Merge branch 'release/v0.7.0'

.Rbuildignore

@@ -1,8 +1,20 @@
-^.*\.Rproj$
+^CRAN-RELEASE$
+## MEMO: While gitignore uses shell glob, Rbuildignore uses regex.
+
 ^\.Rproj\.user$
-^.*\.o$
-^\cleanup*
-^.*\.Rmd
-^\.editorconfig
-^\.travis\.yml
-^\.gitignore
+\.Rproj$
+\.Rmd$
+\.o$
+^docs/
+^man-roxygen/
+^src/stan_files/.*\.o$
+^src/stan_files/.*\.cc$
+^src/stan_files/.*\.hpp$
+^README\.md$
+^LICENSE$
+^\.editorconfig$
+^\.gitignore$
+^\.travis\.yml$
+^_pkgdown\.yml$
+^codecov\.yml$
+^cran-comments\.md$

.gitignore

@@ -1,3 +1,8 @@
+## MEMO: While gitignore uses shell glob, Rbuildignore uses regex.
+
+# RStudio files
+.Rproj.user
+
 # History files
 .Rhistory
 .Rapp.history
@@ -30,13 +35,15 @@ vignettes/*.pdf
 *.utf8.md
 *.knit.md
 
-# Source files
-src/Modules*
+# Source files (new)
+src/stan_files/*.o
+src/stan_files/*.o.tmp
+src/stan_files/*.cc
+src/stan_files/*.hpp
+src/RcppExports.*
 src/hBayesDM.so
 src/hBayesDM.dll
-src/include
-src/RcppExports.*
-
-# RStudio files
-.Rproj.user
+src/init.o
 
+# CRAN-RELEASE
+CRAN-RELEASE

.travis.yml

@@ -1,43 +1,80 @@
 language: r
-r:
-  - oldrel
-  - release
+sudo: false
 
-# Be strict when checking our package
-warnings_are_errors: false
+branches:
+  only:
+    - master
+    - develop
+    - /release\/.*/
+    - /hotfix\/.*/
+    - /bugfix\/.*/
 
-# Sudo is required
-sudo: true
-
-# Use trusty distribution of linux
-dist: trusty
-
-# Use both linux and osx operating systems
-os:
-  - linux
-  - osx
+r_build_args: '--no-build-vignettes'
+r_check_args: '--ignore-vignettes'
 
 # Use cache for packages
 cache:
   apt: true
   packages: true
+  ccache: true
+
+env:
+  global:
+    - MAKEFLAGS="-j 2"
 
-# System dependencies for HTTP calling
-addons:
-  apt:
-    packages:
-      - libgit2-dev
-      - libcurl4-openssl-dev
-      - libxml2-dev
+matrix:
+  include:
+    - name: Ubuntu + g++-7
+      os: linux
+      dist: trusty
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+            - gcc-7
+            - g++-7
+            - gfortran-7
+      env:
+        - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
+    - name: Ubuntu + g++-7 (BUILD_ALL)
+      os: linux
+      dist: trusty
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+            - gcc-7
+            - g++-7
+            - gfortran-7
+      env:
+        - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
+        - BUILD_ALL="true"
+
+before_install:
+  - eval "${MATRIX_EVAL}"
+  - mkdir -p ~/.R/
+  - echo "CC = $CC" >> ~/.R/Makevars
+  - echo "CXX = ${CXX} -fPIC " >> ~/.R/Makevars
+  - echo "CXX14 = ${CXX} -fPIC -flto=2" >> ~/.R/Makevars
+  - echo "CXX14FLAGS = -mtune=native -march=native -Wno-ignored-attributes -O0" >> ~/.R/Makevars
+
+install:
+  - R -e 'install.packages("devtools", quiet = T)' -e 'devtools::install_deps(dep = T, quiet = T)'
 
 script:
-  - travis_wait 30 R CMD build .
+  - travis_wait 42 R CMD build .
+  - travis_wait 59 R CMD check hBayesDM*.tar.gz --as-cran
 
 r_binary_packages:
   - testthat
 
-r_github_packages:
-  - jimhester/covr
+# r_github_packages:
+#   - r-lib/covr
+
+# after_success:
+#   - Rscript -e 'covr::codecov()'
 
-after_success:
-  - Rscript -e 'covr::codecov()'
+after_failure:
+  - cat hBayesDM.Rcheck/00*

