Using jamovi for the Common Statistical Analysis in Pathology

Source: vignettes/pathology_jamovi.Rmd

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

Pearson correlation statistic

Normality test

McNemar test