Merge pull request #268 from NBISweden/olga-survival

Initiate survival session

session-survival/.Rprofile

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+source("renv/activate.R")

session-survival/.gitignore

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+/.quarto/
+renv/

session-survival/_quarto.yml

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+project:
+  type: book
+  output-dir: docs
+
+book:
+  title: "Survival Analysis"
+  author: "Olga Dethlefsen"
+  # date: "8/31/2022"
+  chapters:
+    - index.qmd
+    - intro.qmd
+    - regression.qmd
+    - lab.qmd
+    - references.qmd
+
+bibliography: references.bib
+
+format:
+  html:
+    theme: spacebar
+    code-fold: true
+    mermaid:
+      theme: forest
+
+
+
+
+

session-survival/data/data_cancer_brain.tsv

@@ -0,0 +1,89 @@
+sex	diagnosis	loc	ki	gtv	stereo	status	time
+Female	Meningioma	Infratentorial	90	6.11	SRS	0	57.64
+Male	HG glioma	Supratentorial	90	19.35	SRT	1	8.98
+Female	Meningioma	Infratentorial	70	7.95	SRS	0	26.46
+Female	LG glioma	Supratentorial	80	7.61	SRT	1	47.8
+Male	HG glioma	Supratentorial	90	5.06	SRT	1	6.3
+Female	Meningioma	Supratentorial	80	4.82	SRS	0	52.75
+Male	Meningioma	Supratentorial	80	3.19	SRT	0	55.8
+Male	LG glioma	Supratentorial	80	12.37	SRT	0	42.1
+Female	Meningioma	Supratentorial	70	12.16	SRT	0	34.66
+Male	HG glioma	Supratentorial	100	2.53	SRT	0	11.48
+Male	LG glioma	Supratentorial	80	0.14	SRT	1	35.93
+Female	Meningioma	Infratentorial	90	6.54	SRS	0	34.26
+Female	Meningioma	Infratentorial	90	0.63	SRS	0	32.98
+Male	NA	Supratentorial	90	6.38	SRT	0	50.85
+Female	Meningioma	Supratentorial	60	9.18	SRT	0	41.44
+Female	HG glioma	Supratentorial	70	11.38	SRS	1	7.05
+Female	Other	Infratentorial	60	24	SRT	1	6.82
+Male	HG glioma	Supratentorial	90	10.8	SRT	0	82.56
+Male	Meningioma	Supratentorial	80	13.49	SRS	1	6.92
+Female	Meningioma	Supratentorial	90	2.5	SRT	0	30.16
+Female	Meningioma	Supratentorial	80	2.82	SRS	0	24.39
+Male	HG glioma	Supratentorial	70	14.44	SRT	1	14
+Female	Other	Infratentorial	80	2.11	SRS	0	10.49
+Female	Meningioma	Infratentorial	100	2.13	SRS	1	51.02
+Female	Meningioma	Supratentorial	70	6.48	SRT	1	33.41
+Male	LG glioma	Supratentorial	90	4.23	SRT	1	25.02
+Male	Other	Supratentorial	60	34.64	SRT	1	11.57
+Male	HG glioma	Supratentorial	70	33.69	SRT	1	0.07
+Male	Meningioma	Supratentorial	60	3.81	SRT	0	36.1
+Female	Meningioma	Supratentorial	90	4.72	SRS	0	65.02
+Female	LG glioma	Supratentorial	80	0.85	SRS	1	6.1
+Male	Meningioma	Supratentorial	90	2.56	SRS	0	44.39
+Female	Other	Infratentorial	70	13.45	SRT	1	10.82
+Male	Other	Infratentorial	80	6.81	SRS	0	57.11
+Female	Meningioma	Supratentorial	90	7.3	SRT	0	5.51
+Female	Other	Supratentorial	70	14.26	SRT	0	7.18
