Updated grpLab,sortInd,removed old files & tess3 obj

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Tabulate, analyse and visualise admixture proportions from STRUCTURE, TESS, BAPS, ADMIXTURE and tab-delimited q-matrices
     files
 Version: 2.3.0
-Date: 2019-08-14
+Date: 2019-08-15
 Author: Roy Mathew Francis
 Authors@R: person("Roy", "Francis", email = "roy.m.francis@outlook.com",role = c("aut", "cre"))
 Maintainer: Roy Mathew Francis <roy.m.francis@outlook.com>

NEWS.md → NEWS

@@ -1,5 +1,5 @@
-# pophelper 2.3.0
-
+pophelper 2.3.0
+=================
 * 11-Aug-2019
 * Built on R-3.6.0. Min req R-3.5.0.
 * Removed CLUMPP and DISTRUCT executables
@@ -16,21 +16,21 @@
 * 14-Aug-2019
 * Added arguments 'legendspacing' and 'legendrow' to plotQ()
 
-# pophelper 2.2.9
-
+pophelper 2.2.9
+=================
 * 14-Apr-2019
 * plotQ(): Order of runs in a joined plot was incorrect when k>10 and grplab in use. Fixed.
 
-# pophelper 2.2.8.1
-
+pophelper 2.2.8.1
+=================
 * 16-Mar-2019
 * Fixed 'exportpath' issues in plotQ()
 * Added 'exportpath' to plotQMultiline() and evannoMethod()
 * Added 'exportpath' to tabulateQ()
 * Added 'exportpath' to summariseQ()
 
-# pophelper 2.2.8
-
+pophelper 2.2.8
+=================
 * 15-Mar-2019
 * Dropped dependency on package cairo
 * summariseQ() accepts single run tabulated input
@@ -42,14 +42,14 @@
 * plotQ(): Added argument 'showgrplab'
 * readQ() and readQStructure(): Reads confidence intervals from structure files if available
 
-# pophelper 2.2.7
-
+pophelper 2.2.7
+=================
 * 23-May-2018
 * With joined plots, group labels and sorting, div lines were incorrectly printed causing plots to be misaligned. This has been resolved
 * Removed restriction of setting 'ordergrp=T' when sorting by cluster or 'all'
 
-# pophelper 2.2.6
-
+pophelper 2.2.6
+=================
 * 02-May-2018
 * getDim() adjusted better for shared and unshared individual labels
 * Argument 'grplabface' added to plotQ() to adjust font face of group labels
@@ -58,20 +58,20 @@
 * for-loops in all functions changed to seq_along()
 * sortInd() gets a new argument 'ordergrp' which orders group labels when sorting
 
-# pophelper 2.2.5.1
-
+pophelper 2.2.5.1
+=================
 * 19-Jan-2018
 * Added arguments 'xaxisbreaks' and 'xaxislabels' to evannoMethodStructure()
 
-# pophelper 2.2.5
-
+pophelper 2.2.5
+=================
 * 11-Jan-2018
 * A bug in plotQ() caused strip labels to be incorrect. This has been fixed
 * plotQMultiline() subtitle by default prints the K value of the run
 * plotQ() and plotQMultiline() prints 'Drawing plot ...' when exporting plot
 
-# pophelper 2.2.4
-
+pophelper 2.2.4
+=================
 * 07-Jan-2018
 * Function readQBaps() added to convert BAPS run files to qlist
 * Function readQ() modified to read BAPS run files
@@ -123,14 +123,14 @@
 * grpLabels(): Arguments 'lndlabwithgrplab' and 'indlabsep' added
 * sortInd(): Fixed a bug in sorting where sorting by 'label' didn't work
 
-# pophelper 2.2.3
-
+pophelper 2.2.3
+=================
 * 01-Sep-2017
 * Function readQTess3() added to convert TESS 3 R object to qlist
 * Minor changes in tabulateQ()
 
