions(+) create mode 100644 .Rbuildignore create mode 100644 .Rprofile create mode 100644 .gitignore create mode 100644 DESCRIPTION create mode 100644 LICENSE.md create mode 100644 NAMESPACE create mode 100644 R/baseline_table.R create mode 100644 R/helpers.R create mode 100644 R/regression_model.R create mode 100644 R/regression_table.R create mode 100644 README.md create mode 100644 analyses.qmd create mode 100644 app/functions.R create mode 100644 app/rsconnect/shinyapps.io/agdamsbo/webResearch.dcf create mode 100644 app/server.R create mode 100644 app/ui.R create mode 100644 data.Rds create mode 100644 man/baseline_table.Rd create mode 100644 man/file_extension.Rd create mode 100644 man/getfun.Rd create mode 100644 man/read_input.Rd create mode 100644 man/regression_model.Rd create mode 100644 man/regression_table.Rd create mode 100644 man/write_quarto.Rd create mode 100644 publish_shiny.R create mode 100644 renv.lock create mode 100644 renv/.gitignore create mode 100644 renv/activate.R create mode 100644 toPdfViaTempFile14132-0.html create mode 100644 toPdfViaTempFile14132-1.pdf create mode 100644 webResearch.Rproj diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..ce430ed --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,6 @@ +^renv$ +^renv\.lock$ +^webResearch\.Rproj$ +^\.Rproj\.user$ +^LICENSE\.md$ +^dev$ diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 0000000..81b960f --- /dev/null +++ b/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..5fc2453 --- /dev/null +++ b/.gitignore @@ -0,0 +1,7 @@ +.Rproj.user +dev/ +.Rhistory +.Rdata +.httr-oauth +.DS_Store +.quarto diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..869e9fb --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,26 @@ +Package: webResearch +Title: Browser Based Data Analysis +Version: 0.0.0.9000 +Authors@R: + person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"), + comment = c(ORCID = "0000-0002-7559-1154")) +Description: Browser based basic data analysis and research output. +License: AGPL (>= 3) +Encoding: UTF-8 +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.3.2 +Imports: + assertthat, + dplyr, + glue, + gt, + gtsummary, + haven, + here, + openxlsx2, + quarto, + readODS, + readr +Suggests: + MASS, + styler diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..fab6548 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,659 @@ +GNU Affero General Public License +================================= + +_Version 3, 19 November 2007_ +_Copyright (C) 2007 Free Software Foundation, Inc. <>_ + +Everyone is permitted to copy and distribute verbatim copies of this +license document, but changing it is not allowed. + +## Preamble + +The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + +The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Limitation of Liability. + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR +CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES +ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT +NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR +LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM +TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER +PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16. + +If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + +END OF TERMS AND CONDITIONS + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these +terms. + +To do so, attach the following notices to the program. It is safest to +attach them to the start of each source file to most effectively state +the exclusion of warranty; and each file should have at least the +"copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero 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 Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper +mail. + +If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for +the specific requirements. + +You should also get your employer (if you work as a programmer) or +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. For more information on this, and how to apply and follow +the GNU AGPL, see . diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..cb89686 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,10 @@ +# Generated by roxygen2: do not edit by hand + +export(baseline_table) +export(file_extension) +export(getfun) +export(read_input) +export(regression_model) +export(regression_table) +export(write_quarto) +importFrom(stats,as.formula) diff --git a/R/baseline_table.R b/R/baseline_table.R new file mode 100644 index 0000000..28629ba --- /dev/null +++ b/R/baseline_table.R @@ -0,0 +1,22 @@ +#' Print a flexible baseline characteristics table +#' +#' @param data data set +#' @param fun.args list of arguments passed to +#' @param fun function to +#' @param vars character vector of variables to include +#' +#' @return object of standard class for fun +#' @export +#' +#' @examples +#' mtcars |> baseline_table() +#' mtcars |> baseline_table(fun.args = list(by = "gear")) +baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary, vars = NULL) { + if (!is.null(vars)) { + data <- dplyr::select(dplyr::all_of(vars)) + } + + out <- do.call(fun, c(list(data = data), fun.args)) + return(out) +} + diff --git a/R/helpers.R b/R/helpers.R new file mode 100644 index 0000000..cbb7542 --- /dev/null +++ b/R/helpers.R @@ -0,0 +1,110 @@ +#' Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' +#' +#' @description +#' This function follows the idea from this comment: https://stackoverflow.com/questions/38983179/do-call-a-function-in-r-without-loading-the-package +#' @param x function or function name +#' +#' @return function or character vector +#' @export +#' +#' @examples +#' getfun("stats::lm") +getfun <- function(x) { + if("character" %in% class(x)){ + if (length(grep("::", x)) > 0) { + parts <- strsplit(x, "::")[[1]] + requireNamespace(parts[1]) + getExportedValue(parts[1], parts[2]) + } + }else { + x + } +} + +#' Wrapper to save data in RDS, load into specified qmd and render +#' +#' @param data list to pass to qmd +#' @param fileformat output format. Ignored if file!=NULL +#' @param qmd.file qmd file to render. Default is 'here::here("analyses.qmd")' +#' @param file exact filename (Optional) +#' @param ... Ignored for now +#' +#' @return none +#' @export +#' +write_quarto <- function(data,fileformat,qmd.file=here::here("analyses.qmd"),file=NULL,...){ + if (is.null(file)){ + file <- paste0("analyses.",fileformat) + } + temp <- tempfile(fileext = ".Rds") + # write_rds(mtcars, temp) + # read_rds(temp) + web_data <- data + saveRDS(web_data,file=temp) + + quarto::quarto_render(qmd.file, + output_file = file, + execute_params = list(data.file=temp) + ) +} + +#' Helper to import files correctly +#' +#' @param filenames file names +#' +#' @return character vector +#' @export +#' +#' @examples +#' file_extension(list.files(here::here(""))[[2]])[[1]] +#' file_extension(c("file.cd..ks", "file")) +file_extension <- function(filenames) { + sub( + pattern = "^(.*\\.|[^.]+)(?=[^.]*)", replacement = "", + filenames, + perl = TRUE + ) +} + +#' Flexible file import based on extension +#' +#' @param file file name +#' @param consider.na character vector of strings to consider as NAs +#' +#' @return tibble +#' @export +#' +#' @examples +#' read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv") +read_input <- function(file, consider.na = c("NA", '""', "")) { + ext <- file_extension(file) + + if (ext == "csv") { + df <- readr::read_csv(file = file, na = consider.na) + } else if (ext %in% c("xls", "xlsx")) { + df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na) + } else if (ext == "dta") { + df <- haven::read_dta(file = file) + } else if (ext == "ods") { + df <- readODS::read_ods(file = file) + } else { + stop("Input file format has to be on of: + '.csv', '.xls', '.xlsx', '.dta' or '.ods'") + } + + df +} + +#' Convert string of arguments to list of arguments +#' +#' @description +#' Idea from the answer: https://stackoverflow.com/a/62979238 +#' +#' @param string string to convert to list to use with do.call +#' +#' @return list +#' @export +#' +argsstring2list <- function(string){ + eval(parse(text = paste0("list(", string, ")"))) +} diff --git a/R/regression_model.R b/R/regression_model.R new file mode 100644 index 0000000..602f782 --- /dev/null +++ b/R/regression_model.R @@ -0,0 +1,99 @@ +#' Print a flexible baseline characteristics table +#' +#' @param data data set +#' @param fun Name of function as character vector or function to use for model creation. +#' @param vars character vector of variables to include +#' @param outcome.str Name