major update: add ancombc2 function

.Rbuildignore

@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^data-raw$

DESCRIPTION

@@ -1,32 +1,34 @@
 Package: ANCOMBC
 Type: Package
-Title: Analysis of compositions of microbiomes with bias correction
+Title: Microbiome differential abudance and correlation analyses with bias 
+    correction
 Version: 1.99.1
 Description: ANCOMBC is a package containing differential abundance (DA) and 
     correlation analyses for microbiome data. Specifically, the package includes 
-    Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) and 
+    Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2),
+    Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and 
     Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse 
     Estimation of Correlations among Microbiomes (SECOM) for correlation 
     analysis. Microbiome data are typically subject to two sources of biases: 
     unequal sampling fractions (sample-specific biases) and differential 
     sequencing efficiencies (taxon-specific biases). Methodologies included in 
-    the ANCOMBC package were designed to correct these biases and construct 
+    the ANCOMBC package are designed to correct these biases and construct 
     statistically consistent estimators.
-Date: 2022-06-24
+Date: 2022-10-10
 Authors@R: c(
     person(given = "Huang", 
            family = "Lin", 
            email = "[email protected]", 
            role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-4892-7871")))
 License: Artistic-2.0
-Imports: magrittr, Rdpack, rlang, 
-    microbiome, phyloseq, stats, 
-    DescTools, Hmisc, MASS, doParallel, doRNG, 
-    dplyr, energy, foreach, nlme, nloptr, parallel, tibble, tidyr 
+Imports: mia, stats, 
+    CVXR, DescTools, Hmisc, MASS, Rdpack, S4Vectors, SingleCellExperiment,
+    SummarizedExperiment, doParallel, doRNG, dplyr, emmeans, energy,
+    foreach, lmerTest, magrittr, nlme, nloptr, parallel, rlang, rngtools,
+    tibble, tidyr, utils
 Suggests: knitr, rmarkdown, testthat, 
-    DT, corrplot, ggforce, limma,
-    qwraps2 (>= 0.5.0), tidyverse
+    DT, caret, microbiome, tidyverse
 biocViews: 
     DifferentialExpression, 
     Microbiome, 
@@ -39,3 +41,6 @@ VignetteBuilder: knitr
 RdMacros: Rdpack
 Encoding: UTF-8
 RoxygenNote: 7.2.0
+Depends: 
+    R (>= 4.2.0)
+LazyData: false

NAMESPACE

@@ -2,32 +2,50 @@
 
 export(ancom)
 export(ancombc)
+export(ancombc2)
 export(secom_dist)
 export(secom_linear)
-import(microbiome)
-import(SummarizedExperiment)
-import(phyloseq)
+export(sim_plnm)
+import(mia)
 import(stats, except = filter)
+import(stats, except = filter)
+
+importFrom(CVXR,Minimize)
+importFrom(CVXR,Problem)
+importFrom(CVXR,Variable)
+importFrom(CVXR,matrix_frac)
+importFrom(CVXR,solve)
 importFrom(DescTools,Winsorize)
 importFrom(Hmisc,rcorr)
 importFrom(MASS,ginv)
 importFrom(Rdpack,reprompt)
+importFrom(S4Vectors,DataFrame)
+importFrom(SingleCellExperiment,altExp)
+importFrom(SummarizedExperiment,assay)
+importFrom(SummarizedExperiment,colData)
+importFrom(SummarizedExperiment,rowData)
 importFrom(doParallel,registerDoParallel)
 importFrom(doRNG,"%dorng%")
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,filter)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,right_join)
+importFrom(emmeans,contrast)
+importFrom(emmeans,emmeans)
 importFrom(energy,dcor)
 importFrom(energy,dcor.test)
+importFrom(foreach,"%:%")
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
+importFrom(lmerTest,lmer)
 importFrom(magrittr,"%>%")
 importFrom(nlme,lme)
 importFrom(nloptr,neldermead)
 importFrom(parallel,makeCluster)
 importFrom(parallel,stopCluster)
 importFrom(rlang,.data)
+importFrom(rngtools,setRNG)
 importFrom(tibble,rownames_to_column)
 importFrom(tidyr,pivot_longer)
+importFrom(utils,combn)

NEWS

@@ -1,9 +1,10 @@
-version 2.0.xx (last update 2022-06-07)
-        + Updated ancombc warning messages, added ancom and secom functions
+version 2.0.xx (last update 2022-10-10)
+        + add ancombc2 function
 
 version 1.6.xx (last update 2021-08-13)
         + Fixed bugs
         + Updated warning messages
+        + Add secom functions
 
 version 1.0.0: (2020-10-31)
         + Release!