Merge pull request #87 from snlab-ch/develop

jhollway · web-flow · commit d3dcee689f22 · 2021-04-13T20:39:09.000+02:00
Fixing CRAN submission issues
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,4 @@
 ^docs$
 ^pkgdown$
 ^cran-comments\.md$
+^CRAN-RELEASE$
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -2,18 +2,18 @@
 
 # Checklist:
 
-- [ ] PR form
-  - [ ] I have given this pull request an informative title
-  - [ ] Description above itemizes changes under subtitles, e.g. "## Collection""
+- PR form
+  - [ ] This pull request has an informative title
+  - [ ] Description above itemizes changes under subtitles, e.g. "## Data""
   - [ ] Any closed, fixed, or related issues are referenced and explained in the description above, e.g. "Fixed #0 by adding A"
   - [ ] Package builds on my OS without issues
-- [ ] PR checks all pass for latest commit
+- PR checks all pass for latest commit
+  - [ ] CodeFactor check: Package improves or maintains good style
   - [ ] Package builds on Mac
   - [ ] Package builds on Windows
   - [ ] Package builds on Linux
   - [ ] CodeCov check: Package improves or maintains good test coverage
-  - [ ] CodeFactor check: Package improves or maintains good style
-- [ ] Documentation
+- Documentation
   - [ ] Any new or modified functions or data have roxygen style documentation in their .R scripts
   - [ ] Any longer functions are commented inline so that it is easier to debug in the future
   - [ ] PR description above and the NEWS.md file are aligned
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: migraph
 Title: Multimodal and Multilevel Network Analysis
-Version: 0.6.1
-Date: 2021-04-11
+Version: 0.6.2
+Date: 2021-04-13
 Description: A set of tools that extend common social network analysis packages
    for analysing multimodal and multilevel networks.
    It includes functions for one- and two-mode (and sometimes three-mode) 
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2020 James Hollway
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2020
+COPYRIGHT HOLDER: James Hollway
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2021 James Hollway
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,13 @@
+# migraph 0.6.2
+
+2021-04-13
+
+## Package
+
+* Reran `usethis::use_mit_license("James Hollway")`. MIT License file now contains only the standard two lines.
+* Removed `\dontrun` from examples. `netlm()` now runs in <5 seconds.
+* Fixed missing website item
+
 # migraph 0.6.1
 
 2021-04-11
diff --git a/R/create.R b/R/create.R
@@ -154,9 +154,7 @@ roll_over <- function(w){
 #' #' @importFrom tidygraph as_tbl_graph
 #' #' @importFrom igraph graph_from_incidence_matrix
 #' #' @examples
-#' #' \dontrun{
 #' #' create_nest(10, 12)
-#' #' }
 #' #' @export
 #' create_nest <- function(n1, n2,
 #'                         as = c("tidygraph", "igraph", "matrix")) {
@@ -176,9 +174,7 @@ roll_over <- function(w){
 #' #' @importFrom tidygraph as_tbl_graph
 #' #' @importFrom igraph graph_from_incidence_matrix
 #' #' @examples
-#' #' \dontrun{
 #' #' create_star(1, 12)
-#' #'}
 #' #' @export
 #' create_star <- function(n1 = 1, n2,
 #'                         as = c("tidygraph", "igraph", "matrix")){
diff --git a/R/netlm.R b/R/netlm.R
@@ -10,13 +10,12 @@
 #' @importFrom purrr map
 #' @importFrom stats lm
 #' @examples
-#' \dontrun{
 #' mat1 <- matrix(c(0,1,1,0,0,1,1,1),4,2)
 #' mat2 <- matrix(c(0,1,0,1,0,1,0,1),4,2)
 #' mat3 <- matrix(c(0,0,1,1,0,0,1,1),4,2)
 #' lmat <- list(mat1 = mat1, mat2 = mat2, mat3 = mat3)
-#' example <- netlm(mat1 ~ mat2 + mat3 + lmat)
-#' }
+#' model1 <- netlm(mat1 ~ mat2 + mat3, lmat)
+#' summary(model1)
 #' @export
 netlm <- function(formula, data, ...){
   
@@ -40,15 +39,6 @@ netlm <- function(formula, data, ...){
 #' By default, reps=1000.
 #' @param ... Arguments passed on to `lm()`.
 #' @importFrom stats ecdf lm
-#' @examples
-#' \dontrun{
-#' mat1 <- matrix(c(0,1,1,0,0,1,1,1),4,2)
-#' mat2 <- matrix(c(0,1,0,1,0,1,0,1),4,2)
-#' mat3 <- matrix(c(0,0,1,1,0,0,1,1),4,2)
-#' lmat <- list(mat1 = mat1, mat2 = mat2, mat3 = mat3)
-#' example <- netlm(mat1 ~ mat2 + mat3 + lmat)
-#' summary.netlm(example)
-#' }
 #' @export
 summary.netlm <- function(object, reps = 1000, ...){
   
@@ -115,16 +105,6 @@ summary.netlm <- function(object, reps = 1000, ...){
 #' @param digits the number of significant digits to use when printing.
 #' @param signif.stars logical. If TRUE, ‘significance stars’ are printed for each coefficient.
 #' @importFrom stats printCoefmat
-#' @examples
-#' \dontrun{
-#' mat1 <- matrix(c(0,1,1,0,0,1,1,1),4,2)
-#' mat2 <- matrix(c(0,1,0,1,0,1,0,1),4,2)
-#' mat3 <- matrix(c(0,0,1,1,0,0,1,1),4,2)
-#' lmat <- list(mat1 = mat1, mat2 = mat2, mat3 = mat3)
-#' example <- netlm(mat1 ~ mat2 + mat3 + lmat)
-#' summary.netlm(example)
-#' print.summary.netlm(example)
-#' }
 #' @export
 print.summary.netlm <- function(x,
                                 digits = max(3, getOption("digits") - 3),
diff --git a/cran-comments.md b/cran-comments.md
@@ -11,4 +11,5 @@
 
 0 errors | 0 warnings | 0 notes
 
-* This is a new release.
+* Reran `usethis::use_mit_license("James Hollway")`. MIT License file now contains only the standard two lines.
+* Removed `\dontrun` from examples. `netlm()` now runs in <5 seconds.
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: https://jhollway.github.io/migraph/
+url: https://snlab-ch.github.io/migraph/
 development:
     mode: auto
 template:
@@ -59,4 +59,4 @@ reference:
     desc: "Functions for modelling multimodal and multilevel networks:"
     contents:
       - netlm
-      - blockmodel
+      - starts_with("blockmodel")
