updated on 2019-12-18 14:32:57

sbalci · Dec 18, 2019 · ba67c94 · ba67c94
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diff --git a/.Rprofile b/.Rprofile
@@ -1,9 +1,7 @@
 source("renv/activate.R")
 
 .First <- function(){
-    cat("\nWelcome to histopathology template project", date(), "\n")
+cat("\nWelcome to histopathology template project", date(), "\n")
 }
-
 .Last <- function(){
-    cat("\nGoodbye at ", date(), "\n")
-}
+cat("\nGoodbye at ", date(), "\n")
diff --git a/README.Rmd b/README.Rmd
@@ -65,6 +65,9 @@ https://sbalci.github.io/histopathology-template/
 <!-- 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).
 
 ---
@@ -134,10 +137,11 @@ 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
 

diff --git a/data/histopathology-template2019-12-13.rds b/data/histopathology-template2019-12-13.rds
diff --git a/data/histopathology-template2019-12-13.xlsx b/data/histopathology-template2019-12-13.xlsx
diff --git a/data/mydata.xlsx b/data/mydata.xlsx
diff --git a/figure/DataExplorer 4-1.png b/figure/DataExplorer 4-1.png
diff --git a/figure/DataExplorer 5-1.png b/figure/DataExplorer 5-1.png
diff --git a/figure/DataExplorer 7-1.png b/figure/DataExplorer 7-1.png
diff --git a/figure/DataExplorer 7-2.png b/figure/DataExplorer 7-2.png
diff --git a/figure/DataExplorer 8-1.png b/figure/DataExplorer 8-1.png
diff --git a/figure/DataExplorer 8-2.png b/figure/DataExplorer 8-2.png
diff --git a/figure/DataExplorer 9-1.png b/figure/DataExplorer 9-1.png
diff --git a/figure/Descriptive Statistics Age-1.png b/figure/Descriptive Statistics Age-1.png
diff --git a/figure/Descriptive Statistics Age-2.png b/figure/Descriptive Statistics Age-2.png
diff --git a/figure/Descriptive Statistics Anti-X-intensity-1.png b/figure/Descriptive Statistics Anti-X-intensity-1.png
diff --git a/figure/Descriptive Statistics Anti-X-intensity-2.png b/figure/Descriptive Statistics Anti-X-intensity-2.png
diff --git a/figure/Descriptive Statistics Anti-Y-intensity-1.png b/figure/Descriptive Statistics Anti-Y-intensity-1.png
diff --git a/figure/Descriptive Statistics Anti-Y-intensity-2.png b/figure/Descriptive Statistics Anti-Y-intensity-2.png
diff --git a/figure/Kaplan-Meier Plot Log-Rank Test 2-1.png b/figure/Kaplan-Meier Plot Log-Rank Test 2-1.png
diff --git a/figure/Kaplan-Meier Plot Log-Rank Test TStage-1.png b/figure/Kaplan-Meier Plot Log-Rank Test TStage-1.png
diff --git a/figure/Kaplan-Meier Plot Log-Rank Test-1.png b/figure/Kaplan-Meier Plot Log-Rank Test-1.png
diff --git a/figure/Median Survivals-1.png b/figure/Median Survivals-1.png
diff --git a/figure/generate fake data-1.png b/figure/generate fake data-1.png
diff --git a/figure/inspectdf 5-1.png b/figure/inspectdf 5-1.png
diff --git a/figure/km-1.png b/figure/km-1.png
diff --git a/figure/plot fake data-1.png b/figure/plot fake data-1.png
diff --git a/figure/variable type plot explore-1.png b/figure/variable type plot explore-1.png
diff --git a/figure/variable type plot visdat-1.png b/figure/variable type plot visdat-1.png
diff --git a/figure/xray 2-1.png b/figure/xray 2-1.png
diff --git a/figure/xray 2-2.png b/figure/xray 2-2.png
diff --git a/figure/xray 2-3.png b/figure/xray 2-3.png
diff --git a/figure/xray 2-4.png b/figure/xray 2-4.png
diff --git a/figure/xray 2-5.png b/figure/xray 2-5.png
diff --git a/out/dataMaid_mydata.Rmd b/out/dataMaid_mydata.Rmd
@@ -2,7 +2,7 @@
 dataMaid: yes
 title: mydata
 subtitle: "Autogenerated data summary from dataMaid"
-date: 2019-12-01 21:02:41
+date: 2019-12-13 09:03:42
 output: pdf_document
 geometry: margin=2cm
 documentclass: report
@@ -76,11 +76,11 @@ Please note that all numerical values in the following have been rounded to 2 de
 
 [Age]                    numeric                         50                 0.40 %                
 
-[Race]                   character                        7                 0.40 %    $\times$    
+[Race]                   character                        8                 0.40 %    $\times$    
 
 [PreinvasiveComponent]   character                        3                 0.40 %                
 
-[LVI]                    character                        3                 0.40 %                
+[LVI]                    character                        2                 0.00 %                
 
 [PNI]                    character                        3                 0.40 %                
 
