Report.Rmd

---
title: "Histopathology Research Template"
description: |
  Codes Used in Histopathology Research  
  Data Report for Histopathology Research  
  Example Using Random Generated Fakedata
author: 
  - name: Serdar Balci, MD, Pathologist
    url: https://sbalci.github.io/histopathology-template/
    affiliation: serdarbalci.com
    affiliation_url: https://www.serdarbalci.com/
date: "`r Sys.Date()`"
mail: drserdarbalci@gmail.com
linkedin: "serdar-balci-md-pathologist"
twitter: "serdarbalci"
github: "sbalci"
home: "https://www.serdarbalci.com/"
header-includes:
- \usepackage{pdflscape}
- \newcommand{\blandscape}{\begin{landscape}}
- \newcommand{\elandscape}{\end{landscape}}
- \usepackage{xcolor}
- \usepackage{afterpage}
- \renewcommand{\linethickness}{0.05em}
- \usepackage{booktabs}
- \usepackage{sectsty} \allsectionsfont{\nohang\centering \emph}
- \usepackage{float}
- \usepackage{svg}
always_allow_html: yes
output:
  html_document: 
    toc: yes
    toc_float: yes
    number_sections: yes
    fig_caption: yes
    keep_md: yes
    highlight: kate
    theme: readable
    code_folding: "hide"
    includes:
      after_body: _footer.html
    css: css/style.css
  prettydoc::html_pretty:
    theme: leonids
    highlight: vignette
    toc: true
    number_sections: yes
    css: css/style.css
    includes:
      after_body: _footer.html
  rmarkdown::html_vignette: 
    css: 
    - !expr system.file("rmarkdown/templates/html_vignette/resources/vignette.css", package = "rmarkdown")
  redoc::redoc:
    highlight_outputs: TRUE
    margins: 1 
    line_numbers: FALSE 
  distill::distill_article:
    toc: true
  pdf_document: 
    fig_caption: yes
    highlight: kate
    number_sections: yes
    toc: yes
    latex_engine: lualatex
    toc_depth: 5
    keep_tex: yes
    includes:
      in_header: highlight_echo.tex    
vignette: >
  %\VignetteIndexEntry{Histopathology Research Template}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
bibliography: bib/template.bib
---

```{r pacman, message=FALSE, warning=FALSE, include=FALSE}
# installing necessary packages
if (requireNamespace("magrittr", quietly = TRUE)) {
  `%>%` <- magrittr::`%>%`
}
if (!require("remotes")) install.packages("remotes")
if (!require("pacman")) install.packages("pacman")
if (!require("pak")) install.packages("pak")
if (!require("here")) install.packages("here")
```


<style type="text/css">

h1{
  text-align: center;
}
h2{
  text-align: center;
}
h3{
  text-align: center;
}
h4{
  text-align: center;
}
h4.date{
  text-align: center;
}

</style>

<!-- Open all links in new tab-->  
<base target="_blank"/>  


```{r run all Rmd without knit, eval=FALSE, include=FALSE}
source_rmd <- function(rmd_file){
  knitr::knit(rmd_file, output = tempfile(), envir = globalenv())
}

list_of_Rmd <- list.files(path = here::here("childRmd"), pattern = "Rmd")

list_of_Rmd <- list_of_Rmd[!list_of_Rmd %in% c("_19shinySurvival.Rmd")]

purrr::map(.x = here::here("childRmd", list_of_Rmd), .f = source_rmd)

```



---

$[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3635430.svg)](https://doi.org/10.5281/zenodo.3635430)$

https://doi.org/10.5281/zenodo.3635430

https://osf.io/3tjfk/

[Histopathology Research Template 🔬](https://sbalci.github.io/histopathology-template/)


---



# Introduction

- **State the marker of interest, the study objectives, and hypotheses [@Knijn2015]**.^[From Table 1: Proposed items for reporting histopathology studies. Recommendations for reporting histopathology studies: a proposal Virchows Arch (2015) 466:611–615 DOI 10.1007/s00428-015-1762-3 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460276/]

 


# Materials & Methods

**Describe Materials and Methods as highlighted in [@Knijn2015]**.^[From Table 1: Proposed items for reporting histopathology studies. Recommendations for reporting histopathology studies: a proposal Virchows Arch (2015) 466:611–615 DOI 10.1007/s00428-015-1762-3 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460276/]

- Describe patient characteristics, and inclusion and exclusion criteria

- Describe treatment details

- Describe the type of material used

- Specify how expression of the biomarker was assessed

- Describe the number of independent (blinded) scorers and how they scored

- State the method of case selection, study design, origin of the cases, and time frame