+Female	Meningioma	Supratentorial	80	6.6	SRT	0	14.75
+Male	HG glioma	Supratentorial	90	9.95	SRT	1	6.23
+Male	Other	Infratentorial	80	12.51	SRT	1	29.7
+Female	Meningioma	Supratentorial	90	2.54	SRT	0	45.74
+Female	Meningioma	Supratentorial	80	1.57	SRT	0	2.03
+Male	HG glioma	Supratentorial	90	0.28	SRT	1	16.43
+Female	Meningioma	Supratentorial	70	6.7	SRT	0	14.56
+Male	Meningioma	Supratentorial	80	12.63	SRT	1	4.16
+Male	Other	Infratentorial	90	3.12	SRT	0	18.95
+Male	Meningioma	Supratentorial	60	7.09	SRS	1	31.25
+Male	HG glioma	Supratentorial	80	29.27	SRT	0	5.15
+Female	Meningioma	Supratentorial	80	26.31	SRT	1	39.54
+Male	Meningioma	Supratentorial	70	0.97	SRT	1	1.41
+Female	LG glioma	Supratentorial	80	0.19	SRS	0	11.51
+Female	HG glioma	Supratentorial	90	0.04	SRT	0	31.67
+Female	Meningioma	Infratentorial	90	9.24	SRT	0	26.85
+Male	HG glioma	Supratentorial	90	2.5	SRT	1	9.77
+Male	Meningioma	Infratentorial	80	24.41	SRT	0	39.54
+Female	HG glioma	Supratentorial	80	0.63	SRT	1	16.92
+Male	Other	Infratentorial	90	0.48	SRS	0	54.43
+Male	HG glioma	Infratentorial	80	0.22	SRS	0	33.67
+Male	HG glioma	Supratentorial	80	3.75	SRT	1	19.9
+Female	Other	Supratentorial	80	11.83	SRT	1	22.03
+Female	Meningioma	Supratentorial	90	2.47	SRT	0	17.57
+Female	HG glioma	Supratentorial	80	12.08	SRT	1	7.25
+Male	Meningioma	Supratentorial	80	11.51	SRT	1	14.62
+Female	HG glioma	Supratentorial	40	22.87	SRT	1	3.38
+Male	Meningioma	Supratentorial	80	4.77	SRT	0	67.38
+Male	LG glioma	Supratentorial	80	9.58	SRT	0	78.75
+Female	Meningioma	Supratentorial	100	4	SRT	0	52.23
+Female	HG glioma	Supratentorial	80	7.59	SRT	1	4.56
+Male	Other	Infratentorial	70	0.01	SRS	0	23.67
+Female	Meningioma	Supratentorial	80	6.93	SRS	0	10.1
+Female	Meningioma	Supratentorial	70	3.63	SRT	0	32.82
+Male	Meningioma	Supratentorial	70	8.45	SRT	0	19.41
+Male	Meningioma	Supratentorial	80	20.93	SRT	1	31.15
+Male	LG glioma	Supratentorial	90	2.64	SRT	0	20.13
+Female	HG glioma	Supratentorial	80	0.19	SRT	1	11.02
+Male	Other	Supratentorial	100	24.91	SRT	0	19.74
+Female	Meningioma	Supratentorial	80	31.74	SRT	0	57.25
+Female	Meningioma	Supratentorial	80	2.39	SRS	0	73.74
+Female	Meningioma	Supratentorial	90	7.26	SRT	0	49.05
+Female	Meningioma	Supratentorial	100	9.66	SRT	0	39.25
+Female	Meningioma	Infratentorial	70	2.94	SRS	0	1.54
+Female	HG glioma	Supratentorial	80	15.45	SRT	1	46.16
+Female	Other	Supratentorial	90	1.82	SRT	0	47.11
+Male	LG glioma	Infratentorial	90	30.41	SRT	0	1.18
+Male	HG glioma	Supratentorial	80	0.16	SRT	1	20.69
+Male	HG glioma	Supratentorial	80	19.81	SRT	1	6.39
+Male	Meningioma	Supratentorial	90	2.5	SRT	0	32.82
+Male	Meningioma	Supratentorial	90	2.02	SRS	0	42.07
+Male	Other	Infratentorial	80	0.11	SRT	0	13.9