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Add semi parametric survival analysis (Cox proportional hazards) #5

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merged 24 commits into from
Oct 28, 2024
Merged

Add semi parametric survival analysis (Cox proportional hazards) #5

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bbebf02
add parameter name recoding
FBartos Apr 14, 2024
96a4f73
add basics of semiparametric model
FBartos Sep 5, 2024
61f2b94
update plot menu
FBartos Sep 24, 2024
8f66de0
improve plot
FBartos Sep 30, 2024
f068b01
fix survival plot
FBartos Oct 2, 2024
47e0e0c
fix scaling
FBartos Oct 2, 2024
6130ced
fix plot fill
FBartos Oct 2, 2024
a592252
extend semiparametric
FBartos Oct 2, 2024
a86da56
add diagnostics
FBartos Oct 3, 2024
0e519ef
add residuals and frailties
FBartos Oct 4, 2024
22ab5bd
add frailty handling vol1
FBartos Oct 7, 2024
bc9efad
finish semi-parametric
FBartos Oct 8, 2024
6f61dc1
improve interface
FBartos Oct 10, 2024
199472f
Apply suggestions from code review
FBartos Oct 14, 2024
abbe6e0
Change data-loading and add informative message for frailty waitting
FBartos Oct 21, 2024
f7cd216
disable `cluster` when `exact` method is selected
FBartos Oct 21, 2024
eb1d793
"plotConfidenceInterval" -> "plotCi"
FBartos Oct 21, 2024
9ac82bd
Non-parametric: factors -> strata for consistency
FBartos Oct 21, 2024
0cdbed0
enable `ColorPalette` and `Legend` only when strata is selected
FBartos Oct 21, 2024
557159c
fix ready function
FBartos Oct 21, 2024
4c82b0e
fix residual plots
FBartos Oct 21, 2024
969fb50
Set preferredHeight for variablesForm
boutinb Oct 21, 2024
c177450
fix issues from the review
FBartos Oct 23, 2024
5793f9f
add documentation
FBartos Oct 23, 2024
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2 changes: 2 additions & 0 deletions .Rbuildignore
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@@ -1,3 +1,5 @@
^renv$
^renv\.lock$
^.*\.Rproj$
^\.Rproj\.user$
^\.travis\.yml$
2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -58,3 +58,5 @@ Thumbs.db
# RStudio files
.Rproj.user
_processedLockFile.lock
renv/activate.R
.Rprofile
5 changes: 3 additions & 2 deletions DESCRIPTION
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Expand Up @@ -9,9 +9,10 @@ Maintainer: JASP Team <[email protected]>
Description: Perform analyses of censored time to event data.
License: GPL (>= 2)
Encoding: UTF-8
Depends:
survival
Imports:
survival,
survminer,
ggsurvfit,
jaspBase,
jaspGraphs
Suggests:
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1 change: 1 addition & 0 deletions NAMESPACE
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@@ -1,4 +1,5 @@
import(jaspBase)
import(survival)
export(NonParametricSurvivalAnalysis)
export(SemiParametricSurvivalAnalysis)
export(ParametricSurvivalAnalysis)
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