version 0.5.0

cran · May 18, 2018 · 05637ae · 05637ae
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: DEploid
 Type: Package
 Title: Deconvolute Mixed Genomes with Unknown Proportions
-Version: 0.4.4
+Version: 0.5.0
 Authors@R: c(
     person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="joe.zhu@well.ox.ac.uk"),
     person('Jacob', 'Almagro-Garcia', role=c('aut', 'cph')),
@@ -27,15 +27,15 @@ BugReports: https://github.com/mcveanlab/DEploid-r/issues
 License: GPL (>= 3)
 Depends: R (>= 3.1.0)
 Imports: Rcpp (>= 0.11.2), scales (>= 0.4.0), plotly (>= 4.7.1),
-        magrittr (>= 1.5)
-Suggests: knitr, rmarkdown, testthat (>= 0.9.0)
+        magrittr (>= 1.5), rmarkdown(>= 1.6), htmlwidgets (>= 1.0)
+Suggests: knitr, testthat (>= 0.9.0)
 SystemRequirements: C++11
 VignetteBuilder: knitr
 LinkingTo: Rcpp
 RoxygenNote: 6.0.1
-Date: 2017-08-09
+Date: 2018-05-18
 NeedsCompilation: yes
-Packaged: 2017-09-01 00:24:49 UTC; joezhu
+Packaged: 2018-05-18 00:48:15 UTC; joezhu
 Author: Joe Zhu [aut, cre, cph],
   Jacob Almagro-Garcia [aut, cph],
   Gil McVean [aut, cph],
@@ -46,4 +46,4 @@ Author: Joe Zhu [aut, cre, cph],
   Lutz Kettner [com, cph]
 Maintainer: Joe Zhu <joe.zhu@well.ox.ac.uk>
 Repository: CRAN
-Date/Publication: 2017-09-01 03:09:29 UTC
+Date/Publication: 2018-05-18 03:28:52 UTC
diff --git a/MD5 b/MD5
@@ -1,15 +1,15 @@
-ab020c6fd247593f19934b13a0f9e82d *DESCRIPTION
-60325fac7a82f3e45ef81515447c8dc1 *NAMESPACE
+4fdc1ed1a70c225011e6386926ddf03c *DESCRIPTION
+620dec5abe35747430a215d8d65731bb *NAMESPACE
 3f730ab29544fc1d63946a50242f3a42 *R/DEploidR.R
 7efdf7afe8931c93c9c3cdf32a85fb6b *R/RcppExports.R
 856a9b3317faac53312a512e049ca0f9 *R/dEploid.R
 5a2e60ac3ffc29399ffaa1a2308ba8ae *R/dEploidPlotly.R
 db8dd67bf1ee95720e0b4deeefe17540 *README.md
-4b8735c3042553d77ef67496617e1a7a *build/vignette.rds
+3d5ac8ca720160834e8b1aeedfa70f91 *build/vignette.rds
 461e2dc267742100128d50cd74e757e2 *inst/CITATION
 01c90976b229646ca9b46399709688e3 *inst/doc/dEploid-Arguments.R
 2cbf6a6a60e07984981e6a2329578f8e *inst/doc/dEploid-Arguments.Rmd
-a9c2ba5451ed9582be1822d1ef3c9467 *inst/doc/dEploid-Arguments.html
+f2edea2b41c5cd260b0cf03f43188ef0 *inst/doc/dEploid-Arguments.html
 2cad08193815864d8a26f8ac768ef199 *inst/extdata/PG0390-C.test.alt
 07eccfaeb952de9e0460bcc12d457b22 *inst/extdata/PG0390-C.test.ref
 cdc601c1d8d4eec2bc80512eb8ee6b6b *inst/extdata/PG0390-C.test.vcf.gz
@@ -50,16 +50,16 @@ ccec2bc4b1d1436416711e52b16ef3e0 *src/DEploid/codeCogs/mersenne.hpp
 785e0971c65e88f066c599e4ba8f9324 *src/DEploid/codeCogs/randomSample.hpp
 94c33b48dee38eb7bdc87638e718e09e *src/DEploid/codeCogs/stirling.h
 a3585d8d0b267c7076cc835be837bf5f *src/DEploid/codeCogs/xsub_ln_add1.h
-ccf0d382ab75490ff2169f016cf93b3e *src/DEploid/dEploid.cpp
-3a466176ccc4aaed26325bd05190926e *src/DEploid/dEploidIO.cpp
-19bf6527a2e09276b55f6ead8559b4a4 *src/DEploid/dEploidIO.hpp
+f9b087d7b842b8643f4d25d603743318 *src/DEploid/dEploid.cpp
+bbd1b22c0850d75aa167cc1eaacc5674 *src/DEploid/dEploidIO.cpp
+8b388f005027d34627afff745978bd90 *src/DEploid/dEploidIO.hpp
 ee6cc55608c5471dc7c16aa58087f35b *src/DEploid/debug/mcmcDebug.cpp
 18baed6c81141bf971540f6eeaaffd6b *src/DEploid/debug/vcfReaderDebug.cpp
-7e6d21967aeeb18294f9325b05fecbe7 *src/DEploid/exceptions.hpp
-32c3153abb61241132535cb70e6f11ef *src/DEploid/export/dEploidIOExport.cpp
-d89a3ce3499ae6ad9d49b8212636322b *src/DEploid/export/dEploidIOExportPosteriorProb.cpp
-1175c0426828f9f27d61eff150f2b0a9 *src/DEploid/export/writeMcmcRelated.cpp
-5d8d873e67678af9b2c4cd95f10c6493 *src/DEploid/global.h
+8067e22d89f4b2b23e03ed415a53c172 *src/DEploid/exceptions.hpp
+86ca88bd81de69cd9d83916ea56f6e1e *src/DEploid/export/dEploidIOExport.cpp
