update 28 Jan

.Rprofile

@@ -1,4 +1,4 @@
-source("renv/activate.R")
+# source("renv/activate.R")
 
 .First <- function(){
 cat("\nWelcome to histopathology template project", date(), "\n")

DESCRIPTION

@@ -56,6 +56,5 @@ Suggests:
     janitor,
     bayestestR    
 Remotes:
-    easystats/report,
-
+    easystats/report
 VignetteBuilder: knitr

R/gc_fake_data.R

@@ -52,14 +52,14 @@ fakedata <-
     level(
       x = 1:3,
       prob = c("0.1", "0.4", "0.5"),
-      name = "Anti-X-intensity"
+      name = "AntiX_intensity"
     ),
 
 
     level(
       x = 1:3,
       prob = c("0.3", "0.4", "0.3"),
-      name = "Anti-Y-intensity"
+      name = "AntiY_intensity"
     ),
 
 

README.Rmd

@@ -24,10 +24,20 @@ knitr::opts_chunk$set(
 📸📺🎛🔭🔬💊🔐🍫🌸
 
 
+---
+
 
 https://sbalci.github.io/histopathology-template/
 
 
+---
+
+
+
+<style>.bmc-button img{width: 35px !important;margin-bottom: 1px !important;box-shadow: none !important;border: none !important;vertical-align: middle !important;}.bmc-button{padding: 7px 10px 7px 10px !important;line-height: 35px !important;height:51px !important;min-width:217px !important;text-decoration: none !important;display:inline-flex !important;color:#ffffff !important;background-color:#5F7FFF !important;border-radius: 5px !important;border: 1px solid transparent !important;padding: 7px 10px 7px 10px !important;font-size: 28px !important;letter-spacing:0.6px !important;box-shadow: 0px 1px 2px rgba(190, 190, 190, 0.5) !important;-webkit-box-shadow: 0px 1px 2px 2px rgba(190, 190, 190, 0.5) !important;margin: 0 auto !important;font-family:'Cookie', cursive !important;-webkit-box-sizing: border-box !important;box-sizing: border-box !important;-o-transition: 0.3s all linear !important;-webkit-transition: 0.3s all linear !important;-moz-transition: 0.3s all linear !important;-ms-transition: 0.3s all linear !important;transition: 0.3s all linear !important;}.bmc-button:hover, .bmc-button:active, .bmc-button:focus {-webkit-box-shadow: 0px 1px 2px 2px rgba(190, 190, 190, 0.5) !important;text-decoration: none !important;box-shadow: 0px 1px 2px 2px rgba(190, 190, 190, 0.5) !important;opacity: 0.85 !important;color:#ffffff !important;}</style><link href="https://fonts.googleapis.com/css?family=Cookie" rel="stylesheet"><a class="bmc-button" target="_blank" href="https://www.buymeacoffee.com/bS0teIs"><img src="https://cdn.buymeacoffee.com/buttons/bmc-new-btn-logo.svg" alt="Buy me a coffee"><span style="margin-left:15px;font-size:28px !important;">Buy me a coffee</span></a>
+
+
+---
 
 
 <!-- badges: start -->

README.md

@@ -5,8 +5,19 @@
 
 🔬👀📑🗃📊🏨🗄📇📖⚗📝🎶📈📉📃🖍 🔬🔬🏋🚴🚙👨💻 📸📺🎛🔭🔬💊🔐🍫🌸
 
+-----
+
 <https://sbalci.github.io/histopathology-template/>
 
+-----
+
+<style>.bmc-button img{width: 35px !important;margin-bottom: 1px !important;box-shadow: none !important;border: none !important;vertical-align: middle !important;}.bmc-button{padding: 7px 10px 7px 10px !important;line-height: 35px !important;height:51px !important;min-width:217px !important;text-decoration: none !important;display:inline-flex !important;color:#ffffff !important;background-color:#5F7FFF !important;border-radius: 5px !important;border: 1px solid transparent !important;padding: 7px 10px 7px 10px !important;font-size: 28px !important;letter-spacing:0.6px !important;box-shadow: 0px 1px 2px rgba(190, 190, 190, 0.5) !important;-webkit-box-shadow: 0px 1px 2px 2px rgba(190, 190, 190, 0.5) !important;margin: 0 auto !important;font-family:'Cookie', cursive !important;-webkit-box-sizing: border-box !important;box-sizing: border-box !important;-o-transition: 0.3s all linear !important;-webkit-transition: 0.3s all linear !important;-moz-transition: 0.3s all linear !important;-ms-transition: 0.3s all linear !important;transition: 0.3s all linear !important;}.bmc-button:hover, .bmc-button:active, .bmc-button:focus {-webkit-box-shadow: 0px 1px 2px 2px rgba(190, 190, 190, 0.5) !important;text-decoration: none !important;box-shadow: 0px 1px 2px 2px rgba(190, 190, 190, 0.5) !important;opacity: 0.85 !important;color:#ffffff !important;}</style>
+
+<link href="https://fonts.googleapis.com/css?family=Cookie" rel="stylesheet"><a class="bmc-button" target="_blank" href="https://www.buymeacoffee.com/bS0teIs"><img src="https://cdn.buymeacoffee.com/buttons/bmc-new-btn-logo.svg" alt="Buy me a coffee"><span style="margin-left:15px;font-size:28px !important;">Buy
+me a coffee</span></a>
+
+-----
+
 <!-- badges: start -->
 
