Improve documentation and package imports

.Rinstignore

@@ -0,0 +1 @@
+dev/

DESCRIPTION

@@ -36,57 +36,56 @@ Imports:
     methods,
     S4Vectors,
     crayon,
-    Matrix
+    Matrix,
+    pkgconfig,
+    AnnotationDbi,
+    DESeq2,
+    Rtsne,
+    Seurat,
+    betareg,
+    boot,
+    broom, 
+    class, 
+    clusterProfiler, 
+    e1071, 
+    edgeR,
+    functional, 
+    glmmSeq, 
+    glmmTMB, 
+    limma, 
+    lme4, 
+    matrixStats,
+    msigdbr, 
+    org.Hs.eg.db,
+    org.Mm.eg.db, 
+    pbapply, 
+    pbmcapply,
+    survival,
+    survminer, 
+    sva, 
+    uwot,
+    widyr
 Suggests:
+    tidySummarizedExperiment,
+    tidyHeatmap,
     BiocStyle,
     testthat,
     vctrs,
-    AnnotationDbi,
     BiocManager,
     Rsubread,
-    e1071,
-    edgeR,
-    limma,
-    org.Hs.eg.db,
-    org.Mm.eg.db,
-    sva,
     GGally,
     knitr,
     qpdf,
     covr,
-    Seurat,
     KernSmooth,
-    Rtsne,
     ggplot2,
-    widyr,
-    clusterProfiler,
-    msigdbr,
-    DESeq2,
-    broom,
-    survival,
-    boot,
-    betareg,
-    tidyHeatmap,
     pasilla,
     ggrepel,
-    devtools,
-    functional,
-    survminer,
-    tidySummarizedExperiment,
     markdown,
-    uwot,
-    matrixStats,
     igraph,
-    EGSEA,
     IRanges,
     here,
-    glmmSeq,
-    pbapply,
-    pbmcapply,
-    lme4,
-    glmmTMB,
-    MASS,
-    pkgconfig
+    MASS
 VignetteBuilder: 
     knitr
 RdMacros:

