update vigngette

Author: zhizuio

NEWS.md

@@ -1,52 +1,51 @@
 <div style="text-align: left;">
 
-## GPTCM 1.1.3 (2025-10-01) (GitHub Only)
+### GPTCM 1.1.3 (2025-10-31)
 
 * TODO: update results in vignette
 
 * Remove redundant variables `logPosteriorZeta` and `logPosteriorBeta` in cpp files
 * Remove partial likelihood `loglikelihood0()`, and always use joint likelihood
+* Remove useless func `arms_simple()`
 * Pass more references and using more `const` keyword in functions
 * Update `simData()` by changing xi0 to simulate survival data with censoring rate 0.2
-* Remove `arms_simple`
 * Use `openmp` to parallelize some for-loop
+* Update vignette
 
 * TODO: decide whether keep `kappaIGamma=TRUE` or not
-* TODO: remove redundant arguments "tauSq" and "wSq" after bringing them out of ARMS files
-* TODO: bug for posterior pi_{jl}
 
-## GPTCM 1.1.2 (2025-09-26)
+### GPTCM 1.1.2 (2025-09-26)
 
 * Update simulation examples in vignette due to the change of `mvnfast::rmvn()`
 * Convert line endings in `configure.ac` to LF
 * Improve help documentation
 * Update function `simData()` for any number of clusters 
 * Simplify `BVS.cpp`
 
-## GPTCM 1.1.1 (2025-09-16)
+### GPTCM 1.1.1 (2025-09-16)
 
 * Fix a warning about fallback compilation with Armadillo 14.6.3 from CRAN check on machine `r-devel-linux-x86_64-debian-gcc`
 * Fix issues raised from CRAN reviewer
 * Change `MASS::mvrnorm()` to `mvnfast::rmvn()`
 
-## GPTCM 1.1.0 (2025-09-07) (GitHub Only)
+### GPTCM 1.1.0 (2025-09-07) (GitHub Only)
 
 * First CRAN version
 * Add vignette
 
-## GPTCM 1.0.3 (2025-09-05) (GitHub Only)
+### GPTCM 1.0.3 (2025-09-05) (GitHub Only)
 
 * Fix NOTE about `elapsed time` from Winbuilder checks 
 
-## GPTCM 1.0.2 (2025-09-05) (GitHub Only)
+### GPTCM 1.0.2 (2025-09-05) (GitHub Only)
 
 * Improve help files
 
-## GPTCM 1.0.1 (2025-08-28) (GitHub Only)
+### GPTCM 1.0.1 (2025-08-28) (GitHub Only)
 
 * In `simData()`, suppress intercept when simulating data based on the Cox model
 
-## GPTCM 1.0.0 (2025-08-25) (GitHub Only)
+### GPTCM 1.0.0 (2025-08-25) (GitHub Only)
 
 * First released version at `ocbe-uio` github
 

README.md

@@ -50,7 +50,7 @@ n <- 200 # subjects
 p <- 10 # variable selection predictors
 L <- 3 # cell types
 library(GPTCM)
-set.seed(123)
+set.seed(1234)
 dat <- simData(n, p, L)
 
 # KM curve

man/figures/cran_betas.png

@@ -50,12 +50,11 @@ See more details in [Zhao et al. (2025)](https://doi.org/10.48550/arXiv.2509.010
 rm(list = ls())
 
 # simulate data
-set.seed(123)
 n <- 200 # subjects
 p <- 10 # variable selection predictors
 L <- 3 # cell types
 library(GPTCM)
-set.seed(123)
+set.seed(1234)
 dat <- simData(n, p, L)
 
 # KM curve