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new file mode 100644
index 0000000..6e6b0d3
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new file mode 100644
index 0000000..28835b4
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new file mode 100644
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new file mode 100644
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index 233f069..65edb7c 100644
--- a/.Rproj.user/A70D84A5/sources/prop/INDEX
+++ b/.Rproj.user/A70D84A5/sources/prop/INDEX
@@ -1,3 +1,5 @@
+~%2FRepositories%2Fcure-pipeline%2F.gitignore.R="1ECE0E8B"
+~%2FRepositories%2Fcure-pipeline%2F.gitignore.txt="6B2DD538"
 ~%2FRepositories%2Fcure-pipeline%2FR%2Fcalibration-curve.R="DDEF45DE"
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 ~%2FRepositories%2Fcure-pipeline%2FR%2Fcure-nomo-multi-var.R="0D44D543"
@@ -7,4 +9,5 @@
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 ~%2FRepositories%2Fcure-pipeline%2FR%2Fstability-tests.R="B4356C36"
+~%2FRepositories%2Fcure-pipeline%2FREADME.Rmd="DF2C1924"
 ~%2FRepositories%2Fcure-pipeline%2Fexample.R="5F8A5441"
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+        "scrollLine": "85"
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+    "lastKnownWriteTime": 1610688000,
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 }
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diff --git a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/1E1A0339-contents b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/1E1A0339-contents
index 6cff063..316b3af 100644
--- a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/1E1A0339-contents
+++ b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/1E1A0339-contents
@@ -1,7 +1,6 @@
 # Functions to Run Cure Models (Once or Multiple Times) ------------------------
 # ------------------------------------------------------------------------------
 
-source(here::here("R", "clean-model-results.R"))
 
 # Single Model Run -------------------------------------------------------------
 # Wrapper function for smcure to accept multi-level variables and save necessary 
@@ -96,6 +95,8 @@ multiple_mod_runs <- function(formula,
                               num_repeats = 10, 
                               data = mel) {
 
+  source(here::here("R", "clean-model-results.R"))
+  
   # pull original variables from formula
   mf <- formula
   mf <- eval(mf, parent.frame())
@@ -235,28 +236,4 @@ multiple_mod_runs <- function(formula,
 }
 
 
-# Examples
-
-# data <- ISwR::melanom %>%
-#   mutate(status = case_when(status %in% c(1, 3) ~ 1, 
-#                             TRUE ~ 0)) %>%
-#   mutate(sex = case_when(sex == 2 ~ "male", 
-#                          sex == 1 ~ "female"),
-#          ulc = case_when(ulc == 1 ~ "present", 
-#                          ulc == 2 ~ "absent"))
-# 
-# formula <- Surv(days, status) ~ ulc + sex
-#   
-# x <- multiple_mod_runs(formula,
-#                               nboot = 200,
-#                               eps = 0.0001, 
-#                               num_repeats = 3, 
-#                               data = data)
-# x$model_results
-# 
-# x$var_surv_stab
-# x$p_surv_stab
-# 
-# x$var_cure_stab
-# x$p_cure_stab
   