@@ -106,7 +106,7 @@ Please note that all numerical values in the following have been rounded to 2 de
 
 [Grade\_Level]           character                        4                 0.40 %                
 
-[SurgeryDate]            POSIXct                        220                 0.40 %    $\times$    
+[SurgeryDate]            POSIXct                        218                 0.40 %    $\times$    
 
 [DeathTime]              character                        2                 0.00 %                
 --------------------------------------------------------------------------------------------------
@@ -152,7 +152,7 @@ Mode                           "Male"
 \bminitwo
 ```{r 'Var-3-Sex', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Female", 
-"Male"), class = "factor"), y = c(123L, 126L)), class = "data.frame", row.names = c(NA, 
+"Male"), class = "factor"), y = c(108L, 141L)), class = "data.frame", row.names = c(NA, 
 -2L)), vnam = "Sex")
 ```
 
@@ -176,9 +176,9 @@ Number of missing obs.      1 (0.4 %)
 
 Number of unique values            49
 
-Median                             49
+Median                             51
 
-1st and 3rd quartiles          38; 62
+1st and 3rd quartiles          38; 64
 
 Min. and max.                  25; 73
 -------------------------------------
@@ -190,7 +190,7 @@ Min. and max.                  25; 73
 ggAggHist(data = structure(list(xmin = c(25L, 30L, 35L, 40L, 
 45L, 50L, 55L, 60L, 65L, 70L), xmax = c(30L, 35L, 40L, 45L, 50L, 
 55L, 60L, 65L, 70L, 75L), ymin = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 
-0), ymax = c(29L, 22L, 28L, 31L, 17L, 28L, 25L, 22L, 30L, 17L
+0), ymax = c(27L, 24L, 20L, 24L, 28L, 23L, 24L, 29L, 28L, 22L
 )), class = "data.frame", row.names = c(NA, -10L)), vnam = "Age")
 ```
 
@@ -212,7 +212,7 @@ Variable type               character
 
 Number of missing obs.      1 (0.4 %)
 
-Number of unique values             6
+Number of unique values             7
 
 Mode                          "White"
 -------------------------------------
@@ -221,16 +221,16 @@ Mode                          "White"
 \emini
 \bminitwo
 ```{r 'Var-5-Race', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
-ggAggBarplot(data = structure(list(x = structure(1:6, .Label = c("Asian", 
-"Bi-Racial", "Black", "Hispanic", "Native", "White"), class = "factor"), 
-    y = c(7L, 4L, 37L, 42L, 2L, 157L)), class = "data.frame", row.names = c(NA, 
--6L)), vnam = "Race")
+ggAggBarplot(data = structure(list(x = structure(1:7, .Label = c("Asian", 
+"Bi-Racial", "Black", "Hispanic", "Native", "Other", "White"), class = "factor"), 
+    y = c(10L, 8L, 26L, 38L, 5L, 1L, 161L)), class = "data.frame", row.names = c(NA, 
+-7L)), vnam = "Race")
 ```
 
 \emini
 
 
-- Note that the following levels have at most five observations: \"Bi-Racial\", \"Native\". 
+- Note that the following levels have at most five observations: \"Native\", \"Other\". 
 
 
 
@@ -257,7 +257,7 @@ Mode                         "Absent"
 \bminitwo
 ```{r 'Var-6-PreinvasiveComponent', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent", 
-"Present"), class = "factor"), y = c(205L, 44L)), class = "data.frame", row.names = c(NA, 
+"Present"), class = "factor"), y = c(204L, 45L)), class = "data.frame", row.names = c(NA, 
 -2L)), vnam = "PreinvasiveComponent")
 ```
 
@@ -277,7 +277,7 @@ Feature                        Result
 ------------------------- -----------
 Variable type               character
 
-Number of missing obs.      1 (0.4 %)
+Number of missing obs.        0 (0 %)
 
 Number of unique values             2
 
@@ -289,7 +289,7 @@ Mode                         "Absent"
 \bminitwo
 ```{r 'Var-7-LVI', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent", 
-"Present"), class = "factor"), y = c(138L, 111L)), class = "data.frame", row.names = c(NA, 
+"Present"), class = "factor"), y = c(156L, 94L)), class = "data.frame", row.names = c(NA, 
 -2L)), vnam = "LVI")
 ```
 
@@ -321,7 +321,7 @@ Mode                         "Absent"
 \bminitwo
 ```{r 'Var-8-PNI', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent", 
-"Present"), class = "factor"), y = c(177L, 72L)), class = "data.frame", row.names = c(NA, 
+"Present"), class = "factor"), y = c(158L, 91L)), class = "data.frame", row.names = c(NA, 
 -2L)), vnam = "PNI")
 ```
 
@@ -361,7 +361,7 @@ Mode                           "TRUE"
 \bminitwo