-# pophelper 2.2.2
-
+pophelper 2.2.2
+=================
 * 25-Aug-2017
 * Fixed an issue where 'barbordersize' could not be turned off
 * Changes to plotQ()
@@ -140,8 +140,8 @@
   + Argument 'barbordersize' set to 0 as default
   + Argument 'barbordercolour' set to NA as default
 
-# pophelper 2.2.1
-
+pophelper 2.2.1
+=================
 * 04-Aug-2017
 * Changes to plotQ()
   + Order of arguments changed in plotQ
@@ -191,8 +191,8 @@
   + Argument 'subtitlespacer' added to adjust the space below the subtitle
   + Argument 'subtitleangle' added to adjust the angle of the subtitle
 
-# pophelper 2.2.0
-
+pophelper 2.2.0
+=================
 * 17-May-2017
 * is.qlist() modified to produce error if input does not meet qlist requirements
 * readQ() argument 'indlabfromfile' did not work (fixed)
@@ -243,8 +243,8 @@
   + Argument 'grplabbgcol' added to adjust background colour of group label panel
   + Argument 'outputfilename' added to name exported files
 
-# pophelper 2.1.0
-
+pophelper 2.1.0
+=================
 * 17-Apr-2017
 * Changes to plotQMultiline()
   + Argument 'grplab' added
@@ -291,8 +291,8 @@
   + Default margins slightly increased
   + Minor grid lines removed to reduce clutter
 
-# pophelper 2.0.0
-
+pophelper 2.0.0
+=================
 * 19-Dec-2016
 * checkRuns modified
 * clumppExport.. 'usexe' path issue corrected
@@ -351,13 +351,13 @@
 * checkRuns() renamed to checkQ()
 * Functions related to spatial, plotRunsInterpolate() and plotRunsSpatial() renamed to plotQInterpolate() and plotQSpatial() and moved to a different package pophelperSpatial
 
-# pophelper 1.2.1
-
+pophelper 1.2.1
+=================
 * 05-Sep-2016
 * Fixed a critical bug during parsing in runsToDfStructure() when K=1. Thanks to Emily Humble for reporting this.
 
-# pophelper 1.2.0
-
+pophelper 1.2.0
+=================
 * 25-July-2016
 * exportDistruct() added to generate input files for software DISTRUCT from STRUCTURE, TESS, MATRIX or TAB files.
 * Argument 'indlabfromfile' added to runsToDfStructure() to read individual labels from structure file if available and adds as row names.
@@ -371,25 +371,25 @@
 * Dependency on plyr and reshape removed. 
 * New dependency on tidyr.
 
-# pophelper 1.1.9
-
+pophelper 1.1.9
+=================
 * 31-May-2016
 * For structure files, 'Mean value of alpha' is no longer reported in tabulateRunsStructure(). Reporting of 'Mean value of alpha' and 'Mean value of Fst' may be reimplemented in future if users think it might be be useful.  
 
-# pophelper 1.1.8
-
+pophelper 1.1.8
+=================
 * 19-May-2016
 * In structure files, when more than one line of 'Mean value of alpha' is present, 'mva' was reported as NA. Now, the mean of the values is reported as 'mva'. Thanks to J A Blanco Aguiar for pointing out this issue.
 
-# pophelper 1.1.7
-
+pophelper 1.1.7
+=================
 * 18-May-2016
 * runsToDfStructure() produced NA columns when STRUCTURE file contains probability intervals. Fixed. Thanks to J A Blanco Aguiar for pointing out this issue.  
 * plotMultiline() has a new argument sortlabels to show x-axis labels in the original sort order.
 * A critical loop variable issue fixed in plotMultiline().  
 
-# pophelper 1.1.6
-
+pophelper 1.1.6
+=================
 * 02-Jan-2016
 * Sort individuals by one or all clusters in plotRuns() or plotMultiline().  
 * Subset/reorder populations when using pop labels in plotRuns().  
@@ -398,8 +398,8 @@
 * Argument 'barwidth' deprecated from plotMultiline().  
 * Fixed space, labeller for compatibility with ggplot2 2.0.0.  
 
