In sbalci/histopathology-template: Template of R Codes Used in Histopathology Research.

# 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")

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)

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$$

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

https://osf.io/3tjfk/

Histopathology Research Template 🔬

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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

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Statistical Methods

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Header Codes

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Generate Fake Data

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Import Data

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Study Population

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Ethics and IRB

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Define Variable Types

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Overview the Data

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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]

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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

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Data Dictionary

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Clean and Recode Data

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Impute Missing Data

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Descriptive Statistics

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Survival Analysis

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Interactive Survival Analysis

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Correlation

Models

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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

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Footer

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push all changes to GitHub repository

source(file = here::here("R", "force_git.R"))

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References

sbalci/histopathology-template documentation built on June 29, 2023, 5:52 a.m.