\ No newline at end of file
diff --git a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/7C2EB88F b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/7C2EB88F
deleted file mode 100644
index dc04432..0000000
--- a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/7C2EB88F
+++ /dev/null
@@ -1,25 +0,0 @@
-{
-    "id": "7C2EB88F",
-    "path": "~/Repositories/cure-pipeline/R/calibration-curve.R",
-    "project_path": "R/calibration-curve.R",
-    "type": "r_source",
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new file mode 100644
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--- /dev/null
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+{
+    "id": "868C082D",
+    "path": "~/Repositories/cure-pipeline/R/clean-model-results.R",
+    "project_path": "R/clean-model-results.R",
+    "type": "r_source",
+    "hash": "0",
+    "contents": "",
+    "dirty": false,
+    "created": 1610687727650.0,
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diff --git a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/868C082D-contents b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/868C082D-contents
new file mode 100644
index 0000000..b739b49
--- /dev/null
+++ b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/868C082D-contents
@@ -0,0 +1,18 @@
+
+# Clean Model Results ----------------------------------------------------------
+mmcure <- function(fit_k2_cat) {
+  enframe(fit_k2_cat$b) %>% 
+  left_join(enframe(fit_k2_cat$b_pvalue),
+            by = "name") %>%
+  transmute(name, 
+            value = round(exp(value.x), 2), 
+            pvalue = round(value.y, 2))
+}
+
+mmsurv <- function(fit_k2_cat) {
+  enframe(fit_k2_cat$beta) %>% 
+  left_join(enframe(fit_k2_cat$beta_pvalue), by = "name") %>%
+  transmute(name, 
+            value = round(exp(value.x), 2), 
+            pvalue = round(value.y, 2))
+}
diff --git a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/91B9DCD1 b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/91B9DCD1
new file mode 100644
index 0000000..f769294
--- /dev/null
+++ b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/91B9DCD1
@@ -0,0 +1,25 @@
+{
+    "id": "91B9DCD1",
+    "path": "~/Repositories/cure-pipeline/README.Rmd",
+    "project_path": "README.Rmd",
+    "type": "r_markdown",
+    "hash": "2669428527",
+    "contents": "",
+    "dirty": false,
+    "created": 1610688405206.0,
+    "source_on_save": false,
+    "relative_order": 7,
+    "properties": {
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+        "scrollLine": "17",
+        "source_window_id": ""
+    },
+    "folds": "",
+    "lastKnownWriteTime": 1610690234,
+    "encoding": "UTF-8",
+    "collab_server": "",
+    "source_window": "",
+    "last_content_update": 1610690234968,
+    "read_only": false,
+    "read_only_alternatives": []
+}
\ No newline at end of file
diff --git a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/91B9DCD1-contents b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/91B9DCD1-contents
new file mode 100644
index 0000000..afe65a5
--- /dev/null
+++ b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/91B9DCD1-contents
@@ -0,0 +1,80 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# Cure Model Pipeline
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of this package is to provide an easy way to build, evaluate and visualize mixture cure models ([link to paper draft](https://docs.google.com/document/d/1Lhom9H7Hxb8_C6d55Trs9JHSfJCn1i6yuu_xsDyYqZQ/edit?usp=sharing))
+
+
+## Available Functions
+
+- `fit_cure()` - wrapper for `smcure::smcure()` function that allows you to pass multilevel variables as factors directly (instead of first creating dummy codes). It also saves outputs necessary to create nomogram.
+- `nomogram()-` - accepts an object created by `fit_cure()` and creates graphical nomogram based on model fit
+- `cure_calibration()` - accepts an object created by `fit_cure()` and creates a calibration curve for uncured patients
