general srr

srr standards for the General category have been completed.
ropensci · Mar 12, 2024 · 6eaaa5c · 6eaaa5c
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Showing 19 changed files with 37 additions and 26 deletions.
diff --git a/.Rhistory b/.Rhistory
@@ -1,15 +1,3 @@
-x <- matrix(rnorm(100), ncol = 2)
-y <- rep(c(1,2), each=25)
-result <- kb.test(x, method = "subsampling", b = 0.5)
-expect_s4_class(result, "kb.test")
-expect_equal(result@method, "Kernel-based quadratic distance Normality test")
-expect_equal(class(result@h$h_sel), "numeric")
-result <- kb.test(x, y, method = "subsampling", b = 0.5)
-expect_s4_class(result, "kb.test")
-expect_equal(class(result@h$h_sel), "numeric")
-})
-#' Test for pk.test
-#'
 #'
 #' @srrstats {G5.2,G5.2a,G5.2b} all the error and warning messages are tested
 #' @srrstats {G5.5} random seed
@@ -510,3 +498,15 @@ x <- pkgcheck()
 summary(x)
 x
 roxygen2::roxygenise()
+roxygen2::roxygenise()
+library(pkgcheck)
+x <- pkgcheck()
+x <- pkgcheck()
+summary(x)
+x
+library(autotest)
+b <- autotest_package()
+library(srr)
+srr_stats_pre_submit()
+srr_report()
+roxygen2::roxygenise()
diff --git a/.Rproj.user/F4975BFA/pcs/files-pane.pper b/.Rproj.user/F4975BFA/pcs/files-pane.pper
@@ -5,5 +5,5 @@
             "ascending": true
         }
     ],
-    "path": "~/GitHub/QuadratiK-package/R"
+    "path": "~/GitHub/QuadratiK-package"
 }
diff --git a/.Rproj.user/F4975BFA/pcs/source-pane.pper b/.Rproj.user/F4975BFA/pcs/source-pane.pper
@@ -1,3 +1,3 @@
 {
-    "activeTab": 5
+    "activeTab": 17
 }
diff --git a/.Rproj.user/F4975BFA/saved_source_markers b/.Rproj.user/F4975BFA/saved_source_markers
diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
@@ -15,7 +15,6 @@ C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/pkbd_functions.R="1BEA4C49"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/srr-stats-standards.R="EB260381"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/utility.R="F7DAB755"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/wireless.R="5FF8D491"
-C:/Users/sarac/Documents/GitHub/QuadratiK-package/README.Rmd="DD3767BE"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/_pkgdown.yml="5FD21EDB"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/codecov.yml="C78935A5"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/codemeta.json="35775251"
@@ -36,4 +35,5 @@ C:/Users/sarac/Documents/GitHub/QuadratiK-package/tests/testthat/test-validation
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/TwoSample_test.Rmd="77787FE7"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/kSample_test.Rmd="61D887F6"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/uniformity.Rmd="89CAEE2E"
+C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/wireless_clustering.R="2E11C176"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/wireless_clustering.Rmd="FC40ACF9"
diff --git a/R/QuadratiK-package.R b/R/QuadratiK-package.R
@@ -51,6 +51,7 @@
 #' @srrstats {G1.0} Reference section reports the related literature
 #' @srrstats {G1.1, G1.3} First implementation of provided methods
 #' @srrstats {G1.2} see the 'CONTRIBUTING.md' for states of development
+#' @srrstats {G1.5} vignettes reproduce results in the associated publication
 #' @srrstats {G3.0} in all the codes floating point numbers are not compared
 #' @srrstats {G5.7, G5.9} Verified through the simulation studies in the 
 #'                        indicated references. 

diff --git a/R/kb.test.R b/R/kb.test.R
@@ -171,7 +171,7 @@ setMethod("kb.test", signature(x = "ANY"),
                 if(any(is.na(y))){
                    stop("There are missing values in y!")
                 } else if(any(is.infinite(y) |is.nan(y))){
-                   stop("There are undefined values in y, that is Nan, Inf, -Inf")
+                   stop("There are undefined values in y, that is Nan, Inf")
                 }
              }
 

diff --git a/R/srr-stats-standards.R b/R/srr-stats-standards.R
@@ -3,12 +3,14 @@
 #'
 #'
 #' @srrstatsNA {G1.6} there are no alternative implementations
+#' @srrstatsNA {G2.4, G2.4a, G2.4c, G2.4d, G2.4e} other conversions are not 
+#'             used.
 #' @srrstatsNA {G2.5} there are no input of type factor which should be ordered
 #' @srrstatsNA {G2.6} we check that each univariate input has the expected type
 #' @srrstatsNA {G2.9} there are no conversions needed
 #' @srrstatsNA {G2.10} there is no extraction
 #' @srrstatsNA {G2.11,G2.12} We consider only data.frame with numeric variables
-#' @srrstatsNA {G2.14c,G2.14c} we just report errors in case of missing data
+#' @srrstatsNA {G2.14b,G2.14c} we just report errors in case of missing data
 #' @srrstatsNA {G3.1,G3.1a} methods are not based on covariance computation
 #' @srrstatsNA {G4.0} no outputs are written in local files
 #' @srrstatsNA {G5.0} the functions are tested with simple simulated data sets

