fixed Codemeta json and updated README.Rmd (and .md)

fboehm · Jun 29, 2020 · ec97df0 · ec97df0
1 parent ff81a97
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -45,8 +45,6 @@ LinkingTo:
     Rcpp,
     testthat,
     RcppEigen
-VignetteBuilder:
-    knitr
 Encoding: UTF-8
 Language: en-US 
 LazyData: true

diff --git a/README.Rmd b/README.Rmd
@@ -19,7 +19,9 @@ knitr::opts_chunk$set(
 
 # qtl2pleio
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fboehm/qtl2pleio/master?urlpath=rstudio)
+[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/qtl2pleio)](https://cran.r-project.org/package=qtl2pleio)
+
+[![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fboehm/qtl2pleio/master?urlpath=rstudio)
 [![Travis-CI Build Status](https://travis-ci.org/fboehm/qtl2pleio.svg?branch=master)](https://travis-ci.org/fboehm/qtl2pleio)
 [![Coverage Status](https://img.shields.io/codecov/c/github/fboehm/qtl2pleio/master.svg)](https://codecov.io/github/fboehm/qtl2pleio?branch=master)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
@@ -41,7 +43,7 @@ We eagerly welcome contributions to `qtl2pleio`. All pull requests will be consi
 
 ## Technical support 
 
-For technical support, please open a Github issue. If you're just getting started with `qtl2pleio`, please examine the vignettes. You can also email <[email protected]> for assistance. 
+For technical support, please open a Github issue. If you're just getting started with `qtl2pleio`, please examine the [vignettes](https://fboehm.us/software/qtl2pleio) on the [package's web site](https://fboehm.us/software/qtl2pleio). You can also email <[email protected]> for assistance. 
 
 
 
@@ -68,15 +70,14 @@ To install qtl2pleio, use `install_github()` from the
 
 
 ```{r install-qtl2pleio, eval = FALSE}
-install.packages("devtools")
-devtools::install_github("fboehm/qtl2pleio")
+install.packages("qtl2pleio")
 ```
 
 You may also wish to install the [R/qtl2](https://kbroman.org/qtl2). We
 will use it below.
 
 ```{r install-qtl2, eval = TRUE}
-install.packages("qtl2", repos="http://rqtl.org/qtl2cran")
+install.packages("qtl2")
 ```
 
 
@@ -170,8 +171,9 @@ X <- gemma2::stagger_mats(pp[ , , 50], pp[ , , 50])
 B <- matrix(data = c(-1, -1, -1, -1, 1, 1, 1, 1, -1, -1, -1, -1, 1, 1, 1, 1), nrow = 8, ncol = 2, byrow = FALSE)
 # set.seed to ensure reproducibility
 set.seed(2018-01-30)
+Sig <- calc_Sigma(Vg = diag(2), Ve = diag(2), kinship = kinship[[2]])
 # call to sim1
-Ypre <- sim1(X = X, B = B, Vg = diag(2), Ve = diag(2), kinship = kinship[[2]])
+Ypre <- sim1(X = X, B = B, Sigma = Sig)
 Y <- matrix(Ypre, nrow = 261, ncol = 2, byrow = FALSE)
 rownames(Y) <- rownames(pp)
 colnames(Y) <- c("tr1", "tr2")
@@ -216,7 +218,7 @@ out <- suppressMessages(scan_pvl(probs = pp,
                 pheno = Y,
                 kinship = kinship[[2]], # 2nd entry in kinship list is Chr 3
                 start_snp = 38,
-                n_snp = 25, n_cores = 1
+                n_snp = 25
                 ))
 ```
 
@@ -262,7 +264,7 @@ b_out <- suppressMessages(boot_pvl(probs = pp,
          pheno = Y,
          pleio_peak_index = pleio_index,
          kinship = kinship[[2]], # 2nd element in kinship list is Chr 3
-         nboot_per_job = 10,
+         nboot = 10,
          start_snp = 38,
          n_snp = 25
          ))
@@ -275,9 +277,6 @@ b_out <- suppressMessages(boot_pvl(probs = pp,
 
 
 
-
-
-
 ## Citation information
 
 ```{r cite}

diff --git a/README.md b/README.md
@@ -3,7 +3,9 @@
 
 # qtl2pleio
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fboehm/qtl2pleio/master?urlpath=rstudio)
+[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/qtl2pleio)](https://cran.r-project.org/package=qtl2pleio)
+
+[![Binder](https://static.mybinder.org/badge_logo.svg)](https://static.mybinder.org/v2/gh/fboehm/qtl2pleio/master?urlpath=rstudio)
 [![Travis-CI Build
 Status](https://travis-ci.org/fboehm/qtl2pleio.svg?branch=master)](https://travis-ci.org/fboehm/qtl2pleio)
 [![Coverage
@@ -38,8 +40,10 @@ conduct](https://github.com/fboehm/qtl2pleio/blob/master/CONDUCT.md).
 ## Technical support
 
