In sbalci/histopathR: Template and R Codes Used in Histopathologic Research

Codes for explaining the software and the packages that are used in the analysis^[See childRmd/_23footer.Rmd file for other codes]

Save Final Data {.appendix}

projectName <- list.files(path = here::here(), pattern = "Rproj")
projectName <- gsub(pattern = ".Rproj", replacement = "", x = projectName)

analysisDate <- as.character(Sys.Date())

imageName <- paste0(projectName, analysisDate, ".RData")

save.image(file = here::here("data", imageName))

rdsName <- paste0(projectName, analysisDate, ".rds")

readr::write_rds(x = mydata, path = here::here("data", rdsName))

saveRDS(object = mydata, file = here::here("data", rdsName))

excelName <- paste0(projectName, analysisDate, ".xlsx")

writexl::write_xlsx(mydata, here::here("data", excelName))

print(glue::glue(
    "saved data after analysis to ",
    rownames(file.info(here::here("data", excelName))),
    " : ",
    as.character(
        file.info(here::here("data", excelName))$ctime
    )
    )
)

# pacman::p_load(here, lubridate, glue)
# here::here("data", glue("{today()}_trends.csv"))

---

\pagebreak

Final Data Summary {.appendix}

# use summarytools to generate final data summary
# summarytools::view(summarytools::dfSummary(x = mydata
#                                            , style = "markdown"))

# mydata %>% select(
#     -c(
#         rapor_yil,
#         rapor_no,
#         protokol_no,
#         istek_tarihi,
#         nux_yada_met_varsa_tarihi,
#         son_hastane_vizit_tarihi,
#         Outcome
#     )
# ) -> finalSummary
# 
# summarytools::view(summarytools::dfSummary(x = finalSummary
#                                            , style = "markdown"))

---

\pagebreak

Software and Libraries Used {.appendix}

citation()

The jamovi project (2019). jamovi. (Version 0.9) [Computer Software]. Retrieved from https://www.jamovi.org.
R Core Team (2018). R: A Language and envionment for statistical computing. [Computer software]. Retrieved from https://cran.r-project.org/.
Fox, J., & Weisberg, S. (2018). car: Companion to Applied Regression. [R package]. Retrieved from https://cran.r-project.org/package=car.

report::cite_packages(session = sessionInfo())

report::show_packages(session = sessionInfo()) %>% 
    kableExtra::kable()

# citation("tidyverse")
citation("readxl")
citation("janitor")
citation("report")
citation("finalfit")
citation("ggstatsplot")

knitr::write_bib(x = c(.packages(), "knitr", "shiny"),
                 file = here::here("bib", "packages.bib")
)

---

\pagebreak

Session Info {.appendix}

sessionInfo()

\pagebreak

---

Loaded packages {.appendix}

pacman::p_loaded(all = TRUE)

---

\pagebreak

Notes {.appendix}

Last update on r as.character(Sys.time())

Serdar Balci, MD, Pathologist
[e-mail]
https://rpubs.com/sbalci/CV

---

\pagebreak

Code Appendix

Use following chunk options to include all codes below the report.

r{echo=TRUE, eval=FALSE, ref.label=knitr::all_labels()}

sbalci/histopathR documentation built on Nov. 12, 2024, 12:28 p.m.