Dar lint5

StudentNotebooks/Assignment07_DraftFinalProjectNotebook/lint5-Assignment07-f24.Rmd

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+---
+title: "CTBenchEval App Final Project Report Draft"
+author: "Tianyan"
+date: "`r Sys.Date()`"
+output:
+  pdf_document:
+    toc: yes
+    toc_depth: '3'
+  html_notebook: default
+  html_document:
+    toc: yes
+    toc_depth: 3
+    toc_float: yes
+    number_sections: yes
+    theme: united
+---
+
+# DAR Project and Group Members
+
+* Project name: CTBenchEval
+* Project team members: Xiheng Liu, Yashas Balaji, Ziyi Bao, Corey Curran, Mingyang Li, Corey Curran,  Soumeek Mishra, Samuel Park, Victor Zhao
+
+
+# 0.0 Preliminaries.
+
+This report is generated from an R Markdown file that includes all the R code necessary to produce the results described and embedded in the report.  
+
+```{R, echo=F}
+# Set to TRUE to expand R code blocks; set to FALSE to collapse R code blocks 
+# Code blocks can be surpressed from output for readability using the command code `{R,  echo=show}` in the code block header. 
+show <- FALSE
+```
+
+Executing this R notebook requires some subset of the following packages:
+
+* `ggplot2`
+* `devtools`
+* `conflicted`
+* `rmarkdown`
+* `knitr`
+* `tidyverse`
+* `stringr`
+* `ggbiplot`
+* `pheatmap`
+* `plotrix`
+* `kableExtra` 
+* `coin`
+* `png`
+* `grid`
+
+These will be installed and loaded as necessary (code suppressed). 
+
+
+```{r setup, include=FALSE}
+
+# Required R package installation; RUN THIS BLOCK BEFORE ATTEMPTING TO KNIT THIS NOTEBOOK!!!
+# This section  install packages if they are not already installed. 
+# This block will not be shown in the knit file.
+knitr::opts_chunk$set(echo = TRUE)
+
+# Set the default CRAN repository
+local({r <- getOption("repos")
+       r["CRAN"] <- "http://cran.r-project.org" 
+       options(repos=r)
+})
+
+if (!require("devtools")) {
+  install.packages("devtools")
+  library(devtools)
+}
+# For package conflict resolution (esp. dplyr functions)
+# run con
+if (!require("conflicted")) {
+  devtools::install_github("r-lib/conflicted")
+  library(conflicted)
+}
+
+# Required packages for CTEval analysis
+if (!require("rmarkdown")) {
+  install.packages("rmarkdown")
+  library(rmarkdown)
+}
+
+if (!require("knitr")) {
+  install.packages("knitr")
+  library(knitr)
+}
+if (!require("tidyverse")) {
+  install.packages("tidyverse")
+  library(tidyverse)
+}
+# Our preferences
+conflicts_prefer(dplyr::summarize())
+conflicts_prefer(dplyr::filter())
+conflicts_prefer(dplyr::select())
+conflicts_prefer(dplyr::mutate())
+conflicts_prefer(dplyr::arrange())
+
+if (!require("stringr")) {
+  install.packages("stringr")
+  library(stringr)
+}
+
+if (!require("ggbiplot")) {
+  install.packages("ggbiplot")
+  library(ggbiplot)
+}
+
+if (!require("pheatmap")) {
+  install.packages("pheatmap")
+  library(pheatmap)
+}
+if (!require("plotrix")) {
+  install.packages("plotrix")
+  library(plotrix)
+}
+if (!require("kableExtra")) {
+  install.packages("kableExtra")
+  library(kableExtra)
+} 
+
+if (!require("coin")) {
+  install.packages("coin")
+  library(coin)
+}
+
+if (!require("png")) {
+  install.packages("png")
+  library(png)
+}
+
+if (!require("grid")) {
+  install.packages("grid")
+  library(grid)
+}
+```
+
+# 1.0 Project Introduction
+
+CTBench is a benchmark to assess large language models (LLMs) in aiding clinical study design.
+
+The CTBenchEval project is to further evaluate and improve the CTBench benchmark. CTBenchEval App is one of the approach.
+
+# 2.0 Organization of Report
+
+This report is organize as follows: 
+
+* Section 3.0: User guide of CTBenchEval App
+
+* Section 4.0 Page 1: 'Step 1: Specify Trial'
+
+* Section 5.0 Page 2: 'Step 2: Generate Descriptors' 
+
+* Section 6.0 Page 3: 'Step 3: Evaluate'
+
+# 3.0 User guide of CTBenchEval App
+
+Begin by pressing "Continue to the app" to assess main webpage.
+
+```{R, echo=F}
+# Code
+img <- readPNG("../../StudentNotebooks/FinalProjectNotebook/CTBS_Userguide/lint5_CTBS_01.png")
+grid.raster(img)
+grid.text("LLM output", x = 0.5, y = 0.95, gp = gpar(fontsize = 20))
+```
+
+## 3.1 Data, Code, and Resources
+
+## 3.2 Contribution
+
+## 3.3 Methods Description 
+
+## 3.4 Result and Discussion 
+
+## 3.5 Conclusions, Limitations,  and Future Work.
+
+# 4.0 Page 1: 'Step 1: Specify Trial'
+
+# 5.0 Page 2: 'Step 2: Generate Descriptors' 
+
+# 6.0 Page 3: 'Step 3: Evaluate'
+
+
+
+```{R, echo=F}
+# Code to read in data if appropriate.
+
+```
+
+
+# Bibliography
+Provide a listing of references and other sources.
+
+# Appendix
+