ropensci · eebrown · Oct 11, 2019 · Oct 11, 2019 · Dec 8, 2020
diff --git a/CRAN-RELEASE b/CRAN-RELEASE
@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2020-12-08.
+Once it is accepted, delete this file and tag the release (commit 607fcc8b1c).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tacmagic
 Type: Package
 Title: Positron Emission Tomography Time-Activity Curve Analysis
-Version: 0.3.0
+Version: 0.3.1
 Authors@R: c(person("Eric", "Brown", 
                     role = c("aut", "cre"),
                     email = "eb@ericebrown.com",
@@ -33,7 +33,7 @@ URL: https://github.com/ropensci/tacmagic
 BugReports: https://github.com/ropensci/tacmagic
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
 Imports: 
     graphics, 
     grDevices, 

diff --git a/NAMESPACE b/NAMESPACE
@@ -19,6 +19,7 @@ export(load_tac)
 export(load_voistat)
 export(load_vol)
 export(pos_anyroi)
+export(roi_AAL_full)
 export(roi_ham_full)
 export(roi_ham_pib)
 export(roi_ham_stand)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,11 @@
 # tacmagic News
 
+## tacmagic 0.3.1 (2020-12-08)
+
+### Minor changes
+
+- Make vdiffr plotting tests conditional.
+
 ## tacmagic 0.3.0 (2019-06-06)
 
 ### Major changes

diff --git a/R/ROI_definitions.R b/R/ROI_definitions.R
@@ -143,3 +143,104 @@ roi_ham_pib <- function() {
 
