Release of v0.2.2

wanyuac · Mar 21, 2020 · b0fc3af · b0fc3af
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Analysing association and physical linkage between bacterial genes
 Version: 0.2.2
 Author: Yu Wan
-Maintainer: Yu Wan <wanyuac@gmail.com>
+Maintainer: Yu Wan <wanyuac@126.com>
 Description: Applies univariate linear mixed models (LMMs) to bacterial genotype
     data to find out association between bacterial genes. Users may also incorporate
     physical distances between genes to identify physical linkages between these genes.

diff --git a/R/func__assignPairID.R b/R/func__assignPairID.R
@@ -12,7 +12,7 @@
 #' a0 <- assoc[["lmms.pat"]][["dif"]][["h1"]]
 #' a0 <- assignPairID(lmms = a0, from = 1, paired.rows = TRUE)
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
 #  Copyright 2017 Yu Wan

diff --git a/R/func__betaSignCongruence.R b/R/func__betaSignCongruence.R
@@ -20,7 +20,7 @@
 #'
 #' @return A data frame of percentages as measurements of sign congruence.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
 # Copyright 2018 Yu Wan

diff --git a/R/func__calcGeneFreq.R b/R/func__calcGeneFreq.R
@@ -17,10 +17,10 @@
 #' gf <- calcGeneFreq(x = mapping[, c("gene", "count")], n = 1125)  # assuming
 #' there are 1125 strains
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
-# Copyright 2018 Yu Wan <wanyuac@gmail.com>
+# Copyright 2018 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First edition: 26 May 2017; the latest edition: 4 Sep 2018
 

diff --git a/R/func__corCladeProj.R b/R/func__corCladeProj.R
@@ -24,7 +24,7 @@
 #' clades <- tree2Clades(...)
 #' r <- corCladeProj(clades = clades[["pam"]], projections = C[["C"]], clade.sizes = clades[["sizes"]], n.cores = 8)
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
 #  Copyright 2017 Yu Wan

diff --git a/R/func__corPatternProj.R b/R/func__corPatternProj.R
@@ -14,10 +14,10 @@
 #' @examples a <- lmm(...)
 #' r <- corPatternProj(pat.mat = a$alleles$B, proj.mat = a$struc$C$C)
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #'
-#  Copyright 2018 Yu Wan <wanyuac@gmail.com>
+#  Copyright 2018 Yu Wan <wanyuac@126.com>
 #  Licensed under the Apache License, Version 2.0
 #  First and the latest edition: 25 May 2018
 

diff --git a/R/func__countAlleles.R b/R/func__countAlleles.R
@@ -6,10 +6,10 @@
 #' @param patterns (optional) a data frame consisting of two columns: allele and pattern ID
 #' @param pat.sizes (optional) a two-column data frame (pattern and size) for the number of alleles per pattern
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
-# Copyright 2017 Yu Wan <wanyuac@gmail.com>
+# Copyright 2017 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First version: 26 May 2017; the latest edition: 24 May 2018
 

diff --git a/R/func__distanceAnalyser__evalPL.R b/R/func__distanceAnalyser__evalPL.R
@@ -19,7 +19,7 @@
 #' @param score.dist (optional) A logical parameter specifying whether allelic
 #' physical distances should be taken into account for scoring edges. Default: FALSE.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
 #  Copyright 2017-2019 Yu Wan

diff --git a/R/func__distanceAnalyser__importPhysicalDists.R b/R/func__distanceAnalyser__importPhysicalDists.R
@@ -9,7 +9,7 @@
 #' @param outgroup A vector of strains whose physical distances will be excluded
 #' from the result.
 #' @return A data frame of physical distances.
-#' @author Yu Wan, \email{wanyuac@@gmail.com}
+#' @author Yu Wan, \email{wanyuac@@126.com}
 #' @export
 #  Copyright 2019 Yu Wan
 #  Licensed under the Apache License, Version 2.0

diff --git a/R/func__distanceAnalyser__summariseDist.R b/R/func__distanceAnalyser__summariseDist.R
@@ -28,7 +28,7 @@
 #' @param n.cores Number of computational cores that will be used in parallel for
 #' this function.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
 #  Copyright 2017-2018 Yu Wan

