adding badges

Author: gvegayon

R/aphylo_mcmc.R

@@ -55,7 +55,7 @@ APHYLO_DEFAULT_MCMC_CONTROL <- list(
 #' set.seed(1231)
 #' 
 #' ans_mcmc <- aphylo_mcmc(
-#'   dat ~ mu_d + psi + eta + Pi,
+#'   atree ~ mu_d + psi + eta + Pi,
 #'   control = list(nsteps = 2e5, burnin=1000, thin=200)
 #' )
 #' }

R/prediction_score.R

@@ -90,10 +90,11 @@ prediction_score.default <- function(
     W <- W[ids, ids, drop=FALSE]
 
   # obs <- rowSums(x - expected)
-  obs <- NULL
-  for (p in 1:ncol(x))
-    obs <- cbind(obs, ifelse(expected == 1, 1 - x, x))
-  obs <- sum(obs)
+  # obs <- NULL
+  # for (p in 1:ncol(x))
+  #   obs <- cbind(obs, ifelse(expected == 1, 1 - x, x))
+  obs <- sum(abs(x - expected))
+  # obs <- sum(obs)
   # obs <- t(obs) %*% W %*% obs
 
   # Best case
@@ -228,14 +229,14 @@ prediction_score.aphylo_estimates <- function(
   n <- length(ids)
   if (is.null(alpha0) && loo) {
 
-    alpha0 <- max(sum(expected[ids,] == 0) - 1, 0)
-    alpha0 <- alpha0/(n - 1)
+    alpha0 <- max(sum(expected[ids,] == 0) - ncol(expected), 0)
+    alpha0 <- alpha0/((nrow(expected[ids,]) - 1) * ncol(expected))
 
   }
   if (is.null(alpha1) && loo) {
 
-    alpha1 <- max(sum(expected[ids,]) - 1, 0)
-    alpha1 <- alpha1/(n - 1)
+    alpha1 <- max(sum(expected[ids,]) - ncol(expected), 0)
+    alpha1 <- alpha1/((nrow(expected[ids,]) - 1) * ncol(expected))
 
   }
 

README.Rmd

@@ -5,10 +5,14 @@ output:
     html_preview: false
 ---
 
-[![](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
+<!--[![](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)-->
+
 [![R CI](https://github.com/USCbiostats/aphylo/actions/workflows/ci.yml/badge.svg)](https://github.com/USCbiostats/aphylo/actions/workflows/ci.yml)
 [![Build status](https://ci.appveyor.com/api/projects/status/1xpgpv10yifojyab?svg=true)](https://ci.appveyor.com/project/gvegayon/phylogenetic)
 [![Coverage Status](https://codecov.io/gh/USCbiostats/aphylo/branch/master/graph/badge.svg)](https://codecov.io/gh/USCbiostats/aphylo) [![Integrative Methods of Analysis for Genetic Epidemiology](https://raw.githubusercontent.com/USCbiostats/badges/master/tommy-image-badge.svg)](https://image.usc.edu)
+[![CRAN status](https://www.r-pkg.org/badges/version/aphylo)](https://CRAN.R-project.org/package=aphylo)
+[![status](https://tinyverse.netlify.com/badge/fmcmc)](https://CRAN.R-project.org/package=fmcmc)
+[![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/aphylo)](https://cran.r-project.org/package=aphylo)
 
 # aphylo: Statistical Inference of Annotated Phylogenetic Trees <img src="man/figures/logo.svg" align="right" width="180px"/>
 

README.md

@@ -1,5 +1,6 @@
 
-[![](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
+<!--[![](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)-->
+
 [![R
 CI](https://github.com/USCbiostats/aphylo/actions/workflows/ci.yml/badge.svg)](https://github.com/USCbiostats/aphylo/actions/workflows/ci.yml)
 [![Build
@@ -8,6 +9,11 @@ status](https://ci.appveyor.com/api/projects/status/1xpgpv10yifojyab?svg=true)](
 Status](https://codecov.io/gh/USCbiostats/aphylo/branch/master/graph/badge.svg)](https://codecov.io/gh/USCbiostats/aphylo)
 [![Integrative Methods of Analysis for Genetic
 Epidemiology](https://raw.githubusercontent.com/USCbiostats/badges/master/tommy-image-badge.svg)](https://image.usc.edu)
+[![CRAN
+status](https://www.r-pkg.org/badges/version/aphylo)](https://CRAN.R-project.org/package=aphylo)
+[![status](https://tinyverse.netlify.com/badge/fmcmc)](https://CRAN.R-project.org/package=fmcmc)
+[![CRAN
+downloads](http://cranlogs.r-pkg.org/badges/grand-total/aphylo)](https://cran.r-project.org/package=aphylo)
 
 # aphylo: Statistical Inference of Annotated Phylogenetic Trees <img src="man/figures/logo.svg" align="right" width="180px"/>
 
@@ -35,24 +41,26 @@ Southern California.
 citation(package="aphylo")
 ```
 
+``` 
 
-    To cite aphylo in publications use the following paper:
+To cite aphylo in publications use the following paper:
 
-      Vega Yon GG, Thomas DC, Morrison J, Mi H, Thomas PD, et al. (2021)
-      Bayesian parameter estimation for automatic annotation of gene
-      functions using observational data and phylogenetic trees. PLOS
-      Computational Biology 17(2): e1007948.
-      https://doi.org/10.1371/journal.pcbi.1007948
+  Vega Yon GG, Thomas DC, Morrison J, Mi H, Thomas PD, et al. (2021)
+  Bayesian parameter estimation for automatic annotation of gene
+  functions using observational data and phylogenetic trees. PLOS
+  Computational Biology 17(2): e1007948.
+  https://doi.org/10.1371/journal.pcbi.1007948
 
-    And the actual R package:
+And the actual R package:
 
-    Vega Yon G (2022). _Statistical Inference of Annotated Phylogenetic
-    Trees_. R package version 0.2-1, <URL:
-    https://github.com/USCBiostats/aphylo>.
+Vega Yon G (2022). _Statistical Inference of Annotated Phylogenetic
+Trees_. R package version 0.2-1, <URL:
+https://github.com/USCBiostats/aphylo>.
 
-    To see these entries in BibTeX format, use 'print(<citation>,
-    bibtex=TRUE)', 'toBibtex(.)', or set
-    'options(citation.bibtex.max=999)'.
+To see these entries in BibTeX format, use 'print(<citation>,
+bibtex=TRUE)', 'toBibtex(.)', or set
+'options(citation.bibtex.max=999)'.
+```
 
 ## Install
 
@@ -320,10 +328,10 @@ pred
     ## Prediction score (H0: Observed = Random)
     ## 
     ##  N obs.      : 99
-    ##  alpha(0, 1) : 0.24, 0.73
-    ##  Observed    : 0.71 
-    ##  Random      : 0.61 
-    ##  P(<t)       : 0.1539
+    ## 
+    ##  Observed    : 0.71 ***
+    ##  Random      : NA 
+    ##  P(<t)       : 0.0000
     ## --------------------------------------------------------------------------------
     ## Values scaled to range between 0 and 1, 1 being best.
     ##