add cox ph example

uvastatlab · May 31, 2024 · be7ab43 · be7ab43
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diff --git a/data/leuk.rds b/data/leuk.rds
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diff --git a/docs/data/leuk.rds b/docs/data/leuk.rds
diff --git a/docs/lm.html b/docs/lm.html
@@ -958,7 +958,7 @@ <h3>Linear model with time ordered data</h3>
 <pre class="r"><code>library(car)
 durbinWatsonTest(m)</code></pre>
 <pre><code> lag Autocorrelation D-W Statistic p-value
-   1     -0.05006007      2.079992   0.904
+   1     -0.05006007      2.079992    0.93
  Alternative hypothesis: rho != 0</code></pre>
 <p>Based on our residual versus time plot and the result of the
 Durbin-Watson test, we decide to assume our residual errors are

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diff --git a/docs/refs.bib b/docs/refs.bib
@@ -22,6 +22,14 @@ @book{hosmer2008
  year = 2008
 }
 
+@book{kleinbaum,
+ author = "David G. Kleinbaum, Mitchel Klein",
+ title = "Survival Analysis, a Self-Learning Text, Second Edition",
+ publisher = "Springer",
+ year = 2005
+}
+
+
 @book{bilder2015,
  author = "Christopher R. Bilder and Thomas M. Loughin",
  title = "Analysis of Categorical Data in {R}",
@@ -315,4 +323,36 @@ @Manual{topmodels
     year = {2024},
     note = {R package version 0.3-0/r1791},
     url = {https://R-Forge.R-project.org/projects/topmodels/},
-  }
+  }
+  
+@Manual{survival-package,
+    title = {A Package for Survival Analysis in R},
+    author = {Terry M Therneau},
+    year = {2024},
+    note = {R package version 3.5-8},
+    url = {https://CRAN.R-project.org/package=survival},
+  }
+
+@Manual{survminer,
+    title = {survminer: Drawing Survival Curves using 'ggplot2'},
+    author = {Alboukadel Kassambara and Marcin Kosinski and Przemyslaw Biecek},
+    year = {2021},
+    note = {R package version 0.4.9},
+    url = {https://CRAN.R-project.org/package=survminer},
+  }
+  
+@article{blood,
+    author = {ACUTE LEUKEMIA GROUP B and FREIREICH, EMIL J and GEHAN, EDMUND and FREI, EMIL, III and SCHROEDER, LESLIE R. and WOLMAN, IRVING J. and ANBARI, RACHAD and BURGERT, E. OMAR and MILLS, STEPHEN D. and PINKEL, DONALD and SELAWRY, OLEG S. and MOON, JOHN H. and GENDEL, B. R. and SPURR, CHARLES L. and STORRS, ROBERT and HAURANI, FARID and HOOGSTRATEN, BARTH and LEE, STANLEY},
+    title = "{The Effect of 6-Mercaptopurine on the Duration of Steroid-induced Remissions in Acute Leukemia: A Model for Evaluation of Other Potentially Useful Therapy}",
+    journal = {Blood},
+    volume = {21},
+    number = {6},
+    pages = {699-716},
+    year = {1963},
+    month = {06},
+    abstract = "{The effect of 6-MP therapy on the duration of remissions induced by adrenal corticosteroids has been studied as a model for testing of new agents. Ninetytwo patients under age 20 entered the study and were accepted for analysis. Sixty-two (67 per cent) had complete or partial remissions induced by corticosteroids. Patients in remission were randomly assigned to maintenance therapy with either 6-MP or placebo. The median duration of 6-MP-maintained complete remissions was 33 weeks and for placebo, 9 weeks. A sequential experimental design was used to analyze remission times while the study was in progress. This resulted in the study being stopped after analysis of the remission times of 21 pairs of patients (42 patients). Overall survival was not significantly different for the two treatment programs, since patients maintained on placebo were treated with 6-MP when relapse occurred.The activity of the known active antileukemic compound 6-MP was readily detected by this experimental design without compromise of optimal survival. Such a design should prove useful for the evaluation of new agents and also permit study of the remission maintenance activity of a compound separately from its remission inducing activity.}",
+    issn = {0006-4971},
+    doi = {10.1182/blood.V21.6.699.699},
+    url = {https://doi.org/10.1182/blood.V21.6.699.699},
+    eprint = {https://ashpublications.org/blood/article-pdf/21/6/699/571437/699.pdf},
+}
diff --git a/docs/survival.html b/docs/survival.html
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diff --git a/refs.bib b/refs.bib
@@ -22,6 +22,14 @@ @book{hosmer2008
  year = 2008
 }
 