 <!-- [![CRAN_Release_Badge](http://www.r-pkg.org/badges/version-ago/histopathology-template)](https://CRAN.R-project.org/package=histopathology-template) -->
@@ -60,6 +71,8 @@ Thanks\!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://sayth
 Binder](http://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/sbalci/histopathology-template/master?urlpath=rstudio)
 <!-- badges: end -->
 
+<https://github.com/sbalci/histopathology-template>
+
 This repository is a template for the codes I use in [my and my friends’
 histopathology
 research](https://sbalci.github.io/cv/SerdarBalciMDPathologist.html).
@@ -135,7 +148,7 @@ Run in your own computer R session:
 
 ``` r
 library(shiny)
-runUrl("https://github.com/sbalci/histopathRshiny/raw/master/histopathRshiny.tar")
+runUrl("https://github.com/sbalci/histopathRshiny/raw/master/histopathRshiny.tar.gz")
 ```
 
 Code here: <https://github.com/sbalci/histopathRshiny>

bib/packages.bib

@@ -26,14 +26,14 @@ @Manual{R-finalfit
 Modelling},
   author = {Ewen Harrison and Tom Drake and Riinu Ots},
   year = {2019},
-  note = {R package version 0.9.6},
+  note = {R package version 0.9.7},
   url = {https://github.com/ewenharrison/finalfit},
 }
 @Manual{R-knitr,
   title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
   author = {Yihui Xie},
-  year = {2019},
-  note = {R package version 1.26},
+  year = {2020},
+  note = {R package version 1.27},
   url = {https://CRAN.R-project.org/package=knitr},
 }
 @Manual{R-magrittr,
@@ -60,15 +60,15 @@ @Manual{R-report
 @Manual{R-shiny,
   title = {shiny: Web Application Framework for R},
   author = {Winston Chang and Joe Cheng and JJ Allaire and Yihui Xie and Jonathan McPherson},
-  year = {2019},
-  note = {R package version 1.4.0},
-  url = {https://CRAN.R-project.org/package=shiny},
+  year = {2020},
+  note = {R package version 1.4.0.9001},
+  url = {http://shiny.rstudio.com},
 }
 @Manual{R-survival,
   title = {survival: Survival Analysis},
   author = {Terry M Therneau},
   year = {2019},
-  note = {R package version 3.1-6},
+  note = {R package version 3.1-8},
   url = {https://CRAN.R-project.org/package=survival},
 }
 @Manual{R-tableone,
@@ -86,7 +86,7 @@ @Book{knitr2015
   year = {2015},
   edition = {2nd},
   note = {ISBN 978-1498716963},
-  url = {https://yihui.name/knitr/},
+  url = {https://yihui.org/knitr/},
 }
 @InCollection{knitr2014,
   booktitle = {Implementing Reproducible Computational Research},

childRmd/_11descriptives.Rmd

@@ -28,14 +28,14 @@ tab1 <- arsenal::tableby(
     Group +
     Grade +
     TStage +
-    `Anti-X-intensity` +
-    `Anti-Y-intensity` +
+    # `Anti-X-intensity` +
+    # `Anti-Y-intensity` +
     LymphNodeMetastasis +
     Valid +
     Smoker +
     Grade_Level
   ,
-  data = mydata
+  data = mydata 
 )
 summary(tab1)
 ```

childRmd/_18survival.Rmd

@@ -10,8 +10,6 @@ https://www.datasurg.net/2019/09/12/survival-analysis-with-strata-clusters-frail
 https://link.springer.com/article/10.1007/s00701-019-04096-9
 
 
-
-
 **Calculate survival time**
 
 ```{r define survival time}

childRmd/gc_desc_cont.Rmd

@@ -20,13 +20,13 @@ jmv::descriptives(
 
 \pagebreak
 
-**Descriptive Statistics Anti-X-intensity** 
+**Descriptive Statistics AntiX_intensity** 
 
-```{r Descriptive Statistics Anti-X-intensity}
+```{r Descriptive Statistics AntiX_intensity}
 mydata %>% 
 jmv::descriptives(
     data = .,
-    vars = 'Anti-X-intensity',
+    vars = 'AntiX_intensity',
     hist = TRUE,
     dens = TRUE,
     box = TRUE,
@@ -42,13 +42,13 @@ jmv::descriptives(
 
 \pagebreak
 
-**Descriptive Statistics Anti-Y-intensity** 
+**Descriptive Statistics AntiY_intensity** 
 
-```{r Descriptive Statistics Anti-Y-intensity}
+```{r Descriptive Statistics AntiY_intensity}
 mydata %>% 
 jmv::descriptives(
     data = .,
-    vars = 'Anti-Y-intensity',
+    vars = 'AntiY_intensity',
     hist = TRUE,
     dens = TRUE,
     box = TRUE,