Version 1 (#46)

* first commit

* added pulsar code, tests, docs

* fixed readme, description for travis

* fixed adding pulsar.params to call

* fixed biocview

* update travis.yml

* fix docs to pass checks

* remove writes in tests

* modify test

* merge master

.Rbuildignore

@@ -1,5 +1,5 @@
-^.*\.BatchJobs.*\.R$
-^README\.Rmd$
-^README\.log$
-^figure$
+## Ignore build and temp file
 ^\.travis\.yml$
+^figure*
+^\.README\.RData$
+^README\.Rmd$

.travis.yml

@@ -0,0 +1,5 @@
+language: r
+cache: packages
+sudo: false
+use_bioc: true
+bioc_required: true

DESCRIPTION

@@ -1,24 +1,36 @@
 Package: SpiecEasi
 Title: Sparse Inverse Covariance for Ecological Statistical Inference
-Version: 0.1.4
-Authors.R: c(person("Zachary", "Kurtz", role = c("aut", "cre"),
-    email="zachary.kurtz@med.nyu.edu"), person("Christian",
-    "Mueller", role = c("aut")), person("Emily", "Miraldi",
-    role=c("aut")), person("Richard", "Bonneau", role=c("aut")))
-Description: Estimate networks from the precision matrix of compositional
-    microbial abundance data
+Version: 1.0.0
+Authors@R: c(
+    person("Zachary", "Kurtz", role = c("aut", "cre"), email="zdkurtz@gmail.com"),
+    person("Christian", "Mueller", role = "aut"),
+    person("Emily", "Miraldi",     role="aut"),
+    person("Richard", "Bonneau",   role="aut"),
+    person("Laura", "Tipton",      role="ctb"))
+Description: Estimate networks from the precision matrix of compositional microbial abundance data.
+Encoding: UTF-8
 Depends:
-    R (>= 3.0.0),
+   R (>= 3.3.0),
 Imports:
-    huge,
-    MASS,
-    VGAM,
-    Matrix
+   stats,
+   methods,
+   graphics,
+   grDevices,
+   huge,
+   pulsar,
+   MASS,
+   VGAM,
+   Matrix
 Suggests:
-    parallel,
-    boot,
-    phyloseq,
-    testthat
-License: getOptions('devtools.desc.license')
+   parallel,
+   boot,
+   phyloseq,
+   igraph,
+   batchtools,
+   testthat
+Remotes:
+   bioc::phyloseq
+biocViews:
+License: GPL (>= 2)
 LazyData: true
 RoxygenNote: 6.0.1

NAMESPACE

@@ -9,6 +9,7 @@ S3method(clr,data.frame)
 S3method(clr,default)
 S3method(clr,matrix)
 S3method(spiec.easi,default)
+S3method(spiec.easi,list)
 S3method(spiec.easi,otu_table)
 S3method(spiec.easi,phyloseq)
 export(adj2igraph)
@@ -18,14 +19,19 @@ export(cor2cov)
 export(cov2prec)
 export(fitdistr)
 export(getOptBeta)
+export(getOptCov)
+export(getOptInd)
+export(getOptLambda)
 export(getOptMerge)
+export(getOptNet)
+export(getOptiCov)
+export(getRefit)
+export(getStability)
 export(get_comm_params)
 export(graph2prec)
-export(icov.select)
 export(make_graph)
-export(multivnomial)
+export(multi.spiec.easi)
 export(neff)
-export(norm_diric)
 export(norm_pseudo)
 export(norm_to_total)
 export(prec2cov)
@@ -46,21 +52,41 @@ export(stars.pr)
 export(stars.roc)
 export(symBeta)
 export(synth_comm_from_counts)
-export(tril)
-export(triu)
-export(triu2diag)
 importFrom(MASS,ginv)
-importFrom(Matrix,forceSymmetric)
-importFrom(Matrix,t)
 importFrom(VGAM,dzinegbin)
 importFrom(VGAM,dzipois)
 importFrom(VGAM,qzinegbin)
 importFrom(VGAM,qzipois)
+importFrom(VGAM,rdiric)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,png)
+importFrom(graphics,abline)
+importFrom(graphics,legend)
+importFrom(graphics,par)
+importFrom(graphics,plot)
 importFrom(huge,huge)
 importFrom(huge,huge.npn)
-importFrom(parallel,mclapply)
+importFrom(methods,as)
+importFrom(pulsar,batch.pulsar)
+importFrom(pulsar,pulsar)
+importFrom(stats,cor)
+importFrom(stats,cov)
+importFrom(stats,cov2cor)
 importFrom(stats,dnbinom)
 importFrom(stats,dpois)
+importFrom(stats,lm)
+importFrom(stats,median)
+importFrom(stats,na.exclude)
+importFrom(stats,na.omit)
+importFrom(stats,optim)
+importFrom(stats,pnorm)
+importFrom(stats,ppoints)
+importFrom(stats,qlnorm)
 importFrom(stats,qnbinom)
 importFrom(stats,qpois)
+importFrom(stats,rmultinom)
+importFrom(stats,rnorm)
+importFrom(stats,rpois)
 importFrom(stats,runif)
+importFrom(stats,sd)
+importFrom(stats,var)