- Describe the end of the follow-up period and median follow-up time

- Define all clinical endpoints examined

- Specify all applied statistical methods

- Describe how interactions with other clinical/pathological factors were analyzed

---

## Statistical Methods






----


## Header Codes


```{r header, child = here::here('childRmd', '_01header.Rmd')}
```


---


## Generate Fake Data


```{r generate fake data, child = here::here('childRmd', '_02fakeData.Rmd')}
```


---


## Import Data


```{r importData, child = here::here('childRmd', '_03importData.Rmd')}
```


---

## Study Population


```{r brief summary, child = here::here('childRmd', '_04briefSummary.Rmd')}
```


---

## Ethics and IRB

```{r ethics, child = here::here('childRmd', '_05ethics.Rmd')}
```


---


## Define Variable Types


```{r variable types, child = here::here('childRmd', '_06variableTypes.Rmd')}
```



---


## Overview the Data


```{r overview, child = here::here('childRmd', '_07overView.Rmd')}
```




---

# Statistical Analysis

**Learn these tests as highlighted in [@Schmidt2017].**^[Statistical Literacy Among Academic Pathologists: A Survey Study to Gauge Knowledge of Frequently Used Statistical Tests Among Trainees and Faculty. Archives of Pathology & Laboratory Medicine: February 2017, Vol. 141, No. 2, pp. 279-287. https://doi.org/10.5858/arpa.2016-0200-OA]


---

# Results

**Write results as described in [@Knijn2015]**^[From Table 1: Proposed items for reporting histopathology studies. Recommendations for reporting histopathology studies: a proposal Virchows Arch (2015) 466:611–615 DOI 10.1007/s00428-015-1762-3 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460276/]



- Describe the number of patients included in the analysis and reason for dropout

- Report patient/disease characteristics (including the biomarker of interest) with the number of missing values

- Describe the interaction of the biomarker of interest with established prognostic variables

- Include at least 90 % of initial cases included in univariate and multivariate analyses

- Report the estimated effect (relative risk/odds ratio, confidence interval, and p value) in univariate analysis

- Report the estimated effect (hazard rate/odds ratio, confidence interval, and p value) in multivariate analysis

- Report the estimated effects (hazard ratio/odds ratio, confidence interval, and p value) of other prognostic factors included in multivariate analysis



---


## Data Dictionary

```{r data dictionary, child = here::here('childRmd', '_08dataDictionary.Rmd')}
```

---


## Clean and Recode Data

```{r clean and recode, child = here::here('childRmd', '_09cleanRecode.Rmd')}
```

---

## Impute Missing Data

```{r impute, child = here::here('childRmd', '_10impute.Rmd')}
```

---

\pagebreak


## Descriptive Statistics


```{r descriptives, child = here::here('childRmd', '_11descriptives.Rmd')}
```


---

\newpage
\blandscape

```{r crossTables, child = here::here('childRmd', '_12crossTables.Rmd')}
```

\elandscape


```{r plots, child = here::here('childRmd', '_13plots.Rmd')}
```




```{r pairedTests, child = here::here('childRmd', '_14pairedTests.Rmd')}
```



```{r hypothesisTests, child = here::here('childRmd', '_15hypothesisTests.Rmd')}
```

\newpage
\blandscape



```{r ROC, child = here::here('childRmd', '_16ROC.Rmd')}
```


```{r Decision Tree, child = here::here('childRmd', '_17decisionTree.Rmd')}
```



## Survival Analysis


```{r survival, child = here::here('childRmd', '_18survival.Rmd')}
```


---

# Interactive Survival Analysis

```{r shiny survival, child = here::here('childRmd', '_19shinySurvival.Rmd')}
```


---

\elandscape


# Correlation


```{r correlation, child = here::here('childRmd', '_20correlation.Rmd')}
```


# Models


```{r models, child = here::here('childRmd', '_21models.Rmd')}
```


---

\pagebreak



```{r comments, child = here::here('childRmd', '_22comments.Rmd')}
```

---

\pagebreak


# Discussion

- Interpret the results in context of the working hypothesis elaborated in the introduction and other relevant studies; include a discussion of limitations of the study.

- Discuss potential clinical applications and implications for future research

\pagebreak


# Footer

```{r footer, child = here::here('childRmd', '_23footer.Rmd')}
```

---

\pagebreak


**push all changes to GitHub repository**

```{r git update}
source(file = here::here("R", "force_git.R"))
```


---


# References