diff --git a/src/QuadratiK.dll b/src/QuadratiK.dll
diff --git a/src/RcppExports.o b/src/RcppExports.o
diff --git a/src/kernel_function.o b/src/kernel_function.o
diff --git a/tests/testthat/test-dpkb.R b/tests/testthat/test-dpkb.R
@@ -3,7 +3,8 @@
 #' 
 #' 
 #' 
-#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with fixed seed
+#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with 
+#'                        fixed seed
 #' @srrstats {G5.2,G5.2a,G5.2b} all the error and warning messages are tested
 #' @srrstats {G5.4,G5.4a} correctness tested on simple cases
 #' @srrstats {G5.8, G5.8a,G5.8b,G5.8c} edge conditions

diff --git a/tests/testthat/test-kb.test.R b/tests/testthat/test-kb.test.R
@@ -3,7 +3,8 @@
 #' 
 #' 
 #' 
-#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with fixed seed
+#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with 
+#'                        fixed seed
 #' @srrstats {G5.2,G5.2a,G5.2b} all the error and warning messages are tested
 #' @srrstats {G5.4,G5.4a} correctness tested on simple cases
 #' @srrstats {G5.8, G5.8a,G5.8b,G5.8c} edge conditions

diff --git a/tests/testthat/test-pk.test.R b/tests/testthat/test-pk.test.R
@@ -2,7 +2,8 @@
 #' 
 #' 
 #' 
-#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with fixed seed
+#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with 
+#'                        fixed seed
 #' @srrstats {G5.2,G5.2a,G5.2b} all the error and warning messages are tested
 #' @srrstats {G5.4,G5.4a} correctness tested on simple cases
 #' @srrstats {G5.8, G5.8a,G5.8b,G5.8c} edge conditions

diff --git a/tests/testthat/test-pkbc.R b/tests/testthat/test-pkbc.R
@@ -2,7 +2,8 @@
 #' 
 #' Clustering on the Sphere
 #' 
-#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with fixed seed
+#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with 
+#'                        fixed seed
 #' @srrstats {G5.2,G5.2a,G5.2b} all the error and warning messages are tested
 #' @srrstats {G5.4,G5.4a} correctness tested on simple cases
 #' @srrstats {G5.8, G5.8a,G5.8b,G5.8c} edge conditions

diff --git a/tests/testthat/test-rpkb.R b/tests/testthat/test-rpkb.R
@@ -2,7 +2,8 @@
 #' 
 #' 
 #' 
-#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with fixed seed
+#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with 
+#'                        fixed seed
 #' @srrstats {G5.2,G5.2a,G5.2b} all the error and warning messages are tested
 #' 
 #' @noRd

diff --git a/tests/testthat/test-select_h.R b/tests/testthat/test-select_h.R
@@ -2,7 +2,8 @@
 #' 
 #' 
 #' 
-#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with fixed seed
+#' @srrstats {G5.1, G5.5} data sets are generated using simple functions with 
+#'                        fixed seed
 #' @srrstats {G5.2,G5.2a,G5.2b} all the error and warning messages are tested
 #' @srrstats {G5.8, G5.8a,G5.8b,G5.8c} edge conditions
 #' 

diff --git a/vignettes/wireless_clustering.R b/vignettes/wireless_clustering.R
@@ -2,7 +2,8 @@
 #  #' srr tags
 #  #'
 #  #'
-#  #' @srrstats {G1.5} application to the wireless data set in the associated paper
+#  #' @srrstats {G1.5} application to the wireless data set in the
+#  #'                  associated paper
 
 ## -----------------------------------------------------------------------------
 library(QuadratiK)

diff --git a/vignettes/wireless_clustering.Rmd b/vignettes/wireless_clustering.Rmd
@@ -13,7 +13,8 @@ vignette: >
 #' srr tags
 #' 
 #' 
-#' @srrstats {G1.5} application to the wireless data set in the associated paper
+#' @srrstats {G1.5} application to the wireless data set in the 
+#'                  associated paper
 ```
 We consider the Wireless Indoor Localization Data Set, publicly available in the UCI Machine Learning Repository’s website. This data set is used to study the performance of different indoor localization algorithms. It is available within the ``QuadratiK`` package as ``wireless``. 
 ```{r}