diff --git a/R/func__distanceAnalyser__summariseDistsForEdges.R b/R/func__distanceAnalyser__summariseDistsForEdges.R
@@ -42,7 +42,7 @@
 #'   ds_stats <- ds_stats[, c("Allele_1", "Allele_2", "Co", "S_d", "M", "Mr", "N", "Nr", "Nc_r")]  # For prioritised distances, Nc_r and Ng are mutually exclusive.
 #'
 #'
-#' @author Yu Wan, \email{wanyuac@@gmail.com}
+#' @author Yu Wan, \email{wanyuac@@126.com}
 #' @export summariseDistsForEdges
 #
 #  Copyright 2018 Yu Wan

diff --git a/R/func__extractPairedRows.R b/R/func__extractPairedRows.R
@@ -13,7 +13,7 @@
 #' a <- rbind.data.frame(subset(assoc[["assoc"]], score >= 1.5 | (s_d == 1 & dif == 0)), stringsAsFactors = FALSE)
 #' ap <- extractPairedRows(x = a, pair.id = "pair")
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
 #  Copyright 2017 Yu Wan

diff --git a/R/func__findMinIncClade.R b/R/func__findMinIncClade.R
@@ -38,7 +38,7 @@
 #'
 #' Dependency: parallel
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
 #  Copyright 2017 - 2018 Yu Wan

diff --git a/R/func__findMinIncCladeOfStrains.R b/R/func__findMinIncCladeOfStrains.R
@@ -13,7 +13,7 @@
 #' mic <- findMinIncCladeOfStrains(strains = c("strain1", "strain2"), clade.pam = assoc[["struc"]][["clades"]][["pam"]],
 #' clade.sizes = assoc[["struc"]][["clades"]][["sizes"]])
 #'
-#' @author Yu Wan (\email{wanyuac@gmail.com})
+#' @author Yu Wan (\email{wanyuac@126.com})
 #' @export
 #
 #  Copyright 2017 Yu Wan

diff --git a/R/func__findPhysLink.R b/R/func__findPhysLink.R
@@ -118,7 +118,7 @@
 #' time.end <- Sys.time()
 #' print(time.end - time.start)
 #'
-#' @author Yu Wan, \email{wanyuac@@gmail.com}
+#' @author Yu Wan, \email{wanyuac@@126.com}
 #' @export
 #
 #  Copyright 2017 Yu Wan

diff --git a/R/func__findSeq.R b/R/func__findSeq.R
@@ -26,7 +26,7 @@
 #' bandage.params = "--ifilter 95 --evfilter 1e-3 --pathnodes 6 --minhitcov 0.98 --minpatlen 0.98 --maxpatlen 1.02",
 #' n.cores = 4, del.temp = FALSE)
 #'
-#' @author Yu Wan (\email{wanyuac@gmail.com})
+#' @author Yu Wan (\email{wanyuac@126.com})
 #' @export
 #
 #  Copyright 2017 Yu Wan

diff --git a/R/func__geoTempAnalyser__calcAllelicDiversityPerCountry.R b/R/func__geoTempAnalyser__calcAllelicDiversityPerCountry.R
@@ -23,10 +23,10 @@
 #' are computed.
 #'   s: isolation information of the final set of strains.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #'
-# Copyright 2018 Yu Wan <wanyuac@gmail.com>
+# Copyright 2018 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First and the latest edition: 31 Oct 2018
 

diff --git a/R/func__geoTempAnalyser__countAllelesPerCountry.R b/R/func__geoTempAnalyser__countAllelesPerCountry.R
@@ -14,10 +14,10 @@
 #' @return This function returns a list of two elements: count and mapping, when
 #' freq = FALSE, else, returns a list of three elements: freq, mapping and sample_size_country.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export countAllelesPerCountry
 #'
-# Copyright 2018 Yu Wan <wanyuac@gmail.com>
+# Copyright 2018 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First edition: 16 Aug 2018; the latest update: 1 Nov 2018
 

diff --git a/R/func__geoTempAnalyser__countAllelesPerGeneByCountry.R b/R/func__geoTempAnalyser__countAllelesPerGeneByCountry.R
@@ -9,10 +9,10 @@
 #'
 #' @examples cc <- countAllelesPerGeneByCountry(sam = sam, mapping = assoc$mapping, gm = assoc$genes$all, nul = -35)
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #'
-# Copyright 2018 Yu Wan <wanyuac@gmail.com>
+# Copyright 2018 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First version: 2 Aug 2018; the latest edition: 3 Aug 2018
 

