after benchmarking fixes

DESCRIPTION

@@ -1,10 +1,11 @@
 Package: GeoDiff
 Type: Package
 Title: Count model based differential expression and normalization on GeoMx RNA data
-Version: 1.1.2
+Version: 1.1.3
 Authors@R: c(person("Nicole", "Ortogero", email = "nortogero@nanostring.com", role = c("cre")),
              person("Lei", "Yang", email = "lyang@nanostring.com", role = c("aut")), 
-             person("Zhi", "Yang", email = "zyang@nanostring.com", role = c("aut")))
+             person("Zhi", "Yang", email = "zyang@nanostring.com", role = c("aut")),
+             person("Ned", "Booker", email = "ned@procogia.com", role = c("aut")))
 Description: A series of statistical models using count generating distributions 
     for background modelling, feature and sample QC, normalization and differential 
     expression analysis on GeoMx RNA data. The application of these methods are 
@@ -15,6 +16,7 @@ Imports:
     plyr,
     lme4,
     Rcpp (>= 1.0.4.6), 
+    Rfast,
     withr,
     methods,
     graphics,

NAMESPACE

@@ -1,32 +1,47 @@
 useDynLib(GeoDiff, .registration=TRUE)
 importFrom(Rcpp, evalCpp)
 
-
 import(Biobase)
 import(testthat)
-importFrom(NanoStringNCTools, esBy)
-importFrom(Matrix, bdiag)
-importFrom(lme4, lFormula)
-importFrom(robust, covRob)
-importFrom(graphics, boxplot)
-importFrom(graphics, abline)
-importFrom(withr, local_tempdir)
-importFrom(withr, local_dir)
-importFrom(GeomxTools, featureType)
-
+importClassesFrom(GeomxTools,NanoStringGeoMxSet)
+importFrom(Biobase,AnnotatedDataFrame)
+importFrom(Biobase,annotation)
+importFrom(Biobase,assayDataElement)
+importFrom(Biobase,experimentData)
+importFrom(Biobase,exprs)
+importFrom(Biobase,fData)
+importFrom(Biobase,featureNames)
+importFrom(Biobase,fvarLabels)
+importFrom(Biobase,notes)
+importFrom(Biobase,pData)
+importFrom(Biobase,phenoData)
+importFrom(Biobase,protocolData)
+importFrom(Biobase,sampleNames)
+importFrom(Biobase,varLabels)
+importFrom(GeomxTools,featureType)
+importFrom(Matrix,bdiag)
+importFrom(Rcpp,sourceCpp)
+importFrom(Rfast,colsums)
+importFrom(Rfast,rowsums)
+importFrom(graphics,abline)
+importFrom(graphics,boxplot)
+importFrom(lme4,lFormula)
+importFrom(robust,covRob)
+importFrom(Matrix,Matrix)
+import(Matrix)
 
-exportMethods(aggreprobe)
-exportMethods(fitPoisBG)
-exportMethods(diagPoisBG)
-exportMethods(QuanRange)
-exportMethods(BGScoreTest)
-exportMethods(fitNBth)
-exportMethods(fitPoisthNorm)
-exportMethods(fitNBthDE)
-exportMethods(coefNBth)
-exportMethods(contrastNBth)
-exportMethods(DENBth)
-exportMethods(fitNBthmDE)
+export(BGScoreTest)
+export(DENBth)
+export(QuanRange)
+export(aggreprobe)
+export(coefNBth)
+export(contrastNBth)
+export(diagPoisBG)
+export(fitNBth)
+export(fitNBthDE)
+export(fitNBthmDE)
+export(fitPoisBG)
+export(fitPoisthNorm)
 
 importFrom("stats", "cor", "cov", "dnbinom", "dpois", "mad", "median",
            "model.matrix", "na.omit", "optim", "p.adjust", "pnorm",

NEWS.md

@@ -55,3 +55,6 @@ Revisions
 
 * transfer maintainership
 
+# GeoDiff 1.1.3
+
+* implement code optimizations (mostly RFast and matrix methods) to speed up execution (NBth.R, NBthDE.R, PoisBG.R, PoisthNorm.R, ScoreTest.R). Added error handling, improved matrix methods, accelerated code for NBthDEOptPara.cpp Rcpp code.