NAMESPACE

@@ -16,37 +16,29 @@ S3method(rename,tidybulk)
 S3method(right_join,tidybulk)
 S3method(rowwise,tidybulk)
 S3method(summarise,tidybulk)
+S3method(summarize,tidybulk)
 S3method(ungroup,tidybulk)
 S3method(unnest,nested_tidybulk)
+S3method(validation,tidybulk)
 export("%>%")
 export(adjust_abundance)
 export(aggregate_duplicates)
-export(arrange)
 export(as_SummarizedExperiment)
 export(as_matrix)
 export(as_tibble)
-export(bind_cols)
 export(cluster_elements)
 export(deconvolve_cellularity)
 export(describe_transcript)
-export(distinct)
 export(do)
 export(ensembl_to_symbol)
 export(fill_missing_abundance)
-export(filter)
-export(full_join)
 export(get_bibliography)
-export(group_by)
 export(identify_abundant)
 export(impute_missing_abundance)
-export(inner_join)
 export(keep_abundant)
 export(keep_variable)
-export(left_join)
 export(log10_reverse_trans)
 export(logit_trans)
-export(mutate)
-export(nest)
 export(pivot_sample)
 export(pivot_transcript)
 export(quantile_normalise_abundance)
@@ -56,10 +48,8 @@ export(rename)
 export(resolve_complete_confounders_of_non_interest)
 export(right_join)
 export(rotate_dimensions)
-export(rowwise)
 export(scale_abundance)
 export(select)
-export(summarise)
 export(symbol_to_entrez)
 export(test_differential_abundance)
 export(test_differential_cellularity)
@@ -70,14 +60,16 @@ export(test_stratification_cellularity)
 export(tibble)
 export(tidybulk)
 export(tidybulk_SAM_BAM)
-export(unnest)
+export(validation_default)
 exportMethods(as_SummarizedExperiment)
 exportMethods(quantile_normalise_abundance)
 exportMethods(scale_abundance)
 exportMethods(tidybulk)
 exportMethods(tidybulk_SAM_BAM)
 import(SummarizedExperiment)
+import(e1071)
 import(lifecycle)
+import(lme4)
 import(methods)
 import(parallel)
 import(preprocessCore)
@@ -91,6 +83,9 @@ importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(SummarizedExperiment,rowRanges)
+importFrom(betareg,betareg)
+importFrom(boot,logit)
+importFrom(broom,tidy)
 importFrom(dplyr,across)
 importFrom(dplyr,anti_join)
 importFrom(dplyr,arrange)
@@ -123,7 +118,10 @@ importFrom(dplyr,slice)
 importFrom(dplyr,starts_with)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_all)
+importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
+importFrom(functional,Compose)
+importFrom(glmmTMB,glmmTMBControl)
 importFrom(lifecycle,deprecate_soft)
 importFrom(lifecycle,deprecate_warn)
 importFrom(magrittr,"%$%")
@@ -134,7 +132,12 @@ importFrom(magrittr,extract2)
 importFrom(magrittr,multiply_by)
 importFrom(magrittr,set_colnames)
 importFrom(magrittr,set_rownames)
+importFrom(matrixStats,colSds)
+importFrom(parallel,clusterExport)
+importFrom(parallel,makeCluster)
 importFrom(parallel,mclapply)
+importFrom(pbapply,pblapply)
+importFrom(pbmcapply,pbmclapply)
 importFrom(purrr,as_mapper)
 importFrom(purrr,map)
 importFrom(purrr,map2)
@@ -151,7 +154,6 @@ importFrom(rlang,":=")
 importFrom(rlang,dots_list)
 importFrom(rlang,dots_values)
 importFrom(rlang,enquo)
-importFrom(rlang,enquos)
 importFrom(rlang,flatten_if)
 importFrom(rlang,inform)
 importFrom(rlang,is_spliced)
@@ -178,9 +180,7 @@ importFrom(stats,model.matrix)
 importFrom(stats,na.omit)
 importFrom(stats,p.adjust)
 importFrom(stats,pchisq)
-importFrom(stats,plogis)
 importFrom(stats,prcomp)
-importFrom(stats,qlogis)
 importFrom(stats,rnorm)
 importFrom(stats,sd)
 importFrom(stats,setNames)
@@ -192,6 +192,10 @@ importFrom(stringr,str_remove)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_split)
+importFrom(survival,coxph)
+importFrom(survival,survdiff)
+importFrom(survminer,ggsurvplot)
+importFrom(survminer,surv_fit)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
 importFrom(tibble,rowid_to_column)

R/attach.R

@@ -0,0 +1,22 @@
+core <- c("dplyr", "tidyr", "ttservice")
+
+core_unloaded <- function() {
+  search <- paste0("package:", core)
+  core[!search %in% search()]
+}
+
+
+same_library <- function(pkg) {
+  loc <- if (pkg %in% loadedNamespaces()) 
+    dirname(getNamespaceInfo(pkg, "path"))
+  library(pkg, lib.loc=loc, character.only=TRUE, warn.conflicts=FALSE)
+}
+
+tidyverse_attach <- function() {
+  to_load <- core_unloaded()
+
+  suppressPackageStartupMessages(
+    lapply(to_load, same_library))
+
+  invisible(to_load)
+}

R/cibersort.R

@@ -202,8 +202,11 @@ call_core = function(itor, Y, X, P, pval, CoreAlg){
 }
 
 
+#' @import e1071
+#' @import parallel
+#' @import preprocessCore
 #' @importFrom stats sd
-#' @importFrom utils install.packages
+#' @importFrom matrixStats colSds
 #'
 #' @keywords internal
 #'
@@ -255,12 +258,6 @@ my_CIBERSORT <- function(Y, X, perm=0, QN=TRUE, cores = 3, exp_transform = FALSE
     ))
   Y=Y[,colSums(Y)>0, drop=FALSE]
 
-  # Check if package is installed, otherwise install
-  if (find.package("matrixStats", quiet = TRUE) %>% length %>% equals(0)) {
-    message("tidybulk says: Installing matrixStats needed for cibersort")
-    install.packages("matrixStats", repos = "https://cloud.r-project.org")
-  }
-
   # Eliminate sd == 0
   if(length(which(matrixStats::colSds(Y)==0))>0)
     warning(sprintf(