From ee905cbb1da681a25c76ffa45200277d29ad556b Mon Sep 17 00:00:00 2001
From: Clare <chorscroft@users.noreply.github.com>
Date: Tue, 14 Jul 2020 14:37:42 +0100
Subject: [PATCH] Added information on the create_LDprofile function to the
 details and @seealso section of the documentation

---
 R/Zalpha_BetaCDF.R                  | 4 +++-
 R/Zalpha_Zscore.R                   | 4 +++-
 R/Zalpha_all.R                      | 7 ++++++-
 R/Zalpha_expected.R                 | 5 +++--
 R/Zalpha_log_rsq_over_expected.R    | 4 +++-
 R/Zalpha_rsq_over_expected.R        | 4 +++-
 R/Zbeta_BetaCDF.R                   | 4 +++-
 R/Zbeta_Zscore.R                    | 4 +++-
 R/Zbeta_expected.R                  | 5 +++--
 R/Zbeta_log_rsq_over_expected.R     | 4 +++-
 R/Zbeta_rsq_over_expected.R         | 4 +++-
 man/Zalpha_BetaCDF.Rd               | 6 +++++-
 man/Zalpha_Zscore.Rd                | 6 +++++-
 man/Zalpha_all.Rd                   | 7 ++++++-
 man/Zalpha_expected.Rd              | 6 +++++-
 man/Zalpha_log_rsq_over_expected.Rd | 6 +++++-
 man/Zalpha_rsq_over_expected.Rd     | 6 +++++-
 man/Zbeta_BetaCDF.Rd                | 6 +++++-
 man/Zbeta_Zscore.Rd                 | 6 +++++-
 man/Zbeta_expected.Rd               | 6 +++++-
 man/Zbeta_log_rsq_over_expected.Rd  | 6 +++++-
 man/Zbeta_rsq_over_expected.Rd      | 6 +++++-
 22 files changed, 92 insertions(+), 24 deletions(-)

diff --git a/R/Zalpha_BetaCDF.R b/R/Zalpha_BetaCDF.R
index 4ccfd62..640b13a 100644
--- a/R/Zalpha_BetaCDF.R
+++ b/R/Zalpha_BetaCDF.R
@@ -14,7 +14,8 @@
 #' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 #' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-#' bound of the bin.
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #'
 #' @importFrom stats cor pbeta na.omit
 #'
@@ -43,6 +44,7 @@
 #'  LDprofile$bin,LDprofile$Beta_a,LDprofile$Beta_b,X=c(600,1500))
 #'
 #' @export
+#' @seealso \code{\link{create_LDprofile}}
 Zalpha_BetaCDF<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_Beta_a, LDprofile_Beta_b, minRandL = 4, minRL = 25, X = NULL){
 
   #Check things are in the correct format
diff --git a/R/Zalpha_Zscore.R b/R/Zalpha_Zscore.R
index ecc0c40..d7f25e9 100644
--- a/R/Zalpha_Zscore.R
+++ b/R/Zalpha_Zscