vignettes/pathology_jamovi.Rmd
---
title: "Using jamovi for the Common Statistical Analysis in Pathology"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Using jamovi for the Common Statistical Analysis in Pathology}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
```{r setup}
# library(ClinicoPath)
```
In this page I am going to collect the most common statistical methods used in pathology research and how can one do them in jamovi.
- Recommendations for reporting histopathology studies: a proposal
Virchows Arch (2015) 466:611–615 DOI 10.1007/s00428-015-1762-3
- Statistical Literacy Among Academic Pathologists: A Survey Study to Gauge Knowledge of Frequently Used Statistical Tests Among Trainees and Faculty.
Arch Pathol Lab Med. 2017 Feb;141(2):279-287. doi: 10.5858/arpa.2016-0200-OA
https://www.ncbi.nlm.nih.gov/pubmed/27959584
https://www.archivesofpathology.org/doi/pdf/10.5858/arpa.2016-0200-OA
- Pathologists should probably forget about kappa. Percent agreement, diagnostic specificity and related metrics provide more clinically applicable measures of interobserver variability
Annals of Diagnostic Pathology, Volume 47, August 2020
https://www.sciencedirect.com/science/article/abs/pii/S1092913420301040
# Student t test
# Regression/ANOVA
# Chi-square test
# Mann-Whitney test (rank sum)
# Fisher exact test
# Survival analysis
## Kaplan-Meier/log-rank
## Cox regression
# Multiple comparison adjustment
## Tukey
## Bonferroni
## Newman-Keuls
# Kappa Statistic
# ROC analysis
# Logistic regression
# Spearman rank correlation
# Kruskal-Wallis test
<iframe width="560" height="315" src="https://www.youtube.com/embed/qfs6T311_88" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
# Pearson correlation statistic
# Normality test
# McNemar test