   return(ROIs)
 }
+
+
+## AAL Atlas
+
+#' Return a list of merged ROIs made up of the atomic ROIs in the AAL atlas.
+#' The groupings for major lobes are as described in the PMOD documentation.
+#'
+#'@export
+#'@return A list of lists, where each list is an ROI (e.g.) frontal lobe that
+#' specifies the atomic ROIs from the atlas that make it up.
+#'@family ROI definitions
+#'@references PMOD Groupings of the AAL Atlas.
+#'
+#' Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain. N. Tzourio-Mazoyer, B. Landeau, D. Papathanassiou, F. Crivello, O. Étard, N. Delcroix, B. Mazoyer, and M. Joliot. NeuroImage 2002, 15 :273-289 <doi:10.1006/nimg.2001.0978>
+#'@examples
+#' roi_AAL_full()
+roi_AAL_full <- function() {
+
+   # Precentral_l  Precentral_r  Frontal_Sup_l  Frontal_Sup_r  Frontal_Sup_Orb_l  Frontal_Sup_Orb_r  Frontal_Mid_l  Frontal_Mid_r  Frontal_Mid_Orb_l  Frontal_Mid_Orb_r  Frontal_Inf_Oper_l  Frontal_Inf_Oper_r  Frontal_Inf_Tri_l  Frontal_Inf_Tri_r  Frontal_Inf_Orb_l  Frontal_Inf_Orb_r  Rolandic_Oper_l  Rolandic_Oper_r  Supp_Motor_Area_l  Supp_Motor_Area_r  Olfactory_l  Olfactory_r  Frontal_Sup_Medial_l  Frontal_Sup_Medial_r  Frontal_Med_Orb_l  Frontal_Med_Orb_r  Rectus_l  Rectus_r  Insula_l  Insula_r  Cingulum_Ant_l  Cingulum_Ant_r  Cingulum_Mid_l  Cingulum_Mid_r  Cingulum_Post_l  Cingulum_Post_r  Hippocampus_l  Hippocampus_r  Parahippocampus_l  Parahippocampus_r  Amygdala_l  Amygdala_r  Calcarine_l  Calcarine_r  Cuneus_l  Cuneus_r  Lingual_l  Lingual_r  Occipital_Sup_l  Occipital_Sup_r  Occipital_Mid_l  Occipital_Mid_r  Occipital_Inf_l  Occipital_Inf_r  Fusiform_l  Fusiform_r  Postcentral_l  Postcentral_r  Parietal_Sup_l  Parietal_Sup_r  Parietal_Inf_l  Parietal_Inf_r  Supra_Marginal_l  Supra_Marginal_r  Angular_l  Angular_r  Precuneus_l  Precuneus_r  Paracentral_Lobule_l  Paracentral_Lobule_r  CaudateNucl_l  CaudateNucl_r  Putamen_l  Putamen_r  Pallidum_l  Pallidum_r  Thalamus_l  Thalamus_r  Heschl_l  Heschl_r  Temporal_Sup_l  Temporal_Sup_r  Temporal_Pole_Sup_l  Temporal_Pole_Sup_r  Temporal_Mid_l  Temporal_Mid_r  Temporal_Pole_Mid_l  Temporal_Pole_Mid_r  Temporal_Inf_l  Temporal_Inf_r  Cerebellum_Crus1_l  Cerebellum_Crus1_r  Cerebellum_Crus2_l  Cerebellum_Crus2_r  Cerebellum3_l  Cerebellum3_r  Cerebellum45_l  Cerebellum45_r  Cerebellum6_l  Cerebellum6_r  Cerebellum7_l  Cerebellum7_r  Cerebellum8_l  Cerebellum8_r  Cerebellum9_l  Cerebellum9_r  Cerebellum10_l  Cerebellum10_r  Vermis12  Vermis3  Vermis45  Vermis6  Vermis7  Vermis8  Vermis9  Vermis10  Medulla  Midbrain  Pons  White_matter_l  White_matter_r  CBW
+
+  frontal_def <- c("Precentral", "Frontal_Sup", "Frontal_Sup_Orb",
+                   "Frontal_Mid", "Frontal_Mid_Orb", "Frontal_Inf_Oper",
+                   "Frontal_Inf_Tri", "Frontal_Inf_Orb", "Rolandic_Oper",
+                   "Supp_Motor_Area", "Olfactory", "Frontal_Sup_Medial",
+                   "Frontal_Med_Orb", "Rectus", "Paracentral_Lobule",
+                   "Paracentral_Lobule")
+
+  temporal_def <- c("Hippocampus", "Parahippocampus", "Amygdala", "Fusiform",
+                    "Heschl", "Temporal_Sup", "Temporal_Pole_Sup",
+                    "Temporal_Mid", "Temporal_Pole_Mid", "Temporal_Inf")
+
+  parietal_def <- c("Postcentral", "Parietal_Sup", "Parietal_Inf",
+                    "Supra_Marginal", "Angular", "Precuneus")
+
+  insulacingulate_def <- c("Insula", "Cingulum_Ant", "Cingulum_Mid",
+                            "Cingulum_Post")
+
+  occipital_def <- c("Calcarine", "Cuneus", "Lingual", "Occipital_Sup",
+                     "Occipital_Mid", "Occipital_Inf")
+
+  central_def <- c("CaudateNucl", "Putamen", "Pallidum", "Thalamus")
+
+  cerebellum_def <- c("Cerebellum_Crus1", "Cerebellum_Crus2", "Cerebellum3",
+                     "Cerebellum45", "Cerebellum6", "Cerebellum7",
+                     "Cerebellum8", "Cerebellum9", "Cerebellum10")
+
+  vermis <- c("Vermis12", "Vermis3", "Vermis45", "Vermis6", "Vermis7",
+              "Vermis8", "Vermis9", "Vermis10")
+
+  leftfrontal <- paste(frontal_def, "_l", sep="")
+  rightfrontal <- paste(frontal_def, "_r", sep="")
+  frontal <- c(leftfrontal, rightfrontal)
+
+  lefttemporal <- paste(temporal_def, "_l", sep="")
+  righttemporal <- paste(temporal_def, "_r", sep="")
+  temporal <- c(lefttemporal, righttemporal)
+
+  leftparietal <- paste(parietal_def, "_l", sep="")
+  rightparietal <- paste(parietal_def, "_r", sep="")
+  parietal <- c(leftparietal, rightparietal)
+
+  leftoccipital <- paste(occipital_def, "_l", sep="")
+  rightoccipital <- paste(occipital_def, "_r", sep="")
+  occipital <- c(leftoccipital, rightoccipital)
+
+  leftinsulacingulate <- paste(insulacingulate_def, "_l", sep="")
+  rightinsulacingulate <- paste(insulacingulate_def, "_r", sep="")
+  insulacingulate <- c(leftinsulacingulate, rightinsulacingulate)
+
+  cerebellum <- c(paste(cerebellum_def, "_l", sep=""),
+                  paste(cerebellum_def, "_r", sep=""), vermis)
+
+  central <- c(paste(central_def, "_l", sep=""),
+               paste(central_def, "_r", sep=""))
+
+  #medulla <- c("Medulla")
+  #midbrain <- c("Midbrain")
+  #pons <- c("Pons")
+  wm <- c("White_matter_l", "White_matter_r")
+  #CBW <- c("CBW")
+
+  totalcortical <- c(frontal, temporal, parietal, occipital, insulacingulate)
+
+  ROIs <- list(leftfrontal=leftfrontal, rightfrontal=rightfrontal,
+               lefttemporal=lefttemporal, righttemporal=righttemporal,
+               leftparietal=leftparietal, rightparietal=rightparietal,
+               leftoccipital=leftoccipital, rightoccipital=rightoccipital,
+               leftinsulacingulate=leftinsulacingulate,
+               rightinsulacingulate=rightinsulacingulate,
+
+               frontal=frontal, temporal=temporal, parietal=parietal,
+               occipital=occipital, insulacingulate=insulacingulate,
+
+               totalcortical=totalcortical,
+
+               cerebellum=cerebellum, central=central, wm=wm)
+               #medulla=medulla, midbrain=midbrain, pons=pons, CBW=CBW)
+
+  return(ROIs)
+}
+
diff --git a/codemeta.json b/codemeta.json
@@ -10,7 +10,7 @@
   "codeRepository": "https://github.com/ropensci/tacmagic",
   "issueTracker": "https://github.com/ropensci/tacmagic",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.3.0",
+  "version": "0.3.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -145,7 +145,7 @@
       "sameAs": "https://CRAN.R-project.org/package=R.matlab"
     }
   ],
-  "readme": "https://github.com/ropensci/tacmagic/blob/master/readme.md",
+  "readme": "https://github.com/ropensci/tacmagic/blob/master/README.md",
   "contIntegration": [
     "https://travis-ci.org/ropensci/tacmagic",
     "https://codecov.io/github/ropensci/tacmagic?branch=master"