+391762551ff34224643d84913249c130 *src/DEploid/export/dEploidIOExportPosteriorProb.cpp
+b752b9a30b7f1d6d2a1516c6f7c17b8c *src/DEploid/export/writeMcmcRelated.cpp
+0014dc9c1f11529ce9aff9e4d87b9b9d *src/DEploid/global.h
 7fbc338309ac38fefcd64b04bb903e34 *src/DEploid/gzstream/COPYING.LIB
 d632447d46c9b1d6ab0103de7a665034 *src/DEploid/gzstream/README
 e57e01d94637dbc81291eb52d7b3670c *src/DEploid/gzstream/gzstream.cpp
@@ -69,12 +69,12 @@ caa5ea78d04f32a480fa6d4008817cec *src/DEploid/gzstream/index.html
 72767782fc756a7855f92361e949b499 *src/DEploid/gzstream/test_gunzip.C
 ade409024dc2511702be4b25cec98304 *src/DEploid/gzstream/test_gzip.C
 667c569a5d455053fccbd853ba195eab *src/DEploid/gzstream/version
-1fcb7a50f57a3badf4ddade692ca443a *src/DEploid/ibd.cpp
-0029702d7be9123f533a0ce26c9682ac *src/DEploid/ibd.hpp
-2b1ee219c92cc8dd7a6b4fbdc7b63e7b *src/DEploid/mcmc.cpp
-ea74b841d17de058b166907135a439bf *src/DEploid/mcmc.hpp
-3a6972a6e817a2a722dc2d3ab688f68c *src/DEploid/panel.cpp
-3721743b908e1121992fa6d681becefc *src/DEploid/panel.hpp
+dedc02c768e080760ee5569f5744274a *src/DEploid/ibd.cpp
+13f922ad1069e95703ee636dcb601786 *src/DEploid/ibd.hpp
+66473e89a704d10066934e09f72bfb76 *src/DEploid/mcmc.cpp
+5d026a7999d488828b60255d6f92938f *src/DEploid/mcmc.hpp
+789168f580b87e18556c8565be5d5898 *src/DEploid/panel.cpp
+4a6fd3f945590316bae7f0ef08696fa7 *src/DEploid/panel.hpp
 a6765fb4db45924b1d3b2d7ed6d5b0ae *src/DEploid/random/fastfunc.cpp
 1a598d9c9df966427a64ef6a74ce56d5 *src/DEploid/random/fastfunc.hpp
 d7ee5456f67c91bd7da907001965dd72 *src/DEploid/random/mersenne_twister.cpp
@@ -83,23 +83,23 @@ d7ee5456f67c91bd7da907001965dd72 *src/DEploid/random/mersenne_twister.cpp
 ad21a81bdcb9369d4c7f9b2d54cb37be *src/DEploid/random/random_generator.hpp
 b5d32dc0eb4400054572939f5c403315 *src/DEploid/txtReader.cpp
 cd2210daa2a2d666b2beba31a3005574 *src/DEploid/txtReader.hpp
-2c00720dcfea641dd7931622f088d67b *src/DEploid/updateHap.cpp
-77ea3771b4393f6a04570f4a21a29059 *src/DEploid/updateHap.hpp
+8b598f7198a869188b7d2ae8648e89c4 *src/DEploid/updateHap.cpp
+eca7713b9e03acb7227e81181a8959b3 *src/DEploid/updateHap.hpp
 8d512180b69a43f5c4a1548e50e5eb67 *src/DEploid/utility.cpp
 fb6fff78e8bee8d5095b0a249c6dbec0 *src/DEploid/utility.hpp
 6036bb12ec9dfe238f17c38b9a9e7cd0 *src/DEploid/variantIndex.cpp
-1471e97687dc414aceb0646be8a137de *src/DEploid/variantIndex.hpp
+fb4535fad787c5583ec7bdb123fbbde5 *src/DEploid/variantIndex.hpp
 519c03da78828af6c1ef1c7302cb8361 *src/DEploid/vcfReader.cpp
 3eabace70e4231c03910f01b6a7ba8b1 *src/DEploid/vcfReader.hpp
 4196a245e535a58793960f565f3ddfb5 *src/Makevars
 4196a245e535a58793960f565f3ddfb5 *src/Makevars.win
 2b97b24c7193853b75825b3fb76daa7e *src/RcppExports.cpp
-17ba2d6c2335e792f616c21be67dbcd2 *src/dEploidr.cpp
+a085cb95317364cbdec3355014a52d62 *src/dEploidr.cpp
 c5cc16e00e5cd1b8150a274c1fcfd3ad *src/init.c
 d9780788cb9e10ae63d0cfb4ce81703d *src/r_random_generator.h
 eedb9b59a5a966b63e9e82308caf7349 *src/test_exports.cpp
 e095660d571c0f3ef91ce1211ecb7f76 *tests/testthat.R
-2254c18f55a17646c9bd234fb1e80183 *tests/testthat/test-DEploid_tools.R
+9d2d8716411d1971ee55a3faca5fad34 *tests/testthat/test-DEploid_tools.R
 e6096201933e4b6042e165bca5d80db7 *tests/testthat/test-dEploid.R
 f66b335af2d854e56592824fc8df7a0a *tests/testthat/test-r_random-generator.R
 2cbf6a6a60e07984981e6a2329578f8e *vignettes/dEploid-Arguments.Rmd
diff --git a/NAMESPACE b/NAMESPACE
@@ -5,6 +5,8 @@ importFrom("utils", "read.table")
 importFrom(Rcpp,evalCpp)
 importFrom("magrittr", "%>%")
 importFrom("plotly", "plot_ly", "layout", "add_trace")
+importFrom("rmarkdown", "pandoc_available")
+importFrom("htmlwidgets", "saveWidget")
 useDynLib(DEploid, .registration = TRUE)
 export(dEploid)
 export(plotProportions)

diff --git a/build/vignette.rds b/build/vignette.rds
diff --git a/inst/doc/dEploid-Arguments.html b/inst/doc/dEploid-Arguments.html
diff --git a/src/DEploid/dEploid.cpp b/src/DEploid/dEploid.cpp
@@ -25,7 +25,6 @@
 
 #include <iostream> // std::cout
 #include "mcmc.hpp"
-#include "panel.hpp"
 #include "dEploidIO.hpp"
 
 using namespace std;
@@ -46,10 +45,13 @@ int main( int argc, char *argv[] ){
             return EXIT_SUCCESS;
         }
 
-        if ( dEploidIO.doPainting() ){
+        if ( dEploidIO.doComputeLLK() ){
+            dEploidIO.computeLLKfromInitialHap();
+        } else if ( dEploidIO.doLsPainting() ){
             dEploidIO.chromPainting();
-        } else{
-
+        } else if ( dEploidIO.doIbdPainting() ){
+            dEploidIO.paintIBD();
+        }else{
             if (dEploidIO.useIBD()){ // ibd
                 McmcSample * ibdMcmcSample = new McmcSample();
                 MersenneTwister ibdRg(dEploidIO.randomSeed());
@@ -66,6 +68,8 @@ int main( int argc, char *argv[] ){
                                         false); // use IBD
             mcmcMachinery.runMcmcChain(true, // show progress
                                        false); // use IBD
+
+            dEploidIO.paintIBD();
             delete mcmcSample;
         }
         // Finishing, write log