 For technical support, please open a Github issue. If you’re just
-getting started with `qtl2pleio`, please examine the vignettes. You can
-also email <[email protected]> for assistance.
+getting started with `qtl2pleio`, please examine the
+[vignettes](https://fboehm.us/software/qtl2pleio) on the [package’s web
+site](https://fboehm.us/software/qtl2pleio). You can also email
+<[email protected]> for assistance.
 
 ## Goals
 
@@ -60,15 +64,14 @@ To install qtl2pleio, use `install_github()` from the
 [devtools](https://devtools.r-lib.org) package.
 
 ``` r
-install.packages("devtools")
-devtools::install_github("fboehm/qtl2pleio")
+install.packages("qtl2pleio")
 ```
 
 You may also wish to install the [R/qtl2](https://kbroman.org/qtl2). We
 will use it below.
 
 ``` r
-install.packages("qtl2", repos="http://rqtl.org/qtl2cran")
+install.packages("qtl2")
 ```
 
 ## Example
@@ -159,8 +162,9 @@ X <- gemma2::stagger_mats(pp[ , , 50], pp[ , , 50])
 B <- matrix(data = c(-1, -1, -1, -1, 1, 1, 1, 1, -1, -1, -1, -1, 1, 1, 1, 1), nrow = 8, ncol = 2, byrow = FALSE)
 # set.seed to ensure reproducibility
 set.seed(2018-01-30)
+Sig <- calc_Sigma(Vg = diag(2), Ve = diag(2), kinship = kinship[[2]])
 # call to sim1
-Ypre <- sim1(X = X, B = B, Vg = diag(2), Ve = diag(2), kinship = kinship[[2]])
+Ypre <- sim1(X = X, B = B, Sigma = Sig)
 Y <- matrix(Ypre, nrow = 261, ncol = 2, byrow = FALSE)
 rownames(Y) <- rownames(pp)
 colnames(Y) <- c("tr1", "tr2")
@@ -173,19 +177,18 @@ matrix.
 s1 <- scan1(genoprobs = pr, pheno = Y, kinship = kinship)
 ```
 
-Here is a plot of the
-results.
+Here is a plot of the results.
 
 <img src="https://raw.githubusercontent.com/fboehm/qtl2pleio/master/man/figures/README-1d-lod-plots-1.png" width="100%" />
 
 And here are the observed QTL peaks with LOD \> 8.
 
 ``` r
 find_peaks(s1, map = DOex$pmap, threshold=8)
-#>   lodindex lodcolumn chr      pos      lod
-#> 1        1       tr1   3 82.77806 13.39312
-#> 2        1       tr1   X 97.07206  9.18941
-#> 3        2       tr2   3 82.77806 23.57570
+#>   lodindex lodcolumn chr      pos       lod
+#> 1        1       tr1   3 82.77806 20.703383
+#> 2        2       tr2   3 82.77806 14.417924
+#> 3        2       tr2   X 48.10040  8.231551
 ```
 
 ### Perform two-dimensional scan as first step in pleiotropy vs. separate QTL hypothesis test
@@ -200,7 +203,7 @@ out <- suppressMessages(scan_pvl(probs = pp,
                 pheno = Y,
                 kinship = kinship[[2]], # 2nd entry in kinship list is Chr 3
                 start_snp = 38,
-                n_snp = 25, n_cores = 1
+                n_snp = 25
                 ))
 ```
 
@@ -250,7 +253,7 @@ b_out <- suppressMessages(boot_pvl(probs = pp,
          pheno = Y,
          pleio_peak_index = pleio_index,
          kinship = kinship[[2]], # 2nd element in kinship list is Chr 3
-         nboot_per_job = 10,
+         nboot = 10,
          start_snp = 38,
          n_snp = 25
          ))
@@ -268,8 +271,8 @@ citation("qtl2pleio")
 #> 
 #> To cite qtl2pleio in publications use:
 #> 
-#>   Boehm FJ, Chesler EJ, Yandell BS, Broman KW (2019) Testing
-#>   pleiotropy vs. separate QTL in multiparental populations G3
+#>   Boehm FJ, Chesler EJ, Yandell BS, Broman KW (2019) Testing pleiotropy
+#>   vs. separate QTL in multiparental populations G3
 #>   https://www.g3journal.org/content/9/7/2317
 #> 
 #> A BibTeX entry for LaTeX users is

