PS model working?

implementing parsurv methods Update parsurvival.jl Update parsurvival.jl Update parsurvival.jl Update parsurvival.jl update for chi2 test tweaks for parsurv Update parsurvival.jl
alexpkeil1 · Sep 19, 2023 · 8d83af1 · 8d83af1
1 parent 2ffb60f
commit 8d83af1
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Showing 5 changed files with 401 additions and 39 deletions.
diff --git a/Project.toml b/Project.toml
@@ -15,9 +15,10 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsModels = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
-Documenter = "0.20 - 0.30"
+Documenter = "0.20 - 0.30,1"
 RecipesBase = "^1"
 Reexport = "^1"
 StatsBase = "^0.34"

diff --git a/src/LSurvival.jl b/src/LSurvival.jl
@@ -5,6 +5,7 @@ using RecipesBase
 using Reexport
 using Printf
 using Random, LinearAlgebra, Tables
+using Zygote
 #using Distributions
 #import Distributions: Chisq, Normal
 import SpecialFunctions: gamma_inc, erfinv, erf
@@ -75,6 +76,7 @@ export AbstractPH,
 export kaplan_meier,        # interface for estimating cumulative risk from non-parametric estimator
     aalen_johansen,        # interface for estimating cumulative risk from non-parametric competing risk estimator
     coxph,                 # interface for Cox model
+    survreg,                 # interface for parametric survival model
     risk_from_coxphmodels,  # interface for estimating cumulative risk from hazard specific Cox models
     # deprecated
     coxmodel,            # (deprecated) interface for Cox model
@@ -170,6 +172,7 @@ abstract type AbstractSurvDist end
 include("shared_structs.jl")
 include("distributions.jl")
 include("coxmodel.jl")
+include("parsurvival.jl")
 include("residuals.jl")
 include("npsurvival.jl")
 include("data_generators.jl")

diff --git a/src/examples.jl b/src/examples.jl
@@ -874,11 +874,11 @@ jres.RL[2]
 ###################################################################
 # checking parametric survival against R
 ###################################################################
-
+using RCall
 @rput dat1
 R"""
 library(survival)
 res = survreg(Surv(time , status) ~ x,data = dat1, dist="weibull")
-summary(res)
+ret = summary(res)
 """
-@rget res
+@rget ret