DESCRIPTION

@@ -1,48 +1,109 @@
 Package: hBayesDM
 Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
-Version: 0.6.3
-Date: 2018-10-30
+Version: 0.7.0
+Date: 2018-12-14
 Author:
     Woo-Young Ahn [aut, cre],
     Nate Haines [aut],
     Lei Zhang [aut],
     Harhim Park [ctb],
     Jaeyeong Yang [ctb],
-    Dayeong Min [ctb],
     Jethro Lee [ctb]
 Authors@R: c(
     person("Woo-Young", "Ahn", email = "[email protected]", role = c("aut", "cre")),
     person("Nate", "Haines", email = "[email protected]", role = c("aut")),
     person("Lei", "Zhang", email = "[email protected]", role = c("aut")),
     person("Harhim", "Park", email = "[email protected]", role = c("ctb")),
     person("Jaeyeong", "Yang", email = "[email protected]", role = c("ctb")),
-    person("Dayeong", "Min", email = "[email protected]", role = c("ctb")),
     person("Jethro", "Lee", email = "[email protected]", role = c("ctb")))
 Maintainer: Woo-Young Ahn <[email protected]>
 Description:
     Fit an array of decision-making tasks with computational models in
     a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
     various computational models with a single line of coding.
 Depends:
-    R (>= 3.4.0),
-    Rcpp (>= 0.12.0),
-    methods
+    R (>= 3.4.0)
 Imports:
+    methods,
+    Rcpp (>= 0.12.0),
     rstan (>= 2.18.1),
     loo (>= 2.0),
     grid,
     parallel,
-    ggplot2
+    ggplot2,
+    data.table
 LinkingTo:
-    StanHeaders (>= 2.18.0),
-    rstan (>= 2.18.1),
     BH (>= 1.66.0),
     Rcpp (>= 0.12.0),
-    RcppEigen (>= 0.3.3.3.0)
+    RcppEigen (>= 0.3.3.3.0),
+    rstan (>= 2.18.1),
+    StanHeaders (>= 2.18.0)
 URL: https://rpubs.com/CCSL/hBayesDM
 BugReports: https://github.com/CCS-Lab/hBayesDM/issues
 License: GPL-3
 LazyData: true
 NeedsCompilation: yes
 Encoding: UTF-8
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
+SystemRequirements: GNU make
+Collate:
+    'HDIofMCMC.R'
+    'stanmodels.R'
+    'settings.R'
+    'hBayesDM_model.R'
+    'bandit2arm_delta.R'
+    'bandit4arm2_kalman_filter.R'
+    'bandit4arm_4par.R'
+    'bandit4arm_lapse.R'
+    'bart_par4.R'
+    'choiceRT_ddm.R'
+    'choiceRT_ddm_single.R'
+    'choiceRT_lba.R'
+    'choiceRT_lba_single.R'
+    'cra_exp.R'
+    'cra_linear.R'
+    'dbdm_prob_weight.R'
+    'dd_cs.R'
+    'dd_cs_single.R'
+    'dd_exp.R'
+    'dd_hyperbolic.R'
+    'dd_hyperbolic_single.R'
+    'estimate_mode.R'
+    'extract_ic.R'
+    'gng_m1.R'
+    'gng_m2.R'
+    'gng_m3.R'
+    'gng_m4.R'
+    'hBayesDM.R'
+    'igt_orl.R'
+    'igt_pvl_decay.R'
+    'igt_pvl_delta.R'
+    'igt_vpp.R'
+    'multiplot.R'
+    'peer_ocu.R'
+    'plot.hBayesDM.R'
+    'plotDist.R'
+    'plotHDI.R'
+    'plotInd.R'
+    'printFit.R'
+    'prl_ewa.R'
+    'prl_fictitious.R'
+    'prl_fictitious_multipleB.R'
+    'prl_fictitious_rp.R'
+    'prl_fictitious_rp_woa.R'
+    'prl_fictitious_woa.R'
+    'prl_rp.R'
+    'prl_rp_multipleB.R'
+    'pst_gainloss_Q.R'
+    'ra_noLA.R'
+    'ra_noRA.R'
+    'ra_prospect.R'
+    'rdt_happiness.R'
+    'rhat.R'
+    'ts_par4.R'
+    'ts_par6.R'
+    'ts_par7.R'
+    'ug_bayes.R'
+    'ug_delta.R'
+    'wcs_sql.R'
+    'zzz.R'