Merge pull request #78 from alexzwanenburg/dev1.4.6

Release version 1.4.6

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: familiar
 Title: End-to-End Automated Machine Learning and Model Evaluation
-Version: 1.4.5
+Version: 1.4.6
 Authors@R: c(
     person("Alex", "Zwanenburg",
            email = "[email protected]",

NEWS.md

@@ -1,3 +1,9 @@
+# Version 1.4.6 (Talented Toad)
+
+## Bug fixes
+
+- Fixes unused arguments appearing in documentation.
+
 # Version 1.4.5 (Reminiscing Rat)
 
 ## Bug fixes

R/FamiliarDataComputationVimp.R

@@ -20,10 +20,6 @@ setClass("familiarDataElementVimpData",
 #'@description Aggregate variable importance from models in a
 #'  `familiarEnsemble`.
 #'
-#'@param feature_similarity_table Table containing pairwise distance between
-#'  features. This is used to determine cluster information, and indicate
-#'  co-clustered important features. The table is created by the
-#'  `extract_feature_similarity` method.
 #'@inheritParams extract_data
 #'
 #'@return A list containing variable importance information.

R/Iterations.R

@@ -1,6 +1,6 @@
 #' Internal function for creating or retrieving iteration data
 #'
-#' @param file_dir Path to directory where iteration files are stored.
+#' @param file_paths Set of paths to relevant files and directories.
 #' @param data Data set as loaded using the `.load_data` function.
 #' @param experiment_setup data.table with subsampler information at different
 #'   levels of the experimental design.

R/LearnerMain.R

@@ -226,10 +226,6 @@ setMethod("promote_learner", signature(object="familiarModel"),
 #'
 #' @param data_obj dataObject class object which contains the data on which the
 #'   preset parameters are determined.
-#' @param outcome_type Type of oucome. Default settings are determined, among
-#'   others by the the outcome type. For example, one default signature size
-#'   depends on the number of events for `survival` outcomes, based on rules of
-#'   thumb.
 #' @param restrict_samples Logical indicating whether the signature size should
 #'   be limited by the number of samples in addition to the number of available
 #'   features. This may help convergence of OLS-based methods.

cran-comments.md

@@ -1,4 +1,4 @@
-Update familiar to version 1.4.1
+Update familiar to version 1.4.6
 
 Vignettes are pre-compiled to avoid long compilation times on build (several minutes).
 
@@ -12,51 +12,46 @@ R CMD check was run on R-hub using rhub::check_for_cran(), producing the followi
 
 ----------------------------------
 Windows Server 2022, R-devel, 64 bit:
-0 errors | 0 warnings | 3 notes
+0 errors | 0 warnings | 4 notes
 
 * checking installed package size ... NOTE
   installed size is  5.8Mb
   sub-directories of 1Mb or more:
     R      3.5Mb
     doc    1.0Mb
-    help   1.1Mb
+    help   1.2Mb
 
-**Maintainer**: The size of the R-directory is due to source code. Addressing the size of the R directory would require creating a set of mutually dependent  packages. This would likely result in a larger footprint across the packages.  
+**Maintainer**: The size of the R-directory is due to source code. Addressing the size of the R directory would require creating a set of mutually dependent packages. This would likely result in a larger footprint across the packages.  
 
-* checking HTML version of manual ... [37s] NOTE
+* checking HTML version of manual ... [39s] NOTE
 Skipping checking math rendering: package 'V8' unavailable
 
 **Maintainer**: I am not sure what the cause is, but it might be because the V8 package was not available on rhub.
-
+
+* checking for non-standard things in the check directory ... NOTE
+Found the following files/directories:
+  ''NULL''
+
+**Maintainer**: I am not sure what the cause is. However, NULL is not present as a directory or file.  
+
 * checking for detritus in the temp directory ... NOTE
 Found the following files/directories:
   'lastMiKTeXException'
 
 **Maintainer**: This note only appeared on the Windows server test. It didn't appear locally (Windows 10) or the other builds.
 
 
+
 ----------------------------------
 Fedora Linux, R-devel, clang, gfortran:
-0 errors | 0 warnings | 3 notes
-
-* checking package dependencies ... NOTE
-Packages suggested but not available for checking: 'fastglm'
-
-**Maintainer**: The package uses stats::glm as a fallback if fastglm is not available.
+0 errors | 0 warnings | 1 notes
 
 * checking installed package size ... NOTE
   installed size is  5.8Mb
   sub-directories of 1Mb or more:
     R      3.5Mb
     doc    1.0Mb
-    help   1.1Mb
-
-* checking HTML version of manual ... NOTE
-Skipping checking HTML validation: no command 'tidy' found
-Skipping checking math rendering: package 'V8' unavailable
-
-
-**Maintainer**: I am unsure what causes this note. It doesn't appear locally.
+    help   1.2Mb
 
 
 
@@ -67,10 +62,9 @@ Ubuntu Linux 20.04.1 LTS, R-release, GCC:
 * checking installed package size ... NOTE
   installed size is  5.9Mb
   sub-directories of 1Mb or more:
-    R      3.5Mb
     doc    1.0Mb
-    help   1.2Mb
-
+    help   1.1Mb
+    R      3.6Mb
 
 
 

inst/CITATION

@@ -1,22 +1,19 @@
-citHeader("To cite the \"familiar\" package in publications, please use:")
-
-citEntry(entry = "Misc",
-         title   = paste0(meta$Package, ": ", meta$Title),
-         author  = c(person("Alex", "Zwanenburg"),
-                     person("Steffen", "Löck")),
-         year    = 2021,
-         url     = "https://github.com/alexzwanenburg/familiar",
-         textVersion = paste0("Alex Zwanenburg and Steffen Löck. ",
-                              paste0(meta$Package, ": ", meta$Title), " (2021). ",
-                              "https://github.com/alexzwanenburg/familiar")
+bibentry(
+  bibtype  = "Misc",
+  title    = paste0(meta$Package, ": ", meta$Title),
+  author   = c(
+    person("Alex", "Zwanenburg"),
+    person("Steffen", "Löck")
+  ),
+  year     = 2021,
+  url      = "https://github.com/alexzwanenburg/familiar"
 )
 
-citEntry(entry = "Manual",
-         header  = "If you cite the manual, vignettes or other part of the documentation, please use:",
-         title   = "familiar: Vignettes and Documentation",
-         author  = c(person("Alex", "Zwanenburg")),
-         year    = 2021,
-         url     = "https://github.com/alexzwanenburg/familiar",
-         textVersion = paste0("Alex Zwanenburg. ",
-                              "familiar: Vignettes and Documentation (2021). ",
-                              "https://github.com/alexzwanenburg/familiar"))
+bibentry(
+  bibtype = "Manual",
+  header  = "If you cite the manual, vignettes or other part of the documentation, please use:",
+  title   = "familiar: Vignettes and Documentation",
+  author  = c(person("Alex", "Zwanenburg")),
+  year    = 2021,
+  url     = "https://github.com/alexzwanenburg/familiar",
+)