diff --git a/R/func__geoTempAnalyser__countAllelesPerGeneByYear.R b/R/func__geoTempAnalyser__countAllelesPerGeneByYear.R
@@ -10,10 +10,10 @@
 #' @examples
 #' ac <- countAllelesPerGeneByYear(sam = sam, mapping = assoc$mapping, gm = assoc$genes$all, nul = -30)
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #'
-# Copyright 2018 Yu Wan <wanyuac@gmail.com>
+# Copyright 2018 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First version: 2 Aug 2018; the latest edition: 3 Aug 2018
 

diff --git a/R/func__geoTempAnalyser__countAllelesPerYear.R b/R/func__geoTempAnalyser__countAllelesPerYear.R
@@ -19,10 +19,10 @@
 #' w (weighted counts per strain) and mapping. When combine is a list, another
 #' two elements called comb_count, comb_freq and period are included.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export countAllelesPerYear
 #'
-# Copyright 2018 Yu Wan <wanyuac@gmail.com>
+# Copyright 2018 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First version: 3 Aug 2018; the latest edition: 16 Aug 2018
 

diff --git a/R/func__geoTempAnalyser__getAllelesEarliestAppearance.R b/R/func__geoTempAnalyser__getAllelesEarliestAppearance.R
@@ -10,10 +10,10 @@
 #'
 #' @examples emg_1 <- getAllelesEarliestAppearance(alleles = targets, pam = rp_1$pam, sam = sam)
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #'
-# Copyright 2018 Yu Wan <wanyuac@gmail.com>
+# Copyright 2018 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First and the latest edition: 4 Aug 2018
 #'

diff --git a/R/func__geoTempAnalyser__mkCoocurNetwork.R b/R/func__geoTempAnalyser__mkCoocurNetwork.R
@@ -31,10 +31,10 @@
 #' occurrence count per isolate. However, when years <= 0, the G element is a
 #' single Graph object.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
-#  Copyright 2018 Yu Wan <wanyuac@gmail.com>
+#  Copyright 2018 Yu Wan <wanyuac@126.com>
 #  Licensed under the Apache License, Version 2.0
 #  First edition: 11 Aug 2018, the latest edition: 25 Dec 2018
 

diff --git a/R/func__geoTempAnalyser__tempNet.R b/R/func__geoTempAnalyser__tempNet.R
@@ -41,7 +41,7 @@
 #' @param e.colour.high A character specifying the colour for edges of the highest weight.
 #' @param e.colour.num An integer specifying the number of colours to be assigned.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export tempNet
 #
 #  Copyright 2018 Yu Wan

diff --git a/R/func__getAllelesPerPattern.R b/R/func__getAllelesPerPattern.R
@@ -18,10 +18,10 @@
 #' ap1 <- getAllelesPerPattern(assoc[["mapping"]], sep = ",")
 #' ap2 <- getAllelesPerPattern(assoc[["alleles"]][["alle.pat"]], sep = ",")  # alternatively
 #'
-#' @author Yu Wan (\email{wanyuac@gmail.com})
+#' @author Yu Wan (\email{wanyuac@126.com})
 #' @export
 #
-# Copyright 2017 Yu Wan <wanyuac@gmail.com>
+# Copyright 2017 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First and the lastest edit: 19 Sep 2017
 

diff --git a/R/func__getAssocGenePair.R b/R/func__getAssocGenePair.R
@@ -15,7 +15,7 @@
 #'
 #' @return A data frame from x.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #'
 #  Copyright 2018 Yu Wan

diff --git a/R/func__getGeneClasses.R b/R/func__getGeneClasses.R
@@ -15,10 +15,10 @@
 #' assoc <- lmm(...)
 #' arg_cls <- data.frame(allele = assoc$mapping$allele, class = getGeneClass(x = assoc$mapping$gene), stringsAsFactors = FALSE)
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export getGeneClass
 #
-# Copyright 2018 Yu Wan <wanyuac@gmail.com>
+# Copyright 2018 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First edition: 18 Apr 2018; the lastest edition: 23 July 2018
 

diff --git a/R/func__getRowsXY.R b/R/func__getRowsXY.R
@@ -14,7 +14,7 @@
 #' z <- getRowsXY(df = assoc[["assoc"]], k1 = "IntI1_1.1", k2 = "SulI_1616", c1 = "y", c2 = "x")
 #' z <- getRowsXY(df = assoc[["assoc"]], k1 = "IntI1_1.1", k2 = "SulI_1616", c1 = 1, c2 = 2)
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #'
 #  Copyright 2017 Yu Wan