of outcome variable. Character vector. +#' @param auto.mode Make assumptions on function dependent on outcome data format. +#' @param formula.str Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional. +#' @param args.list List of arguments passed to 'fun' with 'do.call'. +#' +#' @importFrom stats as.formula +#' +#' @return object of standard class for fun +#' @export +#' +#' @examples +#' gtsummary::trial |> +#' regression_model(outcome.str = "age") +#' gtsummary::trial |> +#' regression_model( +#' outcome.str = "age", +#' fun = "stats::lm", +#' formula.str = "{outcome.str}~.", +#' args.list = NULL +#' ) +#' gtsummary::trial |> regression_model( +#' outcome.str = "trt", +#' fun = "stats::glm", +#' args.list = list(family = binomial(link = "logit")) +#' ) +regression_model <- function(data, + outcome.str, + auto.mode = TRUE, + formula.str = NULL, + args.list = NULL, + fun = NULL, + vars = NULL) { + if (!is.null(formula.str)) { + formula.str <- glue::glue(formula.str) + } else { + assertthat::assert_that(outcome.str %in% names(data), + msg = "Outcome variable is not present in the provided dataset" + ) + formula.str <- glue::glue("{outcome.str}~.") + + if (!is.null(vars)) { + if (outcome.str %in% vars){ + vars <- vars[vars %in% outcome.str] + } + data <- data |> dplyr::select(dplyr::all_of(c(vars,outcome.str))) + } + } + + # Formatting character variables as factor + # Improvement should add a missing vector to format as NA + data <- data |> dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) + + # browser() + if (auto.mode) { + if (is.numeric(data[[outcome.str]])){ + fun <- "stats::lm" + } else if (is.factor(data[[outcome.str]])){ + if (length(levels(data[[outcome.str]]))==2){ + fun <- "stats::glm" + args.list = list(family = binomial(link = "logit")) + + } else if (length(levels(data[[outcome.str]]))>2){ + fun <- "MASS::polr" + args.list = list( + Hess = TRUE, + method = "logistic" + ) + } else { + stop("The provided output variable only has one level") + } + } else { + stop("Output variable should be either numeric or factor for auto.mode") + } + + } + + assertthat::assert_that("character" %in% class(fun), + msg = "Please provide the function as a character vector." + ) + + out <- do.call( + getfun(fun), + c( + list(data = data), + list(formula = as.formula(formula.str)), + args.list + ) + ) + + # Recreating the call + # out$call <- match.call(definition=eval(parse(text=fun)), call(fun, data = 'data',formula = as.formula(formula.str),args.list)) + + return(out) +} diff --git a/R/regression_table.R b/R/regression_table.R new file mode 100644 index 0000000..c1639fb --- /dev/null +++ b/R/regression_table.R @@ -0,0 +1,40 @@ +#' Create table of regression model +#' +#' @param data regression model +#' @param args.list list of arguments passed to 'fun'. +#' @param fun function to use for table creation. Default is "gtsummary::tbl_regression". +#' +#' @return object of standard class for fun +#' @export +#' +#' @examples +#' gtsummary::trial |> +#' regression_model( +#' outcome.str = "stage", +#' fun = "MASS::polr" +#' ) |> +#' regression_table(args.list = list(exponentiate = TRUE)) +#' gtsummary::trial |> +#' regression_model( +#' outcome.str = "age", +#' fun = "stats::lm", +#' formula.str = "{outcome.str}~.", +#' args.list = NULL +#' ) |> +#' regression_table() +#' gtsummary::trial |> +#' regression_model( +#' outcome.str = "trt", +#' fun = "stats::glm", +#' args.list = list(family = binomial(link = "logit")) +#' ) |> +#' regression_table() +regression_table <- function(data, args.list = NULL, fun = "gtsummary::tbl_regression") { + + if (any(c(length(class(data))!=1, class(data)!="lm"))){ + args.list <- c(args.list,list(exponentiate=TRUE)) + } + + out <- do.call(getfun(fun), c(list(x = data), args.list)) + return(out) +} diff --git a/README.md b/README.md new file mode 100644 index 0000000..05366f4 --- /dev/null +++ b/README.md @@ -0,0 +1,20 @@ +# webResearch + + + + + +This package is the backbone of the open and freely accessible browser-based data analysis tool with project name "webResearch". + +## Road map + +- A minimally working example + + - Table 1 of baseline characteristics + - Table 2 of main analysis results + - Figure 1 of main results (like forest plot) + - Shiny GUI implementation + +- Fundraising