version 4.0.2

cran · Jun 8, 2017 · bbef1c5 · bbef1c5
1 parent 433d986
commit bbef1c5
Show file tree

Hide file tree

Showing 5 changed files with 64 additions and 55 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,16 +2,16 @@ Package: sidier
 Type: Package
 Title: Substitution and Indel Distances to Infer Evolutionary
         Relationships
-Version: 4.0.1
-Date: 2017-06-01
+Version: 4.0.2
+Date: 2017-06-09
 Author: A. Jesus Muñoz Pajares
 Maintainer: A.J. Muñoz-Pajares <ajesusmp@ugr.es>
 Depends: R (>= 3.4.0)
 Imports: ape, network, igraph, gridBase, grid, ggmap, ggplot2
 Encoding: UTF-8
 Description: Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.
 License: GPL-2
-Packaged: 2017-06-06 18:40:44 UTC; jela
 NeedsCompilation: no
+Packaged: 2017-06-08 14:15:34 UTC; jela
 Repository: CRAN
-Date/Publication: 2017-06-06 22:18:02 UTC
+Date/Publication: 2017-06-08 16:25:20 UTC
diff --git a/MD5 b/MD5
@@ -1,6 +1,6 @@
-c1aea2d242dce8ee64442af759acdc54 *DESCRIPTION
+8c8931e954198e2048dca51cb6861b61 *DESCRIPTION
 69d0de933e40bc432e96576d5a7bbac6 *NAMESPACE
-a142a148d5a10331f3b6416bf5f316a2 *NEWS
+6e60eee04558f99f6fe64c7cbd14a6c7 *NEWS
 c9ea3cf4be143eb2c02e44c3221c63dc *R/BARRIEL.R
 32b62e53b737044422cf1748ef5eff40 *R/FIFTH.R
 9bda2ca4612f5e7ba194a29b97489797 *R/FilterHaplo.R
@@ -12,7 +12,7 @@ e893dc699f837c34d101a1ca88a55d37 *R/GetHaplo.R
 386c77ec4738d99113169c669a80f781 *R/SIC.R
 8c0fe0f7fbea784faa6fe9ec088891ad *R/barcode.gap.R
 42e98eb2c2c25da6cc255b75741aca50 *R/barcode.quality.R
-8c7ae17ca11ab93f1620101be764ef85 *R/barcode.summary.R
+8dcedf184dea978c8ed2f2ccd4d0a0a8 *R/barcode.summary.R
 01224d521741b8d20259429cd408dfb5 *R/colour.scheme.R
 3c8435fe923958534ff55eb6b921ea18 *R/compare.dist.R
 0c241d9d86699c0dd49a34ea6a00ab71 *R/distance.comb.R
@@ -67,7 +67,7 @@ ca6358b5d7c00607648b35c027d8b6c1 *man/mutationSummary.Rd
 b686ef9dd6ac3fad41e45be7c2a48f98 *man/pie.network.Rd
 a606d8ad6be893478f210076e48d6592 *man/pop.dist.Rd
 4c59e980f81f82b3a6c0193d849009be *man/rule.Rd
-8c27d572a9890b432b769e110de28317 *man/sidier-package.Rd
+8711cb88c131b8f31b769d73b010c9fe *man/sidier-package.Rd
 f74de0dc75f1e1c5e550d0fc099f6c73 *man/simplify.network.Rd
 52f560a4e241b00e2c0f5c34da199ee0 *man/simuEvolution.Rd
 8fb865c982c6cb109936d4930e389e87 *man/single.network.Rd

diff --git a/NEWS b/NEWS
@@ -1,3 +1,11 @@
+=========
+sidier 4.0.2
+=========
+
+Released June 09, 2017
+
+. Bug fixed in barcode.summary
+
 =========
 sidier 4.0.1
 =========

diff --git a/R/barcode.summary.R b/R/barcode.summary.R
@@ -12,21 +12,22 @@ SPS<-unique(sps)
 Intra<-mat[which(kk==1 & lower.tri(mat))]
 row.names(mat)[which(kk==1 & lower.tri(mat))]
 colnames(mat)[which(kk==1 & lower.tri(mat))]
-Inter<-mat[which(kk!=1 & lower.tri(mat))]
+Inter<-mat[which(is.na(kk) & lower.tri(mat))]
 mat2<-mat
 mat2[upper.tri(mat,diag=TRUE)]<-NA
 for (i in 1:length(SPS))
   {
-  SUB<-mat2[which(row.names(mat2)==SPS[1]),]
+  SUB<-mat2[which(row.names(mat2)==SPS[i]),]
+  SUB2<-mat[which(row.names(mat)==SPS[i]),]
   if(i==1)
 	{
 	Intra<-list(sort(c(SUB[,which(colnames(SUB)==SPS[1])])))
-	Inter<-list(sort(c(SUB[,which(colnames(SUB)!=SPS[1])])))
+	Inter<-list(sort(c(SUB2[,which(colnames(SUB2)!=SPS[1])])))
 	}
   if(i>1)
 	{
 	Intra[[i]]<-sort(c(SUB[,which(colnames(SUB)==SPS[i])]))
-	Inter[[i]]<-sort(c(SUB[,which(colnames(SUB)!=SPS[i])]))
+	Inter[[i]]<-sort(c(SUB2[,which(colnames(SUB2)!=SPS[i])]))
 	}
   }
 