diff --git a/R/func__importAllelicPAM.R b/R/func__importAllelicPAM.R
@@ -17,10 +17,10 @@
 #' It can be used to filter the allelic PAM for in-group isolates.
 #' @param skip wheter to skip overwriting existant output files.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
-# Copyright 2017 Yu Wan <wanyuac@gmail.com>
+# Copyright 2017 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # An early version: 21 May 2017; the latest edition: 22 Aug 2018
 

diff --git a/R/func__importCoreGenomeSNPs.R b/R/func__importCoreGenomeSNPs.R
@@ -21,10 +21,10 @@
 #' @param annots.file file path of bimbam-formatted SNP annotations. Keep it "" to prevent the function from writing SNP annotations to the hard disk.
 #' @param skip whether to skip overwriting existing output files.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
-# Copyright 2017 Yu Wan <wanyuac@gmail.com>
+# Copyright 2017 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # Last edition: 21 May 2017
 

diff --git a/R/func__importGeneticPAM.R b/R/func__importGeneticPAM.R
@@ -15,10 +15,10 @@
 #' @param sample.order a vector of isolate names for the PAM to be matched with.
 #' It can be used to filter the genetic PAM for in-group isolates.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
-# Copyright 2017 Yu Wan <wanyuac@gmail.com>
+# Copyright 2017 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # An early version: 21 May 2017; the latest edition: 22 Aug 2018
 

diff --git a/R/func__lmm.R b/R/func__lmm.R
@@ -43,7 +43,7 @@
 #' @param save.stages (optional) Whether to turn on stage control or not. Recommend to turn it on when you are not sure whether the pipeline will be finished smoothly.
 #' @param skip (optional) Whether to avoid overwriting existing output files.
 #'
-#' @author Yu Wan, \email{wanyuac@@gmail.com}
+#' @author Yu Wan, \email{wanyuac@@126.com}
 #' @export
 #
 #  Copyright 2017-2019 Yu Wan

diff --git a/R/func__mergeIddAlleles.R b/R/func__mergeIddAlleles.R
@@ -46,10 +46,10 @@
 #'                          stringsAsFactors = FALSE)
 #' lmms_merged <- mergeIddAlleles(assoc = lmms, lmms.only = TRUE)
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
-# Copyright 2017 Yu Wan <wanyuac@gmail.com>
+# Copyright 2017 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 # First edition: 30 June 2017; the latest edition: 21 April 2019.
 

diff --git a/R/func__mkFilterTSV.R b/R/func__mkFilterTSV.R
@@ -12,11 +12,11 @@
 #'
 #' Either allele.mat or pam.a is expected to be used as an input for this function.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
 # First edition: 23 Janury 2017, 21 May 2017; the latest edition: 18 July 2018.
-# Copyright 2017-2018 Yu Wan <wanyuac@gmail.com>
+# Copyright 2017-2018 Yu Wan <wanyuac@126.com>
 # Licensed under the Apache License, Version 2.0
 
 mkFilterTSV <- function(allele.mat = NULL, pam.a = NULL, output = "targeted_isolates_alleles.tsv") {

diff --git a/R/func__networkAnalyser__alleleClusterDistr.R b/R/func__networkAnalyser__alleleClusterDistr.R
@@ -15,7 +15,7 @@
 #'
 #' @return An n-by-m matrix, where n is the sample size and m is the cluster number.
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
 #  Copyright 2019 Yu Wan

diff --git a/R/func__networkAnalyser__allelicCoMatrix.R b/R/func__networkAnalyser__allelicCoMatrix.R
@@ -16,10 +16,10 @@
 #' if hclust.method != NULL; g: a vector (method, dist) for arguments of
 #' column-wise clustering (grouping).
 #'
-#' @author Yu Wan (\email{wanyuac@@gmail.com})
+#' @author Yu Wan (\email{wanyuac@@126.com})
 #' @export
 #
-#  Copyright 2018 Yu Wan <wanyuac@gmail.com>
+#  Copyright 2018 Yu Wan <wanyuac@126.com>
 #  Licensed under the Apache License, Version 2.0
 #  First and the latest edition: 25 Jan 2019