version 0.5.1

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: DEploid
 Type: Package
 Title: Deconvolute Mixed Genomes with Unknown Proportions
-Version: 0.5.0
+Version: 0.5.1
 Authors@R: c(
-    person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="joe.zhu@well.ox.ac.uk"),
+    person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="joe.zhu@bdi.ox.ac.uk"),
     person('Jacob', 'Almagro-Garcia', role=c('aut', 'cph')),
     person('Gil', 'McVean', role=c('aut', 'cph')),
     person('University of Oxford', '', role=c('cph')),
@@ -33,9 +33,9 @@ SystemRequirements: C++11
 VignetteBuilder: knitr
 LinkingTo: Rcpp
 RoxygenNote: 6.0.1
-Date: 2018-05-18
+Date: 2018-10-20
 NeedsCompilation: yes
-Packaged: 2018-05-18 00:48:15 UTC; joezhu
+Packaged: 2018-10-21 09:35:55 UTC; joezhu
 Author: Joe Zhu [aut, cre, cph],
   Jacob Almagro-Garcia [aut, cph],
   Gil McVean [aut, cph],
@@ -44,6 +44,6 @@ Author: Joe Zhu [aut, cre, cph],
   CodeCogs Zyba Ltd [com, cph],
   Deepak Bandyopadhyay [com, cph],
   Lutz Kettner [com, cph]
-Maintainer: Joe Zhu <joe.zhu@well.ox.ac.uk>
+Maintainer: Joe Zhu <joe.zhu@bdi.ox.ac.uk>
 Repository: CRAN
-Date/Publication: 2018-05-18 03:28:52 UTC
+Date/Publication: 2018-10-21 15:40:05 UTC