for further development + +- Implementation with different focus groups and educational formats. diff --git a/analyses.qmd b/analyses.qmd new file mode 100644 index 0000000..2c0ab49 --- /dev/null +++ b/analyses.qmd @@ -0,0 +1,53 @@ +--- +title: "webResearch analysis results" +date: today +execute: + echo: false +params: + data.file: NA +--- + + + + + + + + + + + + +```{r setup} +web_data <- readRDS(file = params$data.file) +# readr::read_rds(file = here::here("data.Rds")) +library(gtsummary) +library(gt) +``` + +## Introduction + + + +## Methods + + +Analyses were conducted in R version `r paste(version["major"],version["minor"],sep=".")` using the web-based data analysis tool 'webResearcher' version `r packageVersion("webResearch")`. + +## Results + +Below is the baseline characteristics plotted. + +```{r} +web_data$table1 +``` + +Here are the regression results. + +```{r} +web_data$table2 +``` + +## Discussion + +Good luck on your further work! diff --git a/app/functions.R b/app/functions.R new file mode 100644 index 0000000..2541691 --- /dev/null +++ b/app/functions.R @@ -0,0 +1,282 @@ + + +######## +#### Current file: R//baseline_table.R +######## + + + + + + + + + + + + + + +baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary, vars = NULL) { + if (!is.null(vars)) { + data <- dplyr::select(dplyr::all_of(vars)) + } + + out <- do.call(fun, c(list(data = data), fun.args)) + return(out) +} + + + +######## +#### Current file: R//helpers.R +######## + + + + + + + + + + + + +getfun <- function(x) { + if("character" %in% class(x)){ + if (length(grep("::", x)) > 0) { + parts <- strsplit(x, "::")[[1]] + requireNamespace(parts[1]) + getExportedValue(parts[1], parts[2]) + } + }else { + x + } +} + + + + + + + + + + + + +write_quarto <- function(data,fileformat,qmd.file=here::here("analyses.qmd"),file=NULL,...){ + if (is.null(file)){ + file <- paste0("analyses.",fileformat) + } + temp <- tempfile(fileext = ".Rds") + # write_rds(mtcars, temp) + # read_rds(temp) + web_data <- data + saveRDS(web_data,file=temp) + + quarto::quarto_render(qmd.file, + output_file = file, + execute_params = list(data.file=temp) + ) +} + + + + + + + + + + + +file_extension <- function(filenames) { + sub( + pattern = "^(.*\\.|[^.]+)(?=[^.]*)", replacement = "", + filenames, + perl = TRUE + ) +} + + + + + + + + + + + +read_input <- function(file, consider.na = c("NA", '""', "")) { + ext <- file_extension(file) + + if (ext == "csv") { + df <- readr::read_csv(file = file, na = consider.na) + } else if (ext %in% c("xls", "xlsx")) { + df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na) + } else if (ext == "dta") { + df <- haven::read_dta(file = file) + } else if (ext == "ods") { + df <- readODS::read_ods(file = file) + } else { + stop("Input file format has to be on of: + '.csv', '.xls', '.xlsx', '.dta' or '.ods'") + } + + df +} + + + +######## +#### Current file: R//regression_model.R +######## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +regression_model <- function(data, + outcome.str, + auto.mode = TRUE, + formula.str = NULL, + args.list = NULL, + fun = NULL, + vars = NULL) { + if (!is.null(formula.str)) { + formula.str <- glue::glue(formula.str) + } else { + assertthat::assert_that(outcome.str %in% names(data), + msg = "Outcome variable is not present in the provided dataset" + ) + formula.str <- glue::glue("{outcome.str}~.") + + if (!is.null(vars)) { + if (outcome.str %in% vars){ + vars <- vars[vars %in% outcome.str] + } + data <- data |> dplyr::select(dplyr::all_of(c(vars,outcome.str))) + } + } + + # Formatting character variables as factor + # Improvement should add a missing vector to format as NA + data <- data |> dplyr::mutate(dplyr::across(dplyr::where(is.character), as.factor)) + + # browser() + if (auto.mode) { + if (is.numeric(data[[outcome.str]])){ + fun <- "stats::lm" + } else if (is.factor(data[[outcome.str]])){ + if (length(levels(data[[outcome.str]]))==2){ + fun <- "stats::glm" + args.list = list(family = binomial(link = "logit")) + + } else if (length(levels(data[[outcome.str]]))>2){ + fun <- "MASS::polr" + args.list = list( + Hess = TRUE, + method = "logistic" + ) + } else { + stop("The provided output variable only has one level") + } + } else { + stop("Output variable should be either numeric or factor for