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1 @@
+Made all calls to vdiffr functions conditional, as requested by Brian Ripley. I tried to see whether setting _R_CHECK_DEPENDS_ONLY_=true would identify this issue, but it did not, so I could not confirm 100% that it is fixed. CHECK produces no errors before or after the change.
diff --git a/man/DVR_all_ref_Logan.Rd b/man/DVR_all_ref_Logan.Rd
diff --git a/man/DVR_ref_Logan.Rd b/man/DVR_ref_Logan.Rd
diff --git a/man/as.tac.Rd b/man/as.tac.Rd
diff --git a/man/batch_load.Rd b/man/batch_load.Rd
diff --git a/man/batch_tm.Rd b/man/batch_tm.Rd
diff --git a/man/batch_voistat.Rd b/man/batch_voistat.Rd
diff --git a/man/cutoff_aiz.Rd b/man/cutoff_aiz.Rd
diff --git a/man/dvr.Rd b/man/dvr.Rd
diff --git a/man/fake_DVR.Rd b/man/fake_DVR.Rd
diff --git a/man/load_tac.Rd b/man/load_tac.Rd
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		This package was submitted to CRAN on 2020-12-08.
		Once it is accepted, delete this file and tag the release (commit 607fcc8b1c).
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Made all calls to vdiffr functions conditional, as requested by Brian Ripley. I tried to see whether setting _R_CHECK_DEPENDS_ONLY_=true would identify this issue, but it did not, so I could not confirm 100% that it is fixed. CHECK produces no errors before or after the change.