MD5

@@ -1,15 +1,15 @@
-4fdc1ed1a70c225011e6386926ddf03c *DESCRIPTION
+fec72e586398468aba8da648f8e12dca *DESCRIPTION
 620dec5abe35747430a215d8d65731bb *NAMESPACE
 3f730ab29544fc1d63946a50242f3a42 *R/DEploidR.R
 7efdf7afe8931c93c9c3cdf32a85fb6b *R/RcppExports.R
 856a9b3317faac53312a512e049ca0f9 *R/dEploid.R
-5a2e60ac3ffc29399ffaa1a2308ba8ae *R/dEploidPlotly.R
-db8dd67bf1ee95720e0b4deeefe17540 *README.md
+d3fac2cb88aea885efd78a57cd3b8a06 *R/dEploidPlotly.R
+86e0f5d855f8f024f1be4513711c735d *README.md
 3d5ac8ca720160834e8b1aeedfa70f91 *build/vignette.rds
 461e2dc267742100128d50cd74e757e2 *inst/CITATION
 01c90976b229646ca9b46399709688e3 *inst/doc/dEploid-Arguments.R
 2cbf6a6a60e07984981e6a2329578f8e *inst/doc/dEploid-Arguments.Rmd
-f2edea2b41c5cd260b0cf03f43188ef0 *inst/doc/dEploid-Arguments.html
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@@ -47,54 +47,95 @@ dd8dd57dee7f3c8d2b45dbf03e8c5163 *src/DEploid/codeCogs/expx2.h
 ae7e51c1268072067ffb113c577f5bb6 *src/DEploid/codeCogs/machine_epsilon.h
 ccec2bc4b1d1436416711e52b16ef3e0 *src/DEploid/codeCogs/mersenne.hpp
 2f8d156a5ffa6d1f3bb302af68b59090 *src/DEploid/codeCogs/poly_eval.h
-785e0971c65e88f066c599e4ba8f9324 *src/DEploid/codeCogs/randomSample.hpp
+3ba8122e26b392c415edec3c7b3ac888 *src/DEploid/codeCogs/randomSample.hpp
 94c33b48dee38eb7bdc87638e718e09e *src/DEploid/codeCogs/stirling.h
 a3585d8d0b267c7076cc835be837bf5f *src/DEploid/codeCogs/xsub_ln_add1.h
-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
-8067e22d89f4b2b23e03ed415a53c172 *src/DEploid/exceptions.hpp
-86ca88bd81de69cd9d83916ea56f6e1e *src/DEploid/export/dEploidIOExport.cpp
+b822188831563922209c5cc0d82499d6 *src/DEploid/dEploidIO.cpp
+71263fc8d2ef0b0c38e6ddaf0d340b34 *src/DEploid/dEploidIO.hpp
+47c3ccc7c67427b403bf67412c19825c *src/DEploid/debug/mcmcDebug.cpp
+f2bc5a44cdf66b26c3657897be89c337 *src/DEploid/debug/vcfReaderDebug.cpp
+2ab6797644a0dd90391e0dfa38ac9a33 *src/DEploid/exceptions.hpp
+aa0d0dbab21a8daecaf3a90cc3986f65 *src/DEploid/export/dEploidIOExport.cpp
 391762551ff34224643d84913249c130 *src/DEploid/export/dEploidIOExportPosteriorProb.cpp
-b752b9a30b7f1d6d2a1516c6f7c17b8c *src/DEploid/export/writeMcmcRelated.cpp
-0014dc9c1f11529ce9aff9e4d87b9b9d *src/DEploid/global.h
+b5bcf7475c1cf98f2869687315ddadc2 *src/DEploid/export/io_unit_tests-dEploidIOExport.gcno
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 7fbc338309ac38fefcd64b04bb903e34 *src/DEploid/gzstream/COPYING.LIB
 d632447d46c9b1d6ab0103de7a665034 *src/DEploid/gzstream/README
-e57e01d94637dbc81291eb52d7b3670c *src/DEploid/gzstream/gzstream.cpp
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 99d59b3af2c3974f943e118556645888 *src/DEploid/gzstream/gzstream.h
 caa5ea78d04f32a480fa6d4008817cec *src/DEploid/gzstream/index.html
+d331a9fa83ed57961829ccd238f5a0d0 *src/DEploid/gzstream/io_unit_tests-gzstream.gcno
 78e2cca98f5d11a43af84eccdd9fb96e *src/DEploid/gzstream/logo.gif
 72767782fc756a7855f92361e949b499 *src/DEploid/gzstream/test_gunzip.C
 ade409024dc2511702be4b25cec98304 *src/DEploid/gzstream/test_gzip.C
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 667c569a5d455053fccbd853ba195eab *src/DEploid/gzstream/version
-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
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+be3900f55cf510e4011fc09aebbd469e *src/DEploid/lasso/dEploidLasso.cpp
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+e77974455e21e3fbc36f3d66a1464cc3 *src/DEploid/lasso/lasso.hpp
+a60b6085198e7396d5392472e7d8f3ad *src/DEploid/lasso/lassoDBG.cpp
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+196cfe16ca992fb0e11539bed7372329 *src/DEploid/mcmc.cpp
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 a6765fb4db45924b1d3b2d7ed6d5b0ae *src/DEploid/random/fastfunc.cpp
 1a598d9c9df966427a64ef6a74ce56d5 *src/DEploid/random/fastfunc.hpp
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 d7ee5456f67c91bd7da907001965dd72 *src/DEploid/random/mersenne_twister.cpp
 5c40c783d72b75abcd7a5264a74d4c1a *src/DEploid/random/mersenne_twister.hpp
 9563d50543ff7687795b66906c787a9f *src/DEploid/random/random_generator.cpp
 ad21a81bdcb9369d4c7f9b2d54cb37be *src/DEploid/random/random_generator.hpp
-b5d32dc0eb4400054572939f5c403315 *src/DEploid/txtReader.cpp
-cd2210daa2a2d666b2beba31a3005574 *src/DEploid/txtReader.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
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-519c03da78828af6c1ef1c7302cb8361 *src/DEploid/vcfReader.cpp
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-4196a245e535a58793960f565f3ddfb5 *src/Makevars
-4196a245e535a58793960f565f3ddfb5 *src/Makevars.win
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+9e33ed23ec1e99b143de552cb4c47f08 *src/DEploid/txtReader.hpp
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+e37dd6a1f4c89bf9c18e7374fb01eab3 *src/DEploid/unit_tests-ibd.gcno
+3440d5ce9043a60fd79d7f712f455fac *src/DEploid/unit_tests-mcmc.gcno
+796723a200a476f32007aa1bd2945fa7 *src/DEploid/unit_tests-panel.gcno
+91efca3bed9b797a4543eb103981c58a *src/DEploid/unit_tests-txtReader.gcno
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+8fa54dd0674c17dd90c0f99607b3640f *src/DEploid/updateHap.cpp
+3c04f03a2e9e8c022ff6138ce0f5dd67 *src/DEploid/updateHap.hpp
+177058e9bd41a4d0905b8cc8b6a9fa50 *src/DEploid/utility.cpp
+20acd35532218e8d275c8b1aff30df36 *src/DEploid/utility.hpp
+6befb905c2f2db83e6703cf5de751983 *src/DEploid/variantIndex.cpp
+1a0ca7691a0ad14a2f03b23511337fc7 *src/DEploid/variantIndex.hpp
+87165591ce55df9e0352b0833d5fd14a *src/DEploid/vcfReader.cpp
+35b5749b31bae39d02661b505450f46c *src/DEploid/vcfReader.hpp
+c4002d59b81406e8bc6fe9eb5535e2c7 *src/Makevars
+c4002d59b81406e8bc6fe9eb5535e2c7 *src/Makevars.win
 2b97b24c7193853b75825b3fb76daa7e *src/RcppExports.cpp
-a085cb95317364cbdec3355014a52d62 *src/dEploidr.cpp
+d8d7321b0ef6566648a7f7c25b3c775c *src/dEploidr.cpp
 c5cc16e00e5cd1b8150a274c1fcfd3ad *src/init.c
 d9780788cb9e10ae63d0cfb4ce81703d *src/r_random_generator.h
 eedb9b59a5a966b63e9e82308caf7349 *src/test_exports.cpp

