replaced cat to message

ichcha-m · Oct 24, 2023 · 8429a1a · 8429a1a
1 parent bd95dc9
commit 8429a1a
Show file tree

Hide file tree

Showing 72 changed files with 110 additions and 116 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: cophescan
 Title: Adaptation of the Coloc Method for PheWAS
-Version: 1.3.1
+Version: 1.3.2
 Authors@R: c(person("Ichcha", "Manipur", role=c("aut","cre"),
     email = "[email protected]"),
     person("Chris", "Wallace", role=c("aut")))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+## cophescan 1.3.2
+
+-   Changed one instance of print() to message()
+
 ## cophescan 1.3.1
 
 -   Changed plotting functions where querytrait and query_trait_names are now required arguments instead of optional in `prepare_plot_data`, `get_beta`, `cophe_plot`, `cophe_heatmap`.

diff --git a/R/metrop_hier_priors.R b/R/metrop_hier_priors.R
@@ -10,7 +10,6 @@
 #' @param avg_pik default: FALSE, estimate the average of the pik
 #' @param avg_posterior default: FALSE, estimate the average of the posterior probabilities of the hypotheses
 #' @param pik default: FALSE, inferred prior probabilities
-#' @param cores default: 1, number of cores
 #' @param alpha_mean prior for the mean of  alpha
 #' @param alpha_sd prior for the standard deviation of  alpha
 #' @param beta_shape prior for the shape (gamma distibution) of beta
@@ -24,7 +23,7 @@
 #' @export
 run_metrop_priors <- function(multi.dat, covar=FALSE, covar_vec=NULL, is_covar_categorical=FALSE, nits=10000,
                               thin=1, posterior=FALSE, avg_pik=TRUE, avg_posterior=TRUE,
-                              pik=FALSE, cores=1, alpha_mean =-10,
+                              pik=FALSE, alpha_mean =-10,
                                alpha_sd=0.5,  beta_shape=2,  beta_scale=2,
                                gamma_shape=2,  gamma_scale=2){
   if (!is.data.frame(multi.dat)){
@@ -65,7 +64,7 @@ run_metrop_priors <- function(multi.dat, covar=FALSE, covar_vec=NULL, is_covar_c
 
   lbf_mat <- as.matrix(pp_df[, c('lBF.Ha', 'lBF.Hc')])
   nsnps <- as.vector(pp_df$nsnps)
-  cat(paste0('Running the cophescan hierarchical model... \nNumber of iterations: ', nits,'\nBurn-in: ', thin, '\nNumber of input QV/QT pairs: ', nrow(pp_df), '\nCovariate included: ', covar ))
+  message(paste0('Running the cophescan hierarchical model... \nNumber of iterations: ', nits,'\nBurn-in: ', thin, '\nNumber of input QV/QT pairs: ', nrow(pp_df), '\nCovariate included: ', covar ))
 
   ## Run hierarchical model
   res.metrop <- metrop_run(lbf_mat = lbf_mat, nsnps = nsnps,

diff --git a/README.md b/README.md
@@ -116,6 +116,6 @@ tail(res.hier.predict, row.names = F)
 
 ------------------------------------------------------------------------
 
-#### [**NEWS: cophescan 1.3.1**](https://ichcha-m.github.io/cophescan/news/index.html)
+#### [NEWS: cophescan 1.3.2](https://ichcha-m.github.io/cophescan/news/index.html)
 
 ------------------------------------------------------------------------
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/FixedPriors_03.html b/docs/articles/FixedPriors_03.html
diff --git a/docs/articles/HP-mcmcDiagnostics-1.png b/docs/articles/HP-mcmcDiagnostics-1.png
diff --git a/docs/articles/HP-unnamed-chunk-8-1.png b/docs/articles/HP-unnamed-chunk-8-1.png
diff --git a/docs/articles/HP-unnamed-chunk-8-2.png b/docs/articles/HP-unnamed-chunk-8-2.png
diff --git a/docs/articles/HP-unnamed-chunk-8-3.png b/docs/articles/HP-unnamed-chunk-8-3.png
diff --git a/docs/articles/HierarchicalPriors_04.html b/docs/articles/HierarchicalPriors_04.html
diff --git a/docs/articles/InputData_02.html b/docs/articles/InputData_02.html
diff --git a/docs/articles/IntroductionCoPheScan_01.html b/docs/articles/IntroductionCoPheScan_01.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -6,7 +6,7 @@ articles:
   HierarchicalPriors_04: HierarchicalPriors_04.html
   InputData_02: InputData_02.html
   IntroductionCoPheScan_01: IntroductionCoPheScan_01.html
-last_built: 2023-10-20T17:39Z
+last_built: 2023-10-24T10:16Z
 urls:
   reference: https://ichcha-m.github.io/cophescan/reference
   article: https://ichcha-m.github.io/cophescan/articles

diff --git a/docs/reference/Hc.cutoff.fdr.html b/docs/reference/Hc.cutoff.fdr.html
diff --git a/docs/reference/adjust_priors.html b/docs/reference/adjust_priors.html
diff --git a/docs/reference/average_piks.html b/docs/reference/average_piks.html
diff --git a/docs/reference/average_piks_list.html b/docs/reference/average_piks_list.html
-Original file line number
+Diff line change
@@ Expand Up / @@ -116,6 +116,6 @@ tail(res.hier.predict, row.names = F) @@
     ------------------------------------------------------------------------
-    #### [**NEWS: cophescan 1.3.1**](https://ichcha-m.github.io/cophescan/news/index.html)
+    #### [NEWS: cophescan 1.3.2](https://ichcha-m.github.io/cophescan/news/index.html)
     ------------------------------------------------------------------------