diff --git a/man/sidier-package.Rd b/man/sidier-package.Rd
@@ -5,55 +5,55 @@
 \title{SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships}
 \description{Package for evolutionary reconstruction and bar code analyses based on substitutions and insertion-deletion (indels) in a distance-based framework. Functions can be classified according to the following groups:
 
-Barcode analysis
-\code{\link{barcode.gap}}
-\code{\link{barcode.quality}}
-\code{\link{barcode.summary}}
-\code{\link{compare.dist}}
-\code{\link{genbank.sp.names}}
-\code{\link{inter.intra.plot}}
-\code{\link{rule}}
+- \emph{Barcode analysis}:
+\code{\link{barcode.gap}}; 
+\code{\link{barcode.quality}}; 
+\code{\link{barcode.summary}}; 
+\code{\link{compare.dist}}; 
+\code{\link{genbank.sp.names}}; 
+\code{\link{inter.intra.plot}}; 
+\code{\link{rule}}. 
 
-Example files
-\code{\link{alignExample}}
-\code{\link{Example_Spatial.plot_Alignment}}
-\code{\link{ex_alignment1}}
-\code{\link{ex_Coords}}
+- \emph{Example files}:
+\code{\link{alignExample}}; 
+\code{\link{Example_Spatial.plot_Alignment}}; 
+\code{\link{ex_alignment1}}; 
+\code{\link{ex_Coords}}.
 
-Indel coding methods
-\code{\link{BARRIEL}}
-\code{\link{FIFTH}}
-\code{\link{MCIC}}
-\code{\link{SIC}}
+- \emph{Indel coding methods}:
+\code{\link{BARRIEL}}; 
+\code{\link{FIFTH}}; 
+\code{\link{MCIC}}; 
+\code{\link{SIC}}.
 
-Matrix/network manipulation
-\code{\link{distance.comb}}
-\code{\link{mergeNodes}}
-\code{\link{nt.gap.comb}}
-\code{\link{simplify.network}}
+- \emph{Matrix/network manipulation}:
+\code{\link{distance.comb}}; 
+\code{\link{mergeNodes}}; 
+\code{\link{nt.gap.comb}}; 
+\code{\link{simplify.network}}.
 
-Network-from-distance methods 
-\code{\link{NINA.thr}}
-\code{\link{perc.thr}}
-\code{\link{zero.thr}}
-\code{\link{single.network}}
-\code{\link{single.network.module}}
+- \emph{Network-from-distance methods}:
+\code{\link{NINA.thr}}; 
+\code{\link{perc.thr}}; 
+\code{\link{zero.thr}}; 
+\code{\link{single.network}}; 
+\code{\link{single.network.module}}.
 
-Network visualization
-\code{\link{mutation.network}}
-\code{\link{pie.network}}
-\code{\link{double.plot}}
-\code{\link{colour.scheme}}
-\code{\link{spatial.plot}}
+- \emph{Network visualization}:
+\code{\link{mutation.network}}; 
+\code{\link{pie.network}}; 
+\code{\link{double.plot}}; 
+\code{\link{colour.scheme}}; 
+\code{\link{spatial.plot}}.
 
-Sequence/haplotype analysis
-\code{\link{FilterHaplo}}
-\code{\link{FindHaplo}}
-\code{\link{GetHaplo}}
-\code{\link{HapPerPop}}
-\code{\link{mutationSummary}}
-\code{\link{pop.dist}}
-\code{\link{simuEvolution}}
+- \emph{Sequence/haplotype analysis}:
+\code{\link{FilterHaplo}}; 
+\code{\link{FindHaplo}}; 
+\code{\link{GetHaplo}}; 
+\code{\link{HapPerPop}}; 
+\code{\link{mutationSummary}}; 
+\code{\link{pop.dist}}; 
+\code{\link{simuEvolution}}.
 
 }
 \details{