auto.mode") + } + + } + + assertthat::assert_that("character" %in% class(fun), + msg = "Please provide the function as a character vector." + ) + + out <- do.call( + getfun(fun), + c( + list(data = data), + list(formula = as.formula(formula.str)), + args.list + ) + ) + + # Recreating the call + # out$call <- match.call(definition=eval(parse(text=fun)), call(fun, data = 'data',formula = as.formula(formula.str),args.list)) + + return(out) +} + + +######## +#### Current file: R//regression_table.R +######## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +regression_table <- function(data, args.list = NULL, fun = "gtsummary::tbl_regression") { + + if (any(c(length(class(data))!=1, class(data)!="lm"))){ + args.list <- c(args.list,list(exponentiate=TRUE)) + } + + out <- do.call(getfun(fun), c(list(x = data), args.list)) + return(out) +} diff --git a/app/rsconnect/shinyapps.io/agdamsbo/webResearch.dcf b/app/rsconnect/shinyapps.io/agdamsbo/webResearch.dcf new file mode 100644 index 0000000..0516923 --- /dev/null +++ b/app/rsconnect/shinyapps.io/agdamsbo/webResearch.dcf @@ -0,0 +1,10 @@ +name: webResearch +title: +username: agdamsbo +account: agdamsbo +server: shinyapps.io +hostUrl: https://api.shinyapps.io/v1 +appId: 13276335 +bundleId: 9334284 +url: https://agdamsbo.shinyapps.io/webResearch/ +version: 1 diff --git a/app/server.R b/app/server.R new file mode 100644 index 0000000..2360550 --- /dev/null +++ b/app/server.R @@ -0,0 +1,116 @@ +# project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R")) +source(here::here("app/functions.R")) + +server <- function(input, output, session) { + v <- shiny::reactiveValues( + list = NULL, + ds = NULL + ) + + ds <- shiny::reactive({ + # input$file1 will be NULL initially. After the user selects + # and uploads a file, head of that data file by default, + # or all rows if selected, will be shown. + + shiny::req(input$file) + + v$ds <- "present" + return(read_input(input$file$datapath)) + }) + + output$include_vars <- shiny::renderUI({ + selectizeInput( + inputId = "include_vars", + selected = NULL, + label = "Covariables to include", + choices = colnames(ds()), + multiple = TRUE + ) + }) + + output$outcome_var <- shiny::renderUI({ + selectInput( + inputId = "outcome_var", + selected = NULL, + label = "Select outcome variable", + choices = colnames(ds()), + multiple = FALSE + ) + }) + + output$data.input <- shiny::renderTable({ + shiny::req(input$file) + ds() + }) + + shiny::observeEvent( + { + input$load + }, + { + shiny::req(input$outcome_var) + + v$list <- ds() |> + (\(data){ + # browser() + list( + data = data, + table1 = data |> baseline_table(), + table2 = data |> + regression_model( + outcome.str = input$outcome_var, + auto.mode = input$regression_auto == 1, + formula.str = input$regression_formula, + fun = input$regression_fun, + args.list = eval(parse(text = paste0("list(", input$regression_args, ")"))), + vars = input$include_vars + ) |> + regression_table() + ) + })() + + output$table1 <- gt::render_gt( + v$list$table1 |> + gtsummary::as_gt() + ) + + output$table2 <- gt::render_gt( + v$list$table2 |> + gtsummary::as_gt() + ) + + } + ) + + + output$uploaded <- shiny::reactive({ + if (is.null(v$ds)) { + "no" + } else { + "yes" + } + }) + + shiny::outputOptions(output, "uploaded", suspendWhenHidden = FALSE) + + ##### + #### Generating output + ##### + + # Downloadable csv of selected dataset ---- + # output$downloadData <- shiny::downloadHandler( + # filename = "index_lookup.csv", + # content = function(file) { + # write.csv(v$index, file, row.names = FALSE) + # } + # ) + + output$report <- downloadHandler( + filename = "analyses.html", + content = function(file) { + v$list |> write_quarto(file = file) + } + ) + + # +} diff --git a/app/ui.R b/app/ui.R new file mode 100644 index 0000000..297f685 --- /dev/null +++ b/app/ui.R @@ -0,0 +1,124 @@ +require(shiny) +require(bslib) +# require(ggplot2) +# source("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/R/index_from_raw.R") +# source("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/R/plot_index.R") +# source(here::here("R/index_from_raw.R")) +# source(here::here("R/plot_index.R")) + +# ui <- fluidPage( + +cards <- list( + bslib::card( + max_height = "200px", + full_screen = TRUE, + bslib::card_header("Data