File version

.Rbuildignore

@@ -9,3 +9,5 @@ $run_dev.*
 ^\.travis\.yml$
 ^appveyor\.yml$
 ^cran-comments\.md$
+^\.github$
+^CRAN-SUBMISSION$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [cran, file_version]
+  pull_request:
+    branches: [cran, file_version]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.gitignore

@@ -0,0 +1,6 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+*.Rproj
+*.DS_Store

DESCRIPTION

@@ -1,12 +1,16 @@
 Package: vici
 Title: Vaccine Induced Cellular Immunogenicity with Bivariate Modeling
-Version: 0.5.4
-Date: 2019-08-21
-Authors@R: person('Boris', 'Hejblum', email = 'boris.hejblum@u-bordeaux.fr', role = c('cre', 'aut'))
+Version: 0.7.3
+Date: 2024-02-02
+Authors@R: c(person('Boris', 'Hejblum', email = 'boris.hejblum@u-bordeaux.fr', role = c('cre', 'aut')),
+             person('Melanie', 'Huchon', email = 'melanie.huchon@u-bordeaux.fr', role = c('aut')),
+             person('Clement', 'Nerestan', email = 'clement.nerestan@u-bordeaux.fr', role = c('aut'))
+           )
 Description: A shiny app for accurate estimation of vaccine induced immunogenicity 
     with bivariate linear modeling. Method is detailed in: Lhomme, Hejblum, Lacabaratz, 
-    Wiedemann, Lelievre, Levy, Thiebaut & Richert (2019). Submitted.
-BugReports: https://github.com/borishejblum/vici/issues
+    Wiedemann, Lelievre, Levy, Thiebaut & Richert (2020). Journal of Immunological Methods, 
+    477:112711. <doi:10.1016/j.jim.2019.112711>.
+BugReports: https://github.com/sistm/vici/issues
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
@@ -21,17 +25,11 @@ Imports:
     stats,
     tidyr,
     utils,
-    covr,
-    testthat,
-    RSelenium,
-    golem,
-    future,
-    pkgload,
-    processx, 
     numDeriv, 
-    methods,
     stringr,
-    MASS, 
-    Matrix, 
-    lmerTest
-RoxygenNote: 7.1.2
+    RColorBrewer,
+    scales,
+    shinyWidgets
+Suggests: 
+    testthat
+RoxygenNote: 7.3.0

NAMESPACE

@@ -5,14 +5,16 @@ export(mod_modelfit_ui)
 export(mod_settings_pan_server)
 export(mod_settings_pan_ui)
 export(run_app)
-import(Matrix)
+import(RColorBrewer)
 import(ggplot2)
 import(ggpubr)
-import(lmerTest)
+import(scales)
 import(shiny)
+import(shinyWidgets)
 importFrom(cowplot,plot_grid)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,png)
+importFrom(nlme,"coef<-")
 importFrom(nlme,Initialize)
 importFrom(nlme,asOneFormula)
 importFrom(nlme,getGroups)
@@ -39,15 +41,18 @@ importFrom(stats,contrasts)
 importFrom(stats,fitted)
 importFrom(stats,formula)
 importFrom(stats,logLik)
+importFrom(stats,model.frame)
 importFrom(stats,model.matrix)
 importFrom(stats,na.fail)
 importFrom(stats,na.omit)
 importFrom(stats,nlminb)
 importFrom(stats,optim)
 importFrom(stats,pt)
+importFrom(stats,qt)
 importFrom(stats,relevel)
 importFrom(stats,sigma)
 importFrom(stats,terms)
+importFrom(stats,update)
 importFrom(stats,vcov)
 importFrom(stringr,str_detect)
 importFrom(tidyr,spread)

NEWS.md

@@ -1,3 +1,11 @@
+# vici 0.7.0
+
+ * Added graphical options
+
+# vici 0.6.0
+
+ * Added support for additional degree of freedom methods 
+
 # vici 0.5.3
 
  * Added source code & CRAN link buttons