+- `multiple_mod_runs()`- allows you to check stability of models but running them multiple times and viewing distributions of variables and p-values. 
+- Coming soon:
+  - k-index and C-index wrapper functions
+  - tidyr function to better clean/view coefficients from cure model
+
+## Example 
+
+```{r, eval = FALSE}
+library(smcure)
+library(ISwR)
+library(gtsummary)
+library(tidyverse)
+
+# Prepare Data --------------------------
+mel <- ISwR::melanom %>%
+  mutate(status = case_when(status %in% c(1, 3) ~ 1, 
+                            TRUE ~ 0)) %>%
+  mutate(thick_cat = 
+              case_when(thick <= 129 ~ "≤ 129", 
+                        thick <= 322 ~ "less equal 322", 
+                        thick > 322 ~ "greater 322")) %>%
+  mutate(thick_cat = fct_relevel(thick_cat, "≤ 129", "≤ 322")) %>%
+  mutate(sex = case_when(sex == 2 ~ "male", 
+                         sex == 1 ~ "female"),
+         ulc = case_when(ulc == 1 ~ "present", 
+                         ulc == 2 ~ "absent"))
+
+# Run Pipeline --------------------------
+fit <- fit_cure(formula = Surv(days, status) ~ ulc + sex + thick_cat + thick ,
+                data = mel)
+cure_nomogram(fit, prediction_time = 300)
+cure_calibration(fit, prediction_time = 300)
+
+
+# Check Stability ----
+formula <- Surv(days, status) ~ ulc + sex
+x <- multiple_mod_runs(formula,
+                              nboot = 200,
+                              eps = 0.0001,
+                              num_repeats = 3,
+                              data = mel)
+x$model_results
+
+x$var_surv_stab
+x$p_surv_stab
+
+x$var_cure_stab
+x$p_cure_stab
+
+```
+
+
diff --git a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/CD6407BC-contents b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/CD6407BC-contents
new file mode 100644
index 0000000..984602d
--- /dev/null
+++ b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/CD6407BC-contents
@@ -0,0 +1,43 @@
+# ignore R data files
+.Rproj.user
+.Rhistory
+.RData
+.rds
+.Ruserdata
+.Rapp.history
+.Rhistory.RData
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# ignore other types of data files
+*.xlsx
+*.xls
+*.csv
+*.dta
+*.sas7bdat
+*.sav
+*.txt
+
+# ignore data folder/symbolic link/sensitive file
+data
+admin
+raw-data
+secure_data
+ext_data
+tmp
+env.json
+archives
+outputs/archive
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# ignore misc files
+~$*.docx
+~$*.xlsx
+~$*.pptx
+~$*.tmp
+Thumbs.db
+.DS_Store
diff --git a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/E5780712 b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/E5780712
index e842fa7..bad9f15 100644
--- a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/E5780712
+++ b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/E5780712
@@ -5,20 +5,20 @@
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     "hash": "0",
     "contents": "",
-    "dirty": true,
+    "dirty": false,
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     "source_on_save": false,
     "relative_order": 5,
     "properties": {
-        "cursorPosition": "31,0",
-        "scrollLine": "10"
+        "cursorPosition": "41,13",
+        "scrollLine": "20"
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-    "lastKnownWriteTime": 1610687370,
+    "lastKnownWriteTime": 1610688082,
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-    "last_content_update": 1610687388996,
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 }
\ No newline at end of file
diff --git a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/E5780712-contents b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/E5780712-contents
index 51993b8..93b45af 100644
--- a/.Rproj.user/A70D84A5/sources/s-D23FE8C5/E5780712-contents
+++ b/.Rproj.user/A70D84A5/sources/s-D23FE8C5/E5780712-contents
@@ -18,15 +18,25 @@ mel <- ISwR::melanom %>%
                          ulc == 2 ~ "absent"))
 