R/dEploidPlotly.R

@@ -108,7 +108,7 @@ plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                                title = "Histogram 0<WSAF<1"){
   tmpWSAFIndex <- 1:length(obsWSAF)
   if (exclusive){
-    tmpWSAFIndex <- which(((obsWSAF < 1) * (obsWSAF > 0)) == 1)
+    tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0) ) == 1)
   }
   xb <- list(
       start = 0,

README.md

@@ -1,10 +1,10 @@
 <img src="inst/extdata/deploid.png" width="180">
 
 [![License (GPL version 3)](https://img.shields.io/badge/license-GPL%20version%203-brightgreen.svg)](http://opensource.org/licenses/GPL-3.0)
-[![Build Status](https://travis-ci.org/mcveanlab/DEploid-r.svg?branch=master)](https://travis-ci.org/mcveanlab/DEploid-r)
+[![Build Status](https://travis-ci.org/DEploid-dev/DEploid-r.svg?branch=master)](https://travis-ci.org/DEploid-dev/DEploid-r)
 [![Build Status](https://ci.appveyor.com/api/projects/status/hi1nq97d5l68qs4r?svg=true)](https://ci.appveyor.com/project/shajoezhu/deploid-r)
-[![Coverage Status](https://coveralls.io/repos/github/mcveanlab/DEploid-r/badge.svg?branch=master)](https://coveralls.io/github/mcveanlab/DEploid-r?branch=master)
-[![codecov](https://codecov.io/gh/mcveanlab/DEploid-r/branch/master/graph/badge.svg)](https://codecov.io/gh/mcveanlab/DEploid-r)
+[![Coverage Status](https://coveralls.io/repos/github/DEploid-dev/DEploid-r/badge.svg?branch=master)](https://coveralls.io/github/DEploid-dev/DEploid-r?branch=master)
+[![codecov](https://codecov.io/gh/DEploid-dev/DEploid-r/branch/master/graph/badge.svg)](https://codecov.io/gh/DEploid-dev/DEploid-r)
 [![CRAN RStudio Mirror Downloads](http://cranlogs.r-pkg.org/badges/DEploid)](https://cran.r-project.org/package=DEploid)
 
 DEploid R package -- Deconvolute Mixed Genomes with Unknown Proportions
@@ -57,6 +57,10 @@ You can freely use all code in this project under the conditions of the GNU GPL
 Citation
 --------
 
+If you use `dEploid` with the flag `-ibd`, please cite the following paper:
+
+Zhu, J. S., J. A. Hendry, J. Almagro-Garcia, R. D. Pearson, R. Amato, A. Miles, D. J. Weiss, T. C. D. Lucas, M. Nguyen, P. W. Gething, D. Kwiatkowski, G. McVean, and for the Pf3k Project. (2018) The origins and relatedness structure of mixed infections vary with local prevalence of *P. falciparum* malaria. *biorxiv*, doi: https://doi.org/10.1101/387266.
+
 If you use `dEploid` in your work, please cite the program:
 
 Zhu, J. S. J. A. Garcia G. McVean. (2017) Deconvoluting multiple infections in *Plasmodium falciparum* from high throughput sequencing data. *bioRxiv* 099499. doi: https://doi.org/10.1101/099499

inst/doc/dEploid-Arguments.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="Sha Zhu" />
 
-<meta name="date" content="2018-05-18" />
+<meta name="date" content="2018-10-21" />
 
 <title>Command Line Arguments</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">Command Line Arguments</h1>
 <h4 class="author"><em>Sha Zhu</em></h4>
-<h4 class="date"><em>2018-05-18</em></h4>
+<h4 class="date"><em>2018-10-21</em></h4>
 
 
 

src/DEploid/codeCogs/randomSample.hpp

@@ -14,8 +14,8 @@
 #ifndef STATS_DISTS_CONTINUOUS_NORMAL_RANDOMSAMPLE_H
 #define STATS_DISTS_CONTINUOUS_NORMAL_RANDOMSAMPLE_H
 
-#include <mersenne.hpp>
 #include <math.h>
+#include "mersenne.hpp"
 
 #define NORMALDENS(x) ((fabs(x) > 8.0) ? 0 : 0.398942280 * exp(- x * x / 2))