overview"), + shiny::uiOutput("data.input") + ), + bslib::card( + # max_height = "200px", + full_screen = TRUE, + bslib::card_header("Baseline characteristics"), + gt::gt_output(outputId = "table1") + ), + bslib::card( + full_screen = TRUE, + bslib::card_header("Multivariable regression table"), + gt::gt_output(outputId = "table2") + ) +) + + +ui <- bslib::page_sidebar( + theme = bslib::bs_theme(bootswatch = "minty"), + title = "webResearcher for easy data analysis", + window_title = "webResearcher", + header = h6("Welcome to the webResearcher tool. This is an early alpha version to act as a proof-of-concept and in no way intended for wider public use."), + + # sidebarPanel( + sidebar = bslib::sidebar( + open = "open", + h4("Upload your dataset"), + + # Input: Select a file ---- + fileInput( + inputId = "file", + label = "Choose data file", + multiple = FALSE, + accept = c( + "text/csv", + "text/comma-separated-values,text/plain", + ".csv", + ".xlsx", + ".xls", + ".dta", + ".ods" + ) + ), + conditionalPanel( + condition = "output.uploaded=='yes'", + h4("Parameter specifications"), + radioButtons( + inputId = "regression_auto", + label = "Automatically choose function", + inline = TRUE, + choiceNames = c( + "Yes", + "No" + ), + choiceValues = c(1, 2) + ), + conditionalPanel( + condition = "input.regression_auto==2", + textInput( + inputId = "regression_formula", + label = "Formula string to render with 'glue::glue'", + value = "{outcome.str}~." + ), + textInput( + inputId = "regression_fun", + label = "Function to use for analysis (needs pasckage and name)", + value = "stats::lm" + ), + textInput( + inputId = "regression_args", + label = "Arguments to pass to the function (provided as a string)", + value = "" + ) + ), + helpText(em("Please specify relevant columns from your data, and press 'Load data'")), + uiOutput("outcome_var"), + radioButtons( + inputId = "all", + label = "Specify covariables", + inline = TRUE, selected = 2, + choiceNames = c( + "Yes", + "No" + ), + choiceValues = c(1, 2) + ), + conditionalPanel( + condition = "input.all==1", + uiOutput("include_vars") + ), + actionButton("load", "Analyse", class = "btn-primary") + ) + # , + + # Horizontal line ---- + # tags$hr(), + # h4("Download results"), + # + # # Button + # downloadButton(outputId="report", + # label= "Download", + # icon = shiny::icon("download")) + ), + layout_columns( + cards[[1]] + ), + layout_columns( + cards[[2]], cards[[3]] + ) +) diff --git a/data.Rds b/data.Rds new file mode 100644 index 0000000000000000000000000000000000000000..6b3ee4e54fab6d0cbcd156a3daeb611f37abf4f5 GIT binary patch literal 1681 zcmV;C25$KuiwFP!000001GQP{Zrer>ULDru+mvgvI*!A?y3$`}^zH7>mdF$-mr2xs9+mOLH4Hw0)i157PD6LCxYOK`uqs z`5)mk*tpolM=7pPH{MiCDRM}&HX7G!#=dUYO`2%kBRs8Ds~bX+NS;9sCOIV!G~3oq z!$Wq$s+qRFLxLfaO>nG3{Ckc8j%AGBKw&Z9DMwyp<(NS&!X`Q9I8q!%Q7lJJsD|$} zM?Xgv*9si-$hpL!ie4bcFvlZk7y-{Hc(OQt25niyh#Ia#TMn8gp(Rf^L@k?yPmG;` z|5<37K`pb0pO$hvbqTJ=g!dWY6)_58=25RWULePdI9Abv9LD3QT}6${sBwkkZ|Gfv z_I2=|hwjh7EA(H0{tc4n9P(V`c)_vC@hkLP^x^&-+*duguMqCb0KcKwkKm4BUj9Um zP0Xp#dkOUkpPL-NVQdQ;H>EieTE0ZyTj=>8KAP`B^H=b{Lv-Fo&U+lcBkn%pzJ`5> z_-_#ZAVAY&_&g$-oHg+mbFZ~^@IHloMtb@jJWp8j-gDNAIR1_`?=^A1GDe;}zaWtq z_y>btj?v0%$ur_dS&$r~K90%#ie*)dUE(fA>u~!>tTRq%(se0K%uo5vb>_+tl_TRm zkty4Jdsnl|dmakiPiE7snIP-)BYS;ll-6Q2>UPRK%nCNAY3ACwYAWdF2};EZ+n%Cal=p{;u`1hpvBp+)`f z@qT%Hz(>(Q#o8$EX{J`@U#cNB4TkK>kdKDsj((t-RyQs2k}>Q@`?F>m?weP*kNCK! 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Passed to 'do.call()'} +\usage{ +getfun(x) +} +\arguments{ +\item{x}{function or function name} +} +\value{ +function or character vector +} +\description{ +This function follows the idea from this comment: https://stackoverflow.com/questions/38983179/do-call-a-function-in-r-without-loading-the-package +} +\examples{ +getfun("stats::lm") +} diff --git a/man/read_input.Rd b/man/read_input.Rd new file mode 100644 index 0000000..020ba8e --- /dev/null +++ b/man/read_input.