Credit @zkamvar & @pitakakariki for their contribs

Closes #3
dwinter · Jun 29, 2015 · 1c542b9 · 1c542b9 · pitakakariki · Jun 29, 2015
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,11 @@ Package: mmod
 Version: 1.3.0
 Date: 2015-05-01
 Title: Modern Measures of Population Differentiation
-Author: David Winter
+Authors@R: c(
+  person("David", "Winter", email = "david.winter@gmail.com", role = c("aut",  "cre")),
+  person("Peter", "Green", email = "pitakakariki@gmail.com", role = "ctb"),
+  person("Zhian", "Kamvar", email = "kamvarz@science.oregonstate.edu", role = "ctb")
+  )
 Maintainer: David Winter <david.winter@gmail.com>
 Depends:
     R (>= 2.6.0),

diff --git a/R/pairwise_D.R b/R/pairwise_D.R
diff --git a/man/D_Jost.Rd b/man/D_Jost.Rd
@@ -40,7 +40,7 @@ D_Jost(nancycats, hsht_mean= "arithmetic")
 Jost, L. (2008), GST and its relatives do not measure differentiation. Molecular Ecology, 17: 4015-4026.
 }
 \seealso{
-Other D: \code{\link{pairwise_D}}, \code{\link{pairwise_D}}
+Other D: \code{\link{pairwise_D}}
 
 Other diffstat: \code{\link{Gst_Hedrick}};
   \code{\link{Gst_Nei}}; \code{\link{Phi_st_Meirmans}};

diff --git a/man/Gst_Hedrick.Rd b/man/Gst_Hedrick.Rd
@@ -40,7 +40,6 @@ Other diffstat: \code{\link{D_Jost}};
   \code{\link{Gst_Nei}}; \code{\link{Phi_st_Meirmans}};
   \code{\link{diff_stats}}
 
-Other Hedrick: \code{\link{pairwise_Gst_Hedrick}},
-  \code{\link{pairwise_Gst_Hedrick}}
+Other Hedrick: \code{\link{pairwise_Gst_Hedrick}}
 }
 
diff --git a/man/Gst_Nei.Rd b/man/Gst_Nei.Rd
@@ -32,7 +32,6 @@ Other diffstat: \code{\link{D_Jost}};
   \code{\link{Gst_Hedrick}}; \code{\link{Phi_st_Meirmans}};
   \code{\link{diff_stats}}
 
-Other Nei: \code{\link{pairwise_Gst_Nei}},
-  \code{\link{pairwise_Gst_Nei}}
+Other Nei: \code{\link{pairwise_Gst_Nei}}
 }
 
diff --git a/man/pairwise_D.Rd b/man/pairwise_D.Rd
@@ -1,11 +1,9 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/pairwise.R, R/pairwise_D.R
+% Please edit documentation in R/pairwise.R
 \name{pairwise_D}
 \alias{pairwise_D}
 \title{Calculates pairwise values of Jost's D}
 \usage{
-pairwise_D(x, linearized = FALSE, hsht_mean = "arithmetic")
-
 pairwise_D(x, linearized = FALSE, hsht_mean = "arithmetic")
 }
 \arguments{
@@ -15,52 +13,26 @@ pairwise_D(x, linearized = FALSE, hsht_mean = "arithmetic")
 
 \item{hsht_mean}{type of mean to use for the global estimates of Hs and Ht
 default it "arithmetic", can also be set to "harmonic".}
-
-\item{hsht_mean}{type of mean to use for the global estimates of Hs and Ht
-default it "arithmetic", can also be set to "harmonic".}
-
-\item{x}{genind object (from package adegenet)}
-
-\item{linearized}{logical, if TRUE will turned linearized D (1/1-D)}
 }
 \value{
-A distance matrix with between-population values of D
-
 A distance matrix with between-population values of D
 }
 \description{
-This function calculates Jost's D, a measure of genetic
-differentiation, between all combinations of populaitons
-in a genind object.
-
 This function calculates Jost's D, a measure of genetic
 differentiation, between all combinations of populaitons
 in a genind object.
 }
 \examples{
 data(nancycats)
 pairwise_D(nancycats[1:26,])
-data(nancycats)
-pairwise_D(nancycats[1:26,])
 }
 \references{
-Jost, L. (2008), GST and its relatives do not measure differentiation. Molecular Ecology, 17: 4015-4026.
-
 Jost, L. (2008), GST and its relatives do not measure differentiation. Molecular Ecology, 17: 4015-4026.
 }
 \seealso{
 Other D: \code{\link{D_Jost}}
 