-# pophelper 1.1.5
-
+pophelper 1.1.5
+=================
 * 18-Oct-2015
 * Handling of Admixture files.  
 * checkRuns modified to use grepl instead of grep and checks for Admixture files too.
@@ -408,18 +408,18 @@
 * plotRunsInterpolate() handles ADMIXTURE files.  
 * Code optimisation.  
 
-# pophelper 1.1.4
-
+pophelper 1.1.4
+=================
 * 27-Sep-2015
 * Fixed runsToDfStructure() error when the structure file has 'Estimated Allele Frequencies in each population' rather than 'each cluster'.
 
-# pophelper 1.1.3
-
+pophelper 1.1.3
+=================
 * 27-Sep-2015
 * Error in plotMultiline() with table files corrected.
 
-# pophelper 1.1.2
-
+pophelper 1.1.2
+=================
 * 17-Sep-2015
 * Error fixed in evannoMethodStructure() when using writetable=T.  
 Error in vapply(x, format, "", ...) : values must be length 1,
@@ -432,8 +432,8 @@ Error in vapply(x, format, "", ...) : values must be length 1,
 Error in theme(legend.key.size = unit(legendsize, "cm")) : 
   could not find function "unit"
 
-# pophelper 1.1.1
-
+pophelper 1.1.1
+=================
 * 31-Mar-2015
 * Function plotRuns() modified.
     + Spacing between bottom plot and second plot was larger than spacing between other plots. This has been corrected.
@@ -448,8 +448,8 @@ Error in theme(legend.key.size = unit(legendsize, "cm")) :
     + Argument basesize added to generally control size of figure elements.
     + Conversion between units and dimensions have been modified.
 
-# pophelper 1.1.0
-
+pophelper 1.1.0
+=================
 * 16-Mar-2015
 * Several changes in code to enable faster runtime.
 * New HTML vignette created.
@@ -470,30 +470,30 @@ Error in theme(legend.key.size = unit(legendsize, "cm")) :
     + Argument 'linetype' added for changing line type of marker line
 * Function analyseRuns() function added. A wrapper for several other functions. Performs a tabulation of runs, summarising of runs, perform Evanno method (for STRUCTURE runs only), exports clumpp output and generates barplots.
 
-# pophelper 1.0.4
-
+pophelper 1.0.4
+=================
 * 18-May-2014
 * Cairo plotting for png exports. Better anti-aliasing.
 * fig aspect ratio issue fixed in function plotRunsInterpolate()
 * Namespace error resolved for some functions.
 * Minor changes to plotRunsInterpolate().
 * plotRunsSpatial() function added. STRUCTURE and TESS runs can be used with a coordinate file to spatially plot the points and colour them into clusters based on the highest probability value. The coordinates can be transformed to UTM coordinates for a better spatial representation.
 
-# pophelper 1.0.3
-
+pophelper 1.0.3
+================= 
 * 11-May-2014
 * Function plotRunsInterpolate() added. STRUCTURE and TESS run files can be used with a coordinate file to spatially interpolate clusters using several interpolation methods such as thin splines, inverse distance weighting and kriging.
 
-# pophelper 1.0.2
-
+pophelper 1.0.2
+=================
 * 25-Apr-2014
 * A bug in functions clumppExportStructure() and clumppExportTess() produced a 'No input' error. This has been fixed. Thanks to Micheal Panasci for pointing this out.
 
-# pophelper 1.0.1
-
+pophelper 1.0.1
+=================
 * parameter sorttable added to functions tabulateRunsStructure() and tabulateRunsTess(). Useful if unsorted table is required.
 
-# pophelper 1.0.0
-
+pophelper 1.0.0
+=================
 * 16-Feb-2014
 * the first version of the `pophelper` package