Fixing slow examples

Author: gumeo

.Rbuildignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^README.Rmd
+^cran-comments\.md$

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: gnonadd
 Type: Package
 Title: Various Non-Additive Models for Genetic Associations
-Version: 1.0.0
+Version: 1.0.1
 Authors@R: c(
      person("Audunn S.", "Snaebjarnarson", , "audunn.snaebjarnarson@decode.is", role = c("aut", "cre")),
      person("Gudmundur", "Einarsson", , "gudmundur.einarsson2@decode.is", role = c("aut")),
      person("Daniel F.", "Gudbjartsson", , "daniel.gudbjartsson@decode.is", role = c("aut"))
      )
 Description: The goal of gnonadd is to simplify workflows in the analysis of non-additive effects of 
     sequence variants. This includes variance effects, correlation effects, interaction 
-    effects and dominance effects.
+    effects and dominance effects. The package also includes convenience functions for visualization.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

R/Env_interaction_CaseControl_all_vs_all.R

@@ -18,16 +18,17 @@
 #' @returns
 #' A dataframe with all possible variant-environmental pairs and their estimated interaction effect
 #' @examples
-#' g_vec <- matrix(0, nrow = 100000, ncol = 3)
+#' N_run <- 50000
+#' g_vec <- matrix(0, nrow = N_run, ncol = 3)
 #' freqs <- runif(ncol(g_vec), min = 0, max = 1)
-#' env_vec <- matrix(0, nrow = 100000, ncol = 3)
+#' env_vec <- matrix(0, nrow = N_run, ncol = 3)
 #' for(i in 1:ncol(g_vec)){
-#'  g_vec[, i] <- rbinom(100000, 2, freqs[i])
+#'  g_vec[, i] <- rbinom(N_run, 2, freqs[i])
 #' }
 #' for( i in 1:ncol(env_vec)){
-#'  env_vec[, i] <- round(runif(100000,min=0,max=6))
+#'  env_vec[, i] <- round(runif(N_run,min=0,max=6))
 #' }
-#' cc_vec <- rbinom(100000,1,0.1 * (1.05 ^ g_vec[, 1]) *
+#' cc_vec <- rbinom(N_run,1,0.1 * (1.05 ^ g_vec[, 1]) *
 #'           (1.06 ^ env_vec[,1]) * (0.95 ^ g_vec[, 2]) *
 #'           (1.1^(g_vec[, 1] * env_vec[, 1])))
 #' res <- pairwise_env_int_CC.calc(cc_vec, g_vec, env_vec)

R/Interactions_CaseControl_all_vs_all.R

@@ -15,12 +15,13 @@
 #' @returns
 #' A dataframe with all possible variant pairs and their estimated interaction effect
 #' @examples
-#' g_vec <- matrix(0, nrow = 100000, ncol = 5)
+#' N_run <- 50000
+#' g_vec <- matrix(0, nrow = N_run, ncol = 5)
 #' freqs <- runif(ncol(g_vec), min = 0,max = 1)
 #' for(i in 1:ncol(g_vec)){
-#'  g_vec[, i] <- rbinom(100000, 2, freqs[i])
+#'  g_vec[, i] <- rbinom(N_run, 2, freqs[i])
 #' }
-#' cc_vec <- rbinom(100000,1,0.1 * (1.05 ^ g_vec[, 1]) *
+#' cc_vec <- rbinom(N_run,1,0.1 * (1.05 ^ g_vec[, 1]) *
 #'           (1.06 ^ g_vec[,2]) * (0.95 ^ g_vec[, 3]) *
 #'           (1.5^(g_vec[,1] * g_vec[,2])))
 #' res <- pairwise_int_CC.calc(cc_vec, g_vec)

README.Rmd

@@ -53,9 +53,15 @@ A more detailed description will be added with further development.
 
 ## Installation
 
-You can install the package via the `remotes` package:
+You can install the latest version of the package via the `remotes` package:
 
 ```{r, eval = FALSE}
 # Use remotes:
 remotes::install_github("DecodeGenetics/gnonadd")
 ```
+
+When the package is on CRAN, you should be able to install it with:
+
+```{r, eval = FALSE}
+install.packages("gnonadd")
+```

README.md

@@ -46,9 +46,16 @@ A more detailed description will be added with further development.
 
 ## Installation
 
-You can install the package via the `remotes` package:
+You can install the latest version of the package via the `remotes`
+package:
 
 ``` r
 # Use remotes:
 remotes::install_github("DecodeGenetics/gnonadd")
 ```
+
+When the package is on CRAN, you should be able to install it with:
+
+``` r
+install.packages("gnonadd")
+```

cran-comments.md

@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release. Gudmundur Einarsson has published two packages to CRAN.