-Other D: \code{\link{D_Jost}}
-
-Other pairwise: \code{\link{pairwise_Gst_Hedrick}},
-  \code{\link{pairwise_Gst_Hedrick}};
-  \code{\link{pairwise_Gst_Nei}},
-  \code{\link{pairwise_Gst_Nei}}
-
-Other pairwise: \code{\link{pairwise_Gst_Hedrick}},
-  \code{\link{pairwise_Gst_Hedrick}};
-  \code{\link{pairwise_Gst_Nei}},
+Other pairwise: \code{\link{pairwise_Gst_Hedrick}};
   \code{\link{pairwise_Gst_Nei}}
 }
 
diff --git a/man/pairwise_Gst_Hedrick.Rd b/man/pairwise_Gst_Hedrick.Rd
@@ -1,58 +1,35 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/pairwise.R, R/pairwise_D.R
+% Please edit documentation in R/pairwise.R
 \name{pairwise_Gst_Hedrick}
 \alias{pairwise_Gst_Hedrick}
 \title{Calculates pairwise values of Hedrick's G'st}
 \usage{
-pairwise_Gst_Hedrick(x, linearized = FALSE)
-
 pairwise_Gst_Hedrick(x, linearized = FALSE)
 }
 \arguments{
 \item{x}{genind object (from package adegenet)}
 
-\item{linearized}{logical, if TRUE will turned linearized G'st (1/()1-G'st))}
-
-\item{x}{genind object (from package adegenet)}
-
 \item{linearized}{logical, if TRUE will turned linearized G'st (1/()1-G'st))}
 }
 \value{
-A distance matrix with between-population values of G''st
-
 A distance matrix with between-population values of G''st
 }
 \description{
-This function calculates Hedrick's G'st, a measure of genetic
-differentiation, between all combinations of populaitons
-in a genind object.
-
 This function calculates Hedrick's G'st, a measure of genetic
 differentiation, between all combinations of populaitons
 in a genind object.
 }
 \examples{
 data(nancycats)
 pairwise_Gst_Hedrick(nancycats[1:26,])
-data(nancycats)
-pairwise_Gst_Hedrick(nancycats[1:26,])
 }
 \references{
-Hedrick, PW. (2005), A Standardized Genetic Differentiation Measure. Evolution 59: 1633-1638.
-
 Hedrick, PW. (2005), A Standardized Genetic Differentiation Measure. Evolution 59: 1633-1638.
 }
 \seealso{
 Other Hedrick: \code{\link{Gst_Hedrick}}
 
-Other Hedrick: \code{\link{Gst_Hedrick}}
-
-Other pairwise: \code{\link{pairwise_D}},
-  \code{\link{pairwise_D}}; \code{\link{pairwise_Gst_Nei}},
-  \code{\link{pairwise_Gst_Nei}}
-
-Other pairwise: \code{\link{pairwise_D}},
-  \code{\link{pairwise_D}}; \code{\link{pairwise_Gst_Nei}},
+Other pairwise: \code{\link{pairwise_D}};
   \code{\link{pairwise_Gst_Nei}}
 }
 
diff --git a/man/pairwise_Gst_Nei.Rd b/man/pairwise_Gst_Nei.Rd
@@ -1,64 +1,37 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/pairwise.R, R/pairwise_D.R
+% Please edit documentation in R/pairwise.R
 \name{pairwise_Gst_Nei}
 \alias{pairwise_Gst_Nei}
 \title{Calculates pairwise values of Nei's Gst}
 \usage{
-pairwise_Gst_Nei(x, linearized = FALSE)
-
 pairwise_Gst_Nei(x, linearized = FALSE)
 }
 \arguments{
 \item{x}{genind object (from package adegenet)}
 
-\item{linearized}{logical, if TRUE will turned linearized Gst (1/(1-Gst))}
-
-\item{x}{genind object (from package adegenet)}
-
 \item{linearized}{logical, if TRUE will turned linearized Gst (1/(1-Gst))}
 }
 \value{
-dist A distance matrix with between-population values of Gst
-
 dist A distance matrix with between-population values of Gst
 }
 \description{
-This function calculates Nei's Gst, a measure of genetic
-differentiation, between all combinations of populaitons
-in a genind object.
-
 This function calculates Nei's Gst, a measure of genetic
 differentiation, between all combinations of populaitons
 in a genind object.
 }
 \examples{
 data(nancycats)
 pairwise_Gst_Nei(nancycats[1:26,])
-data(nancycats)
-pairwise_Gst_Nei(nancycats[1:26,])
 }
 \references{
 Nei M. (1973) Analysis of gene diversity in subdivided populations. PNAS: 3321-3323.
 
-Nei M, Chesser RK. (1983). Estimation of fixation indices and gene diversities. Annals of Human Genetics. 47: 253-259.
-
-Nei M. (1973) Analysis of gene diversity in subdivided populations. PNAS: 3321-3323.
-
 Nei M, Chesser RK. (1983). Estimation of fixation indices and gene diversities. Annals of Human Genetics. 47: 253-259.
 }
 \seealso{
 Other Nei: \code{\link{Gst_Nei}}
 
-Other Nei: \code{\link{Gst_Nei}}
-
-Other pairwise: \code{\link{pairwise_D}},
-  \code{\link{pairwise_D}};
-  \code{\link{pairwise_Gst_Hedrick}},
-  \code{\link{pairwise_Gst_Hedrick}}
-
-Other pairwise: \code{\link{pairwise_D}},
-  \code{\link{pairwise_D}};
-  \code{\link{pairwise_Gst_Hedrick}},
+Other pairwise: \code{\link{pairwise_D}};
   \code{\link{pairwise_Gst_Hedrick}}
 }