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/helpers.R +\name{read_input} +\alias{read_input} +\title{Flexible file import based on extension} +\usage{ +read_input(file, consider.na = c("NA", "\\"\\"", "")) +} +\arguments{ +\item{file}{file name} + +\item{consider.na}{character vector of strings to consider as NAs} +} +\value{ +tibble +} +\description{ +Flexible file import based on extension +} +\examples{ +read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv") +} diff --git a/man/regression_model.Rd b/man/regression_model.Rd new file mode 100644 index 0000000..505cedc --- /dev/null +++ b/man/regression_model.Rd @@ -0,0 +1,54 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/regression_model.R +\name{regression_model} +\alias{regression_model} +\title{Print a flexible baseline characteristics table} +\usage{ +regression_model( + data, + outcome.str = "gear", + outcome.factor = TRUE, + formula.str = NULL, + args.list = list(Hess = TRUE, method = "logistic"), + fun = "MASS::polr", + vars = NULL +) +} +\arguments{ +\item{data}{data set} + +\item{outcome.str}{Name of outcome variable. Character vector.} + +\item{outcome.factor}{Factorize outcome variable. Logical.} + +\item{formula.str}{Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional.} + +\item{args.list}{List of arguments passed to 'fun' with 'do.call'.} + +\item{fun}{Name of function as character vector or function to use for model creation.} + +\item{vars}{character vector of variables to include} +} +\value{ +object of standard class for fun +} +\description{ +Print a flexible baseline characteristics table +} +\examples{ +gtsummary::trial |> + regression_model(outcome.str = "stage", fun = "MASS::polr") +gtsummary::trial |> + regression_model( + outcome.str = "age", + outcome.factor = FALSE, + fun = "stats::lm", + formula.str = "{outcome.str}~.", + args.list = NULL + ) +gtsummary::trial |> regression_model( + outcome.str = "trt", + fun = "stats::glm", + args.list = list(family = binomial(link = "logit")) +) +} diff --git a/man/regression_table.Rd b/man/regression_table.Rd new file mode 100644 index 0000000..c7d57f9 --- /dev/null +++ b/man/regression_table.Rd @@ -0,0 +1,45 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/regression_table.R +\name{regression_table} +\alias{regression_table} +\title{Create table of regression model} +\usage{ +regression_table(data, args.list = NULL, fun = "gtsummary::tbl_regression") +} +\arguments{ +\item{data}{regression model} + +\item{args.list}{list of arguments passed to 'fun'.} + +\item{fun}{function to use for table creation. Default is "gtsummary::tbl_regression".} +} +\value{ +object of standard class for fun +} +\description{ +Create table of regression model +} +\examples{ +gtsummary::trial |> + regression_model( + outcome.str = "stage", + fun = "MASS::polr" + ) |> + regression_table(args.list = list(exponentiate = TRUE)) +gtsummary::trial |> + regression_model( + outcome.str = "age", + outcome.factor = FALSE, + fun = "stats::lm", + formula.str = "{outcome.str}~.", + args.list = NULL + ) |> + regression_table() +gtsummary::trial |> + regression_model( + outcome.str = "trt", + fun = "stats::glm", + args.list = list(family = binomial(link = "logit")) + ) |> + regression_table(args.list = list(exponentiate = TRUE)) +} diff --git a/man/write_quarto.Rd b/man/write_quarto.Rd new file mode 100644 index 0000000..7f3e23d --- /dev/null +++ b/man/write_quarto.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/helpers.R +\name{write_quarto} +\alias{write_quarto} +\title{Wrapper to save data in RDS, load into specified qmd and render} +\usage{ +write_quarto( + data, + fileformat, + qmd.file = here::here("analyses.qmd"), + file = NULL, + ... +) +} +\arguments{ +\item{data}{list to pass to qmd} + +\item{fileformat}{output format. Ignored if file!=NULL} + +\item{qmd.file}{qmd file to render. Default is 'here::here("analyses.qmd")'} + +\item{file}{exact filename (Optional)} + +\item{...}{Ignored for now} +} +\value{ +none +} +\description{ +Wrapper to save data in RDS, load into specified qmd and render +} diff --git a/publish_shiny.R b/publish_shiny.R new file mode 100644 index 0000000..9c6c288 --- /dev/null +++ b/publish_shiny.R @@ -0,0 +1,15 @@ +# Prep for shiny +# system2("cat ./R/index_from_raw.R ./R/plot_index.R ./R/read_file.R > ./R/functions.R") + +project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R")) + +# Typical shiny +shiny::runApp(appDir = here::here("app/"), launch.browser = TRUE) + +project.aid::deploy_shiny( + files = c("server.R", "ui.R"), + account.name = "agdamsbo", + name.app = "webResearch", + name.token = "rsconnect_agdamsbo_token", + name.secret = "rsconnect_agdamsbo_secret" +) diff --git a/renv.lock b/renv.lock new file mode 100644 index 0000000..f60e313 --- /dev/null +++ b/renv.lock @@ -0,0 +1,1730 @@ +{ 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"Version": "2.3.10", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" + }, + "zip": { + "Package": "zip", + "Version": "2.3.