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,5 +1,5 @@
-destination: ~/Documents/website-mediumish/docs/static/software/qtl2pleio
-url: https://fboehm.us/static/software/qtl2pleio
+destination: ~/work/professional-development/fboehm.us/static/software/qtl2pleio
+url: https://fboehm.us/software/qtl2pleio
 
 home:
   links:

diff --git a/codemeta.json b/codemeta.json
@@ -10,14 +10,14 @@
   "codeRepository": "https://github.com/fboehm/qtl2pleio",
   "issueTracker": "https://github.com/fboehm/qtl2pleio/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "1.2.3",
+  "version": "1.3.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
-    "version": "3.6.1",
+    "version": "4.0.0",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 3.6.1 (2019-07-05)",
+  "runtimePlatform": "R version 4.0.0 (2020-04-24)",
   "author": [
     {
       "@type": "Person",
@@ -124,7 +124,14 @@
     {
       "@type": "SoftwareApplication",
       "identifier": "qtl2",
-      "name": "qtl2"
+      "name": "qtl2",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=qtl2"
     }
   ],
   "softwareRequirements": [
@@ -220,49 +227,55 @@
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "stringr",
-      "name": "stringr",
+      "identifier": "tibble",
+      "name": "tibble",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
         "name": "Comprehensive R Archive Network (CRAN)",
         "url": "https://cran.r-project.org"
       },
-      "sameAs": "https://CRAN.R-project.org/package=stringr"
+      "sameAs": "https://CRAN.R-project.org/package=tibble"
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "tibble",
-      "name": "tibble",
+      "identifier": "Matrix",
+      "name": "Matrix",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
         "name": "Comprehensive R Archive Network (CRAN)",
         "url": "https://cran.r-project.org"
       },
-      "sameAs": "https://CRAN.R-project.org/package=tibble"
+      "sameAs": "https://CRAN.R-project.org/package=Matrix"
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "parallel",
-      "name": "parallel"
+      "identifier": "furrr",
+      "name": "furrr",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=furrr"
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "Matrix",
-      "name": "Matrix",
+      "identifier": "future",
+      "name": "future",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
         "name": "Comprehensive R Archive Network (CRAN)",
         "url": "https://cran.r-project.org"
       },
-      "sameAs": "https://CRAN.R-project.org/package=Matrix"
+      "sameAs": "https://CRAN.R-project.org/package=future"
     }
   ],
   "releaseNotes": "https://github.com/fboehm/qtl2pleio/blob/master/NEWS.md",
   "readme": "https://github.com/fboehm/qtl2pleio/blob/master/README.md",
-  "fileSize": "132.497KB",
   "contIntegration": [
     "https://travis-ci.org/fboehm/qtl2pleio",
     "https://codecov.io/github/fboehm/qtl2pleio?branch=master"
@@ -314,5 +327,11 @@
         }
       }
     }
-  ]
+  ],
+  "provider": {
+    "@id": "https://cran.r-project.org",
+    "@type": "Organization",
+    "name": "Comprehensive R Archive Network (CRAN)",
+    "url": "https://cran.r-project.org"
+  }
 }
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,25 +1,14 @@
 ## Test environments
-* local OS X install, R 3.6.1
-* ubuntu 14.04 (on travis-ci), R 3.5.3
+* local ubuntu 20.04 install, R 4.0.0
 * win-builder (devel and release)
 
 ## R CMD check results  
 
-0 errors | 0 warnings | 2 notes
+0 errors | 0 warnings | 1 note
 
-* This is a new release.
+* One note states that "libs" directory is 32.1 Mb in size.
 
-* The package qtl2 is available through a non-CRAN repository.
+* This release updates the CRAN package qtl2pleio.
 
-## Replies to previous CRAN concerns
-
-* This is a resubmission of an initially rejected package. 
-
-* I shortened the title in the file DESCRIPTION
-
-* I removed export tags for some functions that are not needed directly by the user.
-
-* I mistakenly included code that downloaded files to a new directory. I've since deleted those pieces of code.
-
-* I omitted the abbreviation QTL in the DESCRIPTION file.
+* The package qtl2, suggested by qtl2pleio, is newly available through CRAN.
 
diff --git a/man/figures/README-1d-lod-plots-1.png b/man/figures/README-1d-lod-plots-1.png
diff --git a/man/figures/README-profile-plot-1.png b/man/figures/README-profile-plot-1.png