Compare file_version & cran

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

@@ -2,9 +2,15 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
+<<<<<<< HEAD
     branches: [main, master, cran]
   pull_request:
     branches: [main, master, cran]
+=======
+    branches: [main, master, cran, labkey]
+  pull_request:
+    branches: [main, master, cran, labkey]
+>>>>>>> 4b702d8f21a61cae9312b45b8a221d3949aaf732
 
 name: R-CMD-check
 
@@ -28,6 +34,24 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
+<<<<<<< HEAD
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        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@v1
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v1
+=======
 #    steps:
 #      - uses: actions/checkout@v2
 #
@@ -56,3 +80,4 @@ jobs:
 #        with:
 #          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
 #          path: check
+>>>>>>> 4b702d8f21a61cae9312b45b8a221d3949aaf732

.gitignore

@@ -2,5 +2,9 @@
 .Rhistory
 .RData
 .Ruserdata
+<<<<<<< HEAD
+*.DS_Store
+=======
 *.Rproj
-*.DS_Store
+*.DS_Store
+>>>>>>> 4b702d8f21a61cae9312b45b8a221d3949aaf732

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: 0.7.0
+Date: 2022-06-27
+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
@@ -17,21 +21,15 @@ Imports:
     grDevices,
     ggpubr,
     nlme,
+    numDeriv,
     shiny,
     stats,
+    stringr,
     tidyr,
     utils,
-    covr,
-    testthat,
-    RSelenium,
-    golem,
-    future,
-    pkgload,
-    processx, 
-    numDeriv, 
-    methods,
-    stringr,
-    MASS, 
-    Matrix, 
-    lmerTest
-RoxygenNote: 7.1.2
+    scales,
+    shinyWidgets,
+    RColorBrewer
+Suggests:
+    testthat
+RoxygenNote: 7.2.3

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 +1,7 @@
+# vici 0.6.0
+
+ * Added support for additional degree of freedom methods 
+
 # vici 0.5.3
 
  * Added source code & CRAN link buttons

R/BW_functions.R

@@ -1,5 +1,12 @@
 #' Between-Within functions to obtain Denominator degrees of freedom
 #' 
+#' Internal function to calculate Between-Within degrees of freedom
+#' 
+#' @param object a \code{gls} model object.
+#' @param L a numeric vector of the same length as the number of fixed effects from \code{object}.
+#' 
+#' @return a \code{number} object
+#' 
 #' @keywords internal
 #' 
 #' @importFrom stringr str_detect
@@ -15,7 +22,6 @@ ddf_BW <- function(object, L){
 
   for (i in 1:length(sys.parents())){
     if (exists("transformed_data", envir = parent.frame(n=i), inherits=FALSE)){
-      # formul <- get("myformul", envir = parent.frame(n=i),  inherits=FALSE)
       data.obj <- get("transformed_data", envir = parent.frame(n=i),  inherits=FALSE)
     }
     if (exists("input", envir = parent.frame(n=i), inherits=FALSE)){
@@ -29,19 +35,19 @@ ddf_BW <- function(object, L){
   armRef <- input.obj$selectRefArmInter
   n_obs_armRef <- nrow(data.obj[which(data.obj$arm==armRef),])
 
-  n_param_interac <-  length(stringr::str_detect(parameters, ":")[stringr::str_detect(parameters, ":")==TRUE])
+  n_param_interac <-  length(str_detect(parameters, ":")[str_detect(parameters, ":")==TRUE])
 
-  n_param_bkg <- length(stringr::str_detect(parameters, "bkg")[stringr::str_detect(parameters, "bkg")==TRUE])
+  n_param_bkg <- length(str_detect(parameters, "bkg")[str_detect(parameters, "bkg")==TRUE])
 
   # for inter-arm
   if(input.obj$selectModel == "1"){
-    if(stringr::str_detect(est_param, "bkg")){
+    if(str_detect(est_param, "bkg")){
       #ddf_between
       ddf <-  n_obs - n_indiv - n_param
-    }  else if(stringr::str_detect(est_param, ":")){
+    }else if(str_detect(est_param, ":")){
       #ddf_within for stim
       ddf <-  n_obs - n_obs_armRef - n_param_interac
-    } else{
+    }else{
       #ddf_within for stim and arm
       ddf <- n_obs_armRef - n_indiv - (n_param - n_param_interac - n_param_bkg)
     }
@@ -50,7 +56,7 @@ ddf_BW <- function(object, L){
     ddf <-  n_obs - n_indiv - n_param
   }
 
-  ddf
+  return(ddf)
 
 }