Fixing updates

.Rbuildignore

@@ -2,3 +2,8 @@
 ^\.Rproj\.user$
 README\.md
 ^\.travis\.yml$
+data/.Rapp.history
+^refit_sublime\.R$
+^README\.Rmd$
+sublime_train_data\.rda$
+^appveyor\.yml$

.gitignore

@@ -1,4 +1,5 @@
 .Rproj.user
 .Rhistory
 .RData
-*.nii.gz
+*.nii.gz
+data/.Rapp.history

.travis.yml

@@ -1,22 +1,27 @@
 # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
-
 language: R
 sudo: false
 cache: packages
-r_check_args: --as-cran
+
+services:
+  - xvfb
 
 before_script:
-  - "export DISPLAY=:99.0"
-  - "sh -e /etc/init.d/xvfb start"
-  - sleep 3
+  - fname=travis_helpers.sh
+  - wget -O ${fname} http://bit.ly/travis_helpers
+  - cat ${fname}; source ${fname}; rm ${fname}  
+  - codename=`linux_codename`;
+  - if [ "${codename}" = "trusty" ];
+    then
+      start_xvfb ;
+    fi  
+
+os: 
+  - linux
+  - osx
 
 bioc_required: yes
 use_bioc: yes
 r:
 - release
 - devel
-addons:
-  apt:
-    packages:
-    - tcl8.5-dev
-    - tk8.5-dev

DESCRIPTION

@@ -2,8 +2,8 @@ Package: sublime
 Type: Package
 Title: Automatic Lesion Incidence Estimation and Detection using 
     Multi-Modality Longitudinal Magnetic Resonance Images
-Version: 1.3
-Date: 2016-09-29
+Version: 1.6.3
+Date: 2019-10-22
 Authors@R: c(person(given = "Elizabeth M.", "Sweeney",  
   email = "elizabethmargaretsweeney@gmail.com", role = c("aut", "cre")),
   person(given = "John", "Muschelli",  
@@ -16,11 +16,16 @@ Description: Creates probability maps of incident and enlarging lesion voxels
 License: GPL
 LazyData: true
 Depends:
-    oro.nifti
+    oro.nifti,
+    R (>= 2.10)
 Imports:
     downloader,
     graphics,
     stats,
     grDevices,
     AnalyzeFMRI
-RoxygenNote: 5.0.1.9000
+RoxygenNote: 7.0.2
+Encoding: UTF-8
+Suggests: 
+    testthat (>= 2.1.0),
+    neurobase

NAMESPACE

@@ -3,10 +3,11 @@
 export(SuBLIME_prediction)
 export(download_data)
 export(normalize)
+export(sublime_prediction)
 export(voxel_select)
-import(downloader)
 import(oro.nifti)
 importFrom(AnalyzeFMRI,GaussSmoothArray)
+importFrom(downloader,download)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,gray)
 importFrom(grDevices,pdf)

R/SuBLIME_model.R

@@ -1,9 +1,30 @@
-#' @title Sublime Predictive model
+#' @title SuBLIME Predictive model
 #'
 #' @description Predictive model for SuBLIME algorithm
-#' @usage SuBLIME_model
-#' @format An \code{lm} object, but with data an other things, notably 
+#' @usage sublime_model
+#' @format An \code{glm} object, but with data an other things, notably 
 #' qr removed
 #' @references Sweeney, E. M., et al. "Automatic lesion incidence estimation and detection in multiple sclerosis using multisequence longitudinal MRI." American Journal of Neuroradiology 34.1 (2013): 68-73.
-"SuBLIME_model"
+"sublime_model"
+
+
+#' @title SuBLIME Predictive model without PD 
+#'
+#' @description Predictive model for SuBLIME algorithm without PD modality
+#' NOTE: this may perform much worse than the original SuBLIME model
+#' 
+#' @usage nopd_sublime_model
+#' @format An \code{glm} object, but with data an other things, notably 
+#' qr removed
+"nopd_sublime_model"
+
+
+#' @title SuBLIME Predictive model with only T1 and FLAIR
+#'
+#' @description Predictive model for SuBLIME algorithm with only T1 and FLAIR.
+#' NOTE: this may perform much worse than the original SuBLIME model
+#' @usage flairt1_sublime_model
+#' @format An \code{glm} object, but with data an other things, notably 
+#' qr removed
+"flairt1_sublime_model"