 # Run Pipeline --------------------------
-fit <- fit_cure(formula = Surv(days, status) ~ ulc + sex + thick_cat + thick + no,
+fit <- fit_cure(formula = Surv(days, status) ~ ulc + sex + thick_cat + thick ,
                 data = mel)
 
 cure_nomogram(fit, prediction_time = 300)
 
 cure_calibration(fit, prediction_time = 300)
 
-stability <- multiple_mod_runs(formula = Surv(days, status) ~ ulc + sex + thick_cat + thick + no,
-                data = mel, 
-                 num_repeats = 4)
 
-stability
+# Stability example----
+formula <- Surv(days, status) ~ ulc + sex
+x <- multiple_mod_runs(formula,
+                              nboot = 200,
+                              eps = 0.0001,
+                              num_repeats = 3,
+                              data = mel)
+x$model_results
+
+x$var_surv_stab
+x$p_surv_stab
+
+x$var_cure_stab
+x$p_cure_stab
diff --git a/.Rproj.user/shared/notebooks/7EDBDC2F-README/1/A70D84A5D23FE8C5/chunks.json b/.Rproj.user/shared/notebooks/7EDBDC2F-README/1/A70D84A5D23FE8C5/chunks.json
new file mode 100644
index 0000000..faaa042
--- /dev/null
+++ b/.Rproj.user/shared/notebooks/7EDBDC2F-README/1/A70D84A5D23FE8C5/chunks.json
@@ -0,0 +1 @@
+{"chunk_definitions":[],"doc_write_time":1610688452}
\ No newline at end of file
diff --git a/.Rproj.user/shared/notebooks/7EDBDC2F-README/1/s/chunks.json b/.Rproj.user/shared/notebooks/7EDBDC2F-README/1/s/chunks.json
new file mode 100644
index 0000000..faaa042
--- /dev/null
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@@ -0,0 +1 @@
+{"chunk_definitions":[],"doc_write_time":1610688452}
\ No newline at end of file
diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
index 58a4cf0..34a60ff 100644
--- a/.Rproj.user/shared/notebooks/paths
+++ b/.Rproj.user/shared/notebooks/paths
@@ -1,3 +1,5 @@
+/Users/Whiting/Repositories/cure-pipeline/.gitignore.R="49A77F14"
+/Users/Whiting/Repositories/cure-pipeline/.gitignore.txt="2612A3E9"
 /Users/Whiting/Repositories/cure-pipeline/R/calibration-curve.R="B528D07F"
 /Users/Whiting/Repositories/cure-pipeline/R/clean-model-results.R="A08AB9C4"
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@@ -7,4 +9,5 @@
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 /Users/Whiting/Repositories/cure-pipeline/R/stability-tests.R="230A6CB9"
+/Users/Whiting/Repositories/cure-pipeline/README.Rmd="7EDBDC2F"
 /Users/Whiting/Repositories/cure-pipeline/example.R="270BFC7C"
diff --git a/.gitignore.R b/.gitignore.R
new file mode 100644
index 0000000..984602d
--- /dev/null
+++ b/.gitignore.R
@@ -0,0 +1,43 @@
+# ignore R data files
+.Rproj.user
+.Rhistory
+.RData
+.rds
+.Ruserdata
+.Rapp.history
+.Rhistory.RData
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# ignore other types of data files
+*.xlsx
+*.xls
+*.csv
+*.dta
+*.sas7bdat
+*.sav
+*.txt
+
+# ignore data folder/symbolic link/sensitive file
+data
+admin
+raw-data
+secure_data
+ext_data
+tmp
+env.json
+archives
+outputs/archive
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# ignore misc files
+~$*.docx
+~$*.xlsx
+~$*.pptx
+~$*.tmp
+Thumbs.db
+.DS_Store
diff --git a/.gitignore.txt b/.gitignore.txt
new file mode 100644
index 0000000..984602d
--- /dev/null
+++ b/.gitignore.txt
@@ -0,0 +1,43 @@
+# ignore R data files
+.Rproj.user
+.Rhistory
+.RData
+.rds
+.Ruserdata
+.Rapp.history
+.Rhistory.RData
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# ignore other types of data files
+*.xlsx
+*.xls
+*.csv
+*.dta
+*.sas7bdat
+*.sav
+*.txt
+
+# ignore data folder/symbolic link/sensitive file
+data
+admin
+raw-data
+secure_data
+ext_data
+tmp
+env.json
+archives
+outputs/archive
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# ignore misc files
+~$*.docx
+~$*.xlsx
+~$*.pptx
+~$*.tmp
+Thumbs.db
+.DS_Store
diff --git a/R/example-script.R b/R/example-script.R
index ee7fb1a..93b45af 100644
--- a/R/example-script.R
+++ b/R/example-script.R
@@ -18,14 +18,25 @@ mel <- ISwR::melanom %>%
                          ulc == 2 ~ "absent"))
 
 # Run Pipeline --------------------------
-fit <- fit_cure(formula = Surv(days, status) ~ ulc + sex + thick_cat + thick + no,
+fit <- fit_cure(formula = Surv(days, status) ~ ulc + sex + thick_cat + thick ,
                 data = mel)
 
 cure_nomogram(fit, prediction_time = 300)
 
 cure_calibration(fit, prediction_time = 300)
 