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 0000000..0ec0cbb --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..0eb5108 --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1305 @@ + +local({ + + # the requested version of renv + version <- "1.0.11" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + # retrieve package database + db <- tryCatch( + as.data.frame( + do.call(utils::available.packages, args), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + token <- renv_bootstrap_github_token() + if (nzchar(Sys.which("curl")) && nzchar(token)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_read_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_read_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_read_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/toPdfViaTempFile14132-0.html b/toPdfViaTempFile14132-0.html new file mode 100644 index 0000000..8185489 --- /dev/null +++ b/toPdfViaTempFile14132-0.html @@ -0,0 +1,1658 @@ + + + + + + + + + + + + +webResearch analysis results + + + + + + + + + +
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webResearch analysis results

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Published
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November 8, 2024

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Introduction

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Methods

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Analyses were conducted in R version 4.4.1 using the web-based data analysis tool ‘webResearcher’ version 0.0.0.9000.

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Results

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Below is the baseline characteristics plotted.

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CharacteristicN = 2001
Chemotherapy Treatment
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    Drug A98 (49%)
    Drug B102 (51%)
Age47 (38, 57)
    Unknown11
Marker Level (ng/mL)0.64 (0.22, 1.41)
    Unknown10
T Stage
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    T153 (27%)
    T254 (27%)
    T343 (22%)
    T450 (25%)
Grade
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    I68 (34%)
    II68 (34%)
    III64 (32%)
Tumor Response61 (32%)
    Unknown7
Patient Died112 (56%)
Months to Death/Censor22.4 (15.9, 24.0)
1 n (%); Median (Q1, Q3)
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Here are the regression results.

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+ + + ++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
CharacteristicBeta95% CI1p-value
trt
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    Drug A——
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    Drug B-0.41-4.9, 4.10.9
Marker Level (ng/mL)-0.14-2.8, 2.5>0.9
T Stage
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    T1——
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    T22.1-4.0, 8.10.5
    T32.4-4.2, 9.10.5
    T4-3.2-9.7, 3.40.3
Grade
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    I——
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    II0.18-5.5, 5.8>0.9
    III1.7-3.7, 7.10.5
Tumor Response5.00.00, 100.050
Patient Died3.1-3.7, 9.90.4
Months to Death/Censor-0.14-0.79, 0.510.7
1 CI = Confidence Interval
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Discussion

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Good luck on your further work!

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+ + + + diff --git a/toPdfViaTempFile14132-1.pdf b/toPdfViaTempFile14132-1.pdf new file mode 100644 index 0000000..e69de29 diff --git a/webResearch.Rproj b/webResearch.Rproj new file mode 100644 index 0000000..69fafd4 --- /dev/null +++ b/webResearch.Rproj @@ -0,0 +1,22 @@ +Version: 1.0 + +RestoreWorkspace: No +SaveWorkspace: No +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes +LineEndingConversion: Posix + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace