---

title: "Prognostic Performance"

author: "Pranjal"

date: "2/21/2019"

output: html_document

---

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = TRUE)

```

## Initial Setup and Package Loads in R 

Packages used for the analysis.

```{r initial_setup, cache=FALSE, message = FALSE, warning = FALSE}

library(glmnet);library(survival);library(survminer);library(readxl);library(ggplot2); library(GGally)

library(knitr); library(rmdformats); library(magrittr)

library(skimr); library(Hmisc); library(Epi); library(vcd)

library(tidyverse) 

source("Love-boost.R")

## Global options

options(max.print="75")

opts_chunk$set(comment=NA,

               message=FALSE,

               warning=FALSE)

opts_knit$set(width=75)

skimr::skim_with(numeric = list(hist = NULL),

                 integer = list(hist = NULL))

```

## Loading the Raw Data into R 

Loading raw dataset into R.

Training Data from CCF with minimum and max. survival time.

```{r}

train <- read.csv("dataset_train.csv")

train$censor <- ifelse(train$status == 1,'Censor','Dead')

```

```{r}

ggbarplot(train, x = "Cases", y = "RRS",

          fill = "censor",               # change fill color by cyl

          color = FALSE,            # Set bar border colors to white

          palette = "jco",            # jco journal color palett.

          sort.val = "desc",          # Sort the value in dscending order

          sort.by.groups = FALSE,     # Don't sort inside each group

     #     x.text.angle = 90           # Rotate vertically x axis texts

          )

```

# TCGA DATASET

```{r train_set}

TCGA <- read.csv("dataset_nsclc.csv")

TCGA$censor <- ifelse(TCGA$status == 1,'Censor','Dead')

```

```{r}

ggbarplot(TCGA, x = "Cases", y = "RRS",

          fill = "censor",               # change fill color by cyl

          color = FALSE,            # Set bar border colors to white

          palette = "jco",            # jco journal color palett.

          sort.val = "desc",          # Sort the value in dscending order

          sort.by.groups = FALSE,     # Don't sort inside each group

     #     x.text.angle = 90           # Rotate vertically x axis texts

          )

```

# UPENN DATASET

```{r }

UPENN <- read.csv("dataset_upenn.csv")

UPENN$censor <- ifelse(UPENN$status == 1,'Censor','Dead')

```

```{r}

ggbarplot(UPENN, x = "Cases", y = "RRS",

          fill = "censor",               # change fill color by cyl

          color = FALSE,            # Set bar border colors to white

          palette = "jco",            # jco journal color palett.

          sort.val = "desc",          # Sort the value in dscending order

          sort.by.groups = FALSE,     # Don't sort inside each group

     #     x.text.angle = 90           # Rotate vertically x axis texts

          )

```