-stability <- multiple_mod_runs(formula = Surv(days, status) ~ ulc + sex + thick_cat + thick + no,
-                data = mel)
 
-stability
+# Stability example----
+formula <- Surv(days, status) ~ ulc + sex
+x <- multiple_mod_runs(formula,
+                              nboot = 200,
+                              eps = 0.0001,
+                              num_repeats = 3,
+                              data = mel)
+x$model_results
+
+x$var_surv_stab
+x$p_surv_stab
+
+x$var_cure_stab
+x$p_cure_stab
diff --git a/R/model-fitting.R b/R/model-fitting.R
index 6cff063..316b3af 100644
--- a/R/model-fitting.R
+++ b/R/model-fitting.R
@@ -1,7 +1,6 @@
 # Functions to Run Cure Models (Once or Multiple Times) ------------------------
 # ------------------------------------------------------------------------------
 
-source(here::here("R", "clean-model-results.R"))
 
 # Single Model Run -------------------------------------------------------------
 # Wrapper function for smcure to accept multi-level variables and save necessary 
@@ -96,6 +95,8 @@ multiple_mod_runs <- function(formula,
                               num_repeats = 10, 
                               data = mel) {
 
+  source(here::here("R", "clean-model-results.R"))
+  
   # pull original variables from formula
   mf <- formula
   mf <- eval(mf, parent.frame())
@@ -235,28 +236,4 @@ multiple_mod_runs <- function(formula,
 }
 
 
-# Examples
-
-# data <- ISwR::melanom %>%
-#   mutate(status = case_when(status %in% c(1, 3) ~ 1, 
-#                             TRUE ~ 0)) %>%
-#   mutate(sex = case_when(sex == 2 ~ "male", 
-#                          sex == 1 ~ "female"),
-#          ulc = case_when(ulc == 1 ~ "present", 
-#                          ulc == 2 ~ "absent"))
-# 
-# formula <- Surv(days, status) ~ ulc + sex
-#   
-# x <- multiple_mod_runs(formula,
-#                               nboot = 200,
-#                               eps = 0.0001, 
-#                               num_repeats = 3, 
-#                               data = data)
-# x$model_results
-# 
-# x$var_surv_stab
-# x$p_surv_stab
-# 
-# x$var_cure_stab
-# x$p_cure_stab
   
\ No newline at end of file
diff --git a/README.Rmd b/README.Rmd
new file mode 100644
index 0000000..afe65a5
--- /dev/null
+++ b/README.Rmd
@@ -0,0 +1,80 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# Cure Model Pipeline
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of this package is to provide an easy way to build, evaluate and visualize mixture cure models ([link to paper draft](https://docs.google.com/document/d/1Lhom9H7Hxb8_C6d55Trs9JHSfJCn1i6yuu_xsDyYqZQ/edit?usp=sharing))
+
+
+## Available Functions
+
+- `fit_cure()` - wrapper for `smcure::smcure()` function that allows you to pass multilevel variables as factors directly (instead of first creating dummy codes). It also saves outputs necessary to create nomogram.
+- `nomogram()-` - accepts an object created by `fit_cure()` and creates graphical nomogram based on model fit
+- `cure_calibration()` - accepts an object created by `fit_cure()` and creates a calibration curve for uncured patients
+- `multiple_mod_runs()`- allows you to check stability of models but running them multiple times and viewing distributions of variables and p-values. 
+- Coming soon:
+  - k-index and C-index wrapper functions
+  - tidyr function to better clean/view coefficients from cure model
+
+## Example 
+
+```{r, eval = FALSE}
+library(smcure)
+library(ISwR)
+library(gtsummary)
+library(tidyverse)
+
+# Prepare Data --------------------------
+mel <- ISwR::melanom %>%
+  mutate(status = case_when(status %in% c(1, 3) ~ 1, 
+                            TRUE ~ 0)) %>%
+  mutate(thick_cat = 
+              case_when(thick <= 129 ~ "≤ 129", 
+                        thick <= 322 ~ "less equal 322", 
+                        thick > 322 ~ "greater 322")) %>%
+  mutate(thick_cat = fct_relevel(thick_cat, "≤ 129", "≤ 322")) %>%
+  mutate(sex = case_when(sex == 2 ~ "male", 
+                         sex == 1 ~ "female"),
+         ulc = case_when(ulc == 1 ~ "present", 
+                         ulc == 2 ~ "absent"))
+
+# Run Pipeline --------------------------
+fit <- fit_cure(formula = Surv(days, status) ~ ulc + sex + thick_cat + thick ,
+                data = mel)
+cure_nomogram(fit, prediction_time = 300)
+cure_calibration(fit, prediction_time = 300)
+
+
+# Check Stability ----
+formula <- Surv(days, status) ~ ulc + sex
+x <- multiple_mod_runs(formula,
+                              nboot = 200,
+                              eps = 0.0001,
+                              num_repeats = 3,
+                              data = mel)
+x$model_results
+
+x$var_surv_stab
+x$p_surv_stab
+
+x$var_cure_stab
+x$p_cure_stab
+
+```
+
+
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..103a200
--- /dev/null
+++ b/README.md
@@ -0,0 +1,74 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# Cure Model Pipeline
+
+<!-- badges: start -->
+
+<!-- badges: end -->
+
+The goal of this package is to provide an easy way to build, evaluate
+and visualize mixture cure models ([link to paper
+draft](https://docs.google.com/document/d/1Lhom9H7Hxb8_C6d55Trs9JHSfJCn1i6yuu_xsDyYqZQ/edit?usp=sharing))
+
+## Available Functions
+
+  - `fit_cure()` - wrapper for `smcure::smcure()` function that allows
+    you to pass multilevel variables as factors directly (instead of
+    first creating dummy codes). It also saves outputs necessary to
+    create nomogram.
+  - `nomogram()-` - accepts an object created by `fit_cure()` and
+    creates graphical nomogram based on model fit
+  - `cure_calibration()` - accepts an object created by `fit_cure()` and
+    creates a calibration curve for uncured patients
+  - `multiple_mod_runs()`- allows you to check stability of models but
+    running them multiple times and viewing distributions of variables
+    and p-values.
+  - Coming soon:
+      - k-index and C-index wrapper functions
+      - tidyr function to better clean/view coefficients from cure model
+
+## Example
+
+``` r
+library(smcure)
+library(ISwR)
+library(gtsummary)
+library(tidyverse)
+
+# Prepare Data --------------------------
+mel <- ISwR::melanom %>%
+  mutate(status = case_when(status %in% c(1, 3) ~ 1, 
+                            TRUE ~ 0)) %>%
+  mutate(thick_cat = 
+              case_when(thick <= 129 ~ "≤ 129", 
+                        thick <= 322 ~ "less equal 322", 
+                        thick > 322 ~ "greater 322")) %>%
+  mutate(thick_cat = fct_relevel(thick_cat, "≤ 129", "≤ 322")) %>%
+  mutate(sex = case_when(sex == 2 ~ "male", 
+                         sex == 1 ~ "female"),
+         ulc = case_when(ulc == 1 ~ "present", 
+                         ulc == 2 ~ "absent"))
+
+# Run Pipeline --------------------------
+fit <- fit_cure(formula = Surv(days, status) ~ ulc + sex + thick_cat + thick ,
+                data = mel)
+cure_nomogram(fit, prediction_time = 300)
+cure_calibration(fit, prediction_time = 300)
+
+
+# Check Stability ----
+formula <- Surv(days, status) ~ ulc + sex
+x <- multiple_mod_runs(formula,
+                              nboot = 200,
+                              eps = 0.0001,
+                              num_repeats = 3,
+                              data = mel)
+x$model_results
+
+x$var_surv_stab
+x$p_surv_stab
+
+x$var_cure_stab
+x$p_cure_stab
+```