 ```{r 'Var-10-Death', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("FALSE", 
-"TRUE"), class = "factor"), y = c(64L, 185L)), class = "data.frame", row.names = c(NA, 
+"TRUE"), class = "factor"), y = c(76L, 173L)), class = "data.frame", row.names = c(NA, 
 -2L)), vnam = "Death")
 ```
 
@@ -425,7 +425,7 @@ Mode                              "3"
 \bminitwo
 ```{r 'Var-12-Grade', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("1", 
-"2", "3"), class = "factor"), y = c(78L, 71L, 100L)), class = "data.frame", row.names = c(NA, 
+"2", "3"), class = "factor"), y = c(66L, 76L, 107L)), class = "data.frame", row.names = c(NA, 
 -3L)), vnam = "Grade")
 ```
 
@@ -457,7 +457,7 @@ Mode                              "4"
 \bminitwo
 ```{r 'Var-13-TStage', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:4, .Label = c("1", 
-"2", "3", "4"), class = "factor"), y = c(21L, 49L, 56L, 124L)), class = "data.frame", row.names = c(NA, 
+"2", "3", "4"), class = "factor"), y = c(36L, 58L, 57L, 99L)), class = "data.frame", row.names = c(NA, 
 -4L)), vnam = "TStage")
 ```
 
@@ -493,7 +493,7 @@ Reference category                  1
 \bminitwo
 ```{r 'Var-14-Anti-X-intensity', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("1", 
-"2", "3"), class = "factor"), y = c(31L, 103L, 115L)), class = "data.frame", row.names = c(NA, 
+"2", "3"), class = "factor"), y = c(29L, 104L, 116L)), class = "data.frame", row.names = c(NA, 
 -3L)), vnam = "Anti-X-intensity")
 ```
 
@@ -529,7 +529,7 @@ Reference category                  1
 \bminitwo
 ```{r 'Var-15-Anti-Y-intensity', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("1", 
-"2", "3"), class = "factor"), y = c(76L, 98L, 75L)), class = "data.frame", row.names = c(NA, 
+"2", "3"), class = "factor"), y = c(82L, 87L, 80L)), class = "data.frame", row.names = c(NA, 
 -3L)), vnam = "Anti-Y-intensity")
 ```
 
@@ -561,7 +561,7 @@ Mode                         "Absent"
 \bminitwo
 ```{r 'Var-16-LymphNodeMetastasis', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("Absent", 
-"Present"), class = "factor"), y = c(154L, 95L)), class = "data.frame", row.names = c(NA, 
+"Present"), class = "factor"), y = c(134L, 115L)), class = "data.frame", row.names = c(NA, 
 -2L)), vnam = "LymphNodeMetastasis")
 ```
 
@@ -585,15 +585,15 @@ Number of missing obs.      1 (0.4 %)
 
 Number of unique values             2
 
-Mode                           "TRUE"
+Mode                          "FALSE"
 -------------------------------------
 
 
 \emini
 \bminitwo
 ```{r 'Var-17-Valid', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("FALSE", 
-"TRUE"), class = "factor"), y = c(121L, 128L)), class = "data.frame", row.names = c(NA, 
+"TRUE"), class = "factor"), y = c(134L, 115L)), class = "data.frame", row.names = c(NA, 
 -2L)), vnam = "Valid")
 ```
 
@@ -625,7 +625,7 @@ Mode                          "FALSE"
 \bminitwo
 ```{r 'Var-18-Smoker', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:2, .Label = c("FALSE", 
-"TRUE"), class = "factor"), y = c(130L, 119L)), class = "data.frame", row.names = c(NA, 
+"TRUE"), class = "factor"), y = c(135L, 114L)), class = "data.frame", row.names = c(NA, 
 -2L)), vnam = "Smoker")
 ```
 
@@ -657,7 +657,7 @@ Mode                           "high"
 \bminitwo
 ```{r 'Var-19-Grade-Level', echo=FALSE, fig.width=4, fig.height=3, message=FALSE, warning=FALSE}
 ggAggBarplot(data = structure(list(x = structure(1:3, .Label = c("high", 
-"low", "moderate"), class = "factor"), y = c(105L, 74L, 70L)), class = "data.frame", row.names = c(NA, 
+"low", "moderate"), class = "factor"), y = c(108L, 75L, 66L)), class = "data.frame", row.names = c(NA, 
 -3L)), vnam = "Grade_Level")
 ```
 
@@ -714,15 +714,15 @@ Report generation information:
 
  *  Created by Serdar BALCI old (username: `serdarbalciold`).
 
- *  Report creation time: Sun Dec 01 2019 21:02:42
+ *  Report creation time: Fri Dec 13 2019 09:03:42
 
  *  Report was run from directory: `/Users/serdarbalciold/histopathology-template/childRmd`
 
  *  dataMaid v1.3.2 [Pkg: 2019-07-27 from CRAN (R 3.6.0)]
 
  *  R version 3.6.0 (2019-04-26).
 
- *  Platform: x86_64-apple-darwin15.6.0 (64-bit)(macOS  10.15.1).
+ *  Platform: x86_64-apple-darwin15.6.0 (64-bit)(macOS  10.15.2).
 
  *  Function call: `dataMaid::makeDataReport(data = mydata, render = FALSE, file = here::here("out", 
     "dataMaid_mydata.Rmd"), replace = TRUE, quiet = TRUE, openResult = FALSE)`