+@book{kleinbaum,
+ author = "David G. Kleinbaum, Mitchel Klein",
+ title = "Survival Analysis, a Self-Learning Text, Second Edition",
+ publisher = "Springer",
+ year = 2005
+}
+
+
 @book{bilder2015,
  author = "Christopher R. Bilder and Thomas M. Loughin",
  title = "Analysis of Categorical Data in {R}",
@@ -315,4 +323,36 @@ @Manual{topmodels
     year = {2024},
     note = {R package version 0.3-0/r1791},
     url = {https://R-Forge.R-project.org/projects/topmodels/},
-  }
+  }
+  
+@Manual{survival-package,
+    title = {A Package for Survival Analysis in R},
+    author = {Terry M Therneau},
+    year = {2024},
+    note = {R package version 3.5-8},
+    url = {https://CRAN.R-project.org/package=survival},
+  }
+
+@Manual{survminer,
+    title = {survminer: Drawing Survival Curves using 'ggplot2'},
+    author = {Alboukadel Kassambara and Marcin Kosinski and Przemyslaw Biecek},
+    year = {2021},
+    note = {R package version 0.4.9},
+    url = {https://CRAN.R-project.org/package=survminer},
+  }
+  
+@article{blood,
+    author = {ACUTE LEUKEMIA GROUP B and FREIREICH, EMIL J and GEHAN, EDMUND and FREI, EMIL, III and SCHROEDER, LESLIE R. and WOLMAN, IRVING J. and ANBARI, RACHAD and BURGERT, E. OMAR and MILLS, STEPHEN D. and PINKEL, DONALD and SELAWRY, OLEG S. and MOON, JOHN H. and GENDEL, B. R. and SPURR, CHARLES L. and STORRS, ROBERT and HAURANI, FARID and HOOGSTRATEN, BARTH and LEE, STANLEY},
+    title = "{The Effect of 6-Mercaptopurine on the Duration of Steroid-induced Remissions in Acute Leukemia: A Model for Evaluation of Other Potentially Useful Therapy}",
+    journal = {Blood},
+    volume = {21},
+    number = {6},
+    pages = {699-716},
+    year = {1963},
+    month = {06},
+    abstract = "{The effect of 6-MP therapy on the duration of remissions induced by adrenal corticosteroids has been studied as a model for testing of new agents. Ninetytwo patients under age 20 entered the study and were accepted for analysis. Sixty-two (67 per cent) had complete or partial remissions induced by corticosteroids. Patients in remission were randomly assigned to maintenance therapy with either 6-MP or placebo. The median duration of 6-MP-maintained complete remissions was 33 weeks and for placebo, 9 weeks. A sequential experimental design was used to analyze remission times while the study was in progress. This resulted in the study being stopped after analysis of the remission times of 21 pairs of patients (42 patients). Overall survival was not significantly different for the two treatment programs, since patients maintained on placebo were treated with 6-MP when relapse occurred.The activity of the known active antileukemic compound 6-MP was readily detected by this experimental design without compromise of optimal survival. Such a design should prove useful for the evaluation of new agents and also permit study of the remission maintenance activity of a compound separately from its remission inducing activity.}",
+    issn = {0006-4971},
+    doi = {10.1182/blood.V21.6.699.699},
+    url = {https://doi.org/10.1182/blood.V21.6.699.699},
+    eprint = {https://ashpublications.org/blood/article-pdf/21/6/699/571437/699.pdf},
+}