version 1.0.5

DESCRIPTION

@@ -1,23 +1,20 @@
 Package: MetaLonDA
 Type: Package
-Title: Metagenomics Longitudinal Differential Abundant Method
-Version: 1.0.4
-Date: 2017-07-26
+Title: Metagenomics Longitudinal Differential Abundance Method
+Version: 1.0.5
+Date: 2017-10-18
 Author: Ahmed Metwally, Patricia Finn, Yang Dai, David Perkins
 Maintainer: Ahmed Metwally <ametwa2@uic.edu>
-Description: Identify the time intervals when the microbial features are
-    differentially abundant between two phenotypic groups using negative binomial
-    smoothing spline ANOVA (Ahmed Metwally, Patricia Finn, Yang Dai, David Perkins, ACM BCB’17).
+Description: Identify time intervals of differentially abundant metagenomic features in longitudinal studies <doi:10.1145/3107411.3107429>.
 License: GPL-2
-Depends: R(>= 3.1.2)
-Imports: ggplot2, gss, plyr, caTools, parallel, doParallel
+Depends: R(>= 3.2.0)
+Imports: ggplot2, gss, plyr, caTools, parallel, doParallel,
+        metagenomeSeq, DESeq2, edgeR
 Suggests: knitr, rmarkdown
-VignetteBuilder: knitr
-URL: https://bitbucket.org/ametwally/metalonda
 Repository: CRAN
 NeedsCompilation: no
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.0.1
-Packaged: 2017-07-28 16:22:36 UTC; ahmedmetwally
-Date/Publication: 2017-07-28 17:27:33 UTC
+Packaged: 2017-10-20 15:23:40 UTC; ahmedmetwally
+Date/Publication: 2017-10-20 20:36:01 UTC

MD5

@@ -1,25 +1,23 @@
-1709aa26fb4395837866ae2bd12abe23 *DESCRIPTION
-8ce1b4fd1cbfcc9d5b398c465956c0e7 *NAMESPACE
-a32e1440ccf46b0d8ac15a336975b96c *R/CurveFitting.R
-a448bf28feaa0e67556d92e56d9dc6ee *R/Metalonda.R
-abf21a118c902980620185939aadebc7 *R/Permutation.R
-c30d41ecb4efdfb9bd187255b107972e *R/Visualization.R
+e957731f61503d887106cbde7168a717 *DESCRIPTION
+fb48afc4efd890f82dde5fc84d02849a *NAMESPACE
+a88ac42c120effed14c31e61d9ed694e *R/CurveFitting.R
+a194a3e4cf23076feaebf68c330d5937 *R/Metalonda.R
+a3d5a8aa94f98416121d075d21104896 *R/Normalization.R
+824b78e4827c59feaaae0c1eb8584a28 *R/Permutation.R
+9c3854773257e87dd4a3a4dc981e8a24 *R/Visualization.R
 69f35f3adb87ac4c2d8985fda6782dd4 *R/metalonda_test_data.R
-3366039b41c4e42ab445451bf40e268b *build/vignette.rds
 173a19ff73e64e4126b88c5c54164993 *data/metalonda_test_data.RData
-fe2caa47e63e11d7ebb8fd5b4183da39 *inst/doc/metalonda.R
-52069ef7bcc0ab5af15e5d493ba2107d *inst/doc/metalonda.Rmd
-c1a2599203b3c9cfa0367b47df4f1bc7 *inst/doc/metalonda.html
-66cf0cf147ae829b8ee3f52b1c141075 *man/areaPermutation.Rd
-fb7cdb8dda8f4a6653fc6cd1e611f413 *man/curveFitting.Rd
-1ee8b6feb041bcb6be7128457c8beb3a *man/findSigInterval.Rd
-1963cbf2a34a3f7ccc6e34ccfa3ebde0 *man/intervalArea.Rd
-4acf96dcc9cd0d25065593463c94c1ba *man/metalonda.Rd
-5e22eface25c90323d3162cde09d2560 *man/metalondaAll.Rd
-aa7a4a3b7d71b40d7343ea864b2bf2c9 *man/metalonda_test_data.Rd
-3c90794d061ea738a568ca0a477e1779 *man/permutation.Rd
-7e8b8a82d6653b036798ce9796c7f9ae *man/visualizeARHistogram.Rd
-14c32bb18bd4c931590947a5b428ad49 *man/visualizeArea.Rd
-1777d079c31410477ecad1a030f873ec *man/visualizeFeature.Rd
-7bead32b79bea5992f9ddc5281491da0 *man/visualizeFeatureSpline.Rd
-52069ef7bcc0ab5af15e5d493ba2107d *vignettes/metalonda.Rmd
+cde06f2321589f8404dd5c627ca19edb *man/areaPermutation.Rd
+625e54a4040ef4ebfd549233ce4cfb94 *man/curveFitting.Rd
+fb53395fc2b723cf2472947ba16170d3 *man/findSigInterval.Rd
+9b5b272a958e9affe0ca077683f070d6 *man/intervalArea.Rd
+ad0b35fc2cb201b590a6d79d3ae04959 *man/metalonda.Rd
+6128c195e1ccc4851752ceee27d951f3 *man/metalondaAll.Rd
+36892b451bf76a659402bc17b2ac4f09 *man/metalonda_test_data.Rd
+1f368ea253ab297ace72cf1283758871 *man/normalize.Rd
+790abc90c296c835fc34a54cc1bbaf69 *man/permutation.Rd
+a63bd3590a3776ec6fb72d746d659214 *man/visualizeARHistogram.Rd
+32ea5bebfb4ae1d60cc7c39516597f95 *man/visualizeArea.Rd
+8d72f18cc08070db702ff2c48f4e79de *man/visualizeFeature.Rd
+b4e435fc7cb695d2ca8e3049ede186da *man/visualizeFeatureSpline.Rd
+f46b25f4ce23aee80b2d2c3a5d4e16b6 *man/visualizeTimeIntervals.Rd

NAMESPACE

@@ -1,23 +1,25 @@
-# Generated by roxygen2: do not edit by hand
-
-export(areaPermutation)
-export(curveFitting)
-export(findSigInterval)
-export(intervalArea)
-export(metalonda)
-export(metalondaAll)
-export(permutation)
-export(visualizeARHistogram)
-export(visualizeArea)
-export(visualizeFeature)
-export(visualizeFeatureSpline)
-import(caTools)
-import(doParallel)
-import(ggplot2)
-import(grDevices)
-import(graphics)
-import(gss)
-import(parallel)
-import(plyr)
-import(stats)
-import(utils)
+# Generated by roxygen2: do not edit by hand
+
+export(areaPermutation)
+export(curveFitting)
+export(findSigInterval)
+export(intervalArea)
+export(metalonda)
+export(metalondaAll)
+export(normalize)
+export(permutation)
+export(visualizeARHistogram)
+export(visualizeArea)
+export(visualizeFeature)
+export(visualizeFeatureSpline)
+export(visualizeTimeIntervals)
+import(caTools)
+import(doParallel)
+import(ggplot2)
+import(grDevices)
+import(graphics)
+import(gss)
+import(parallel)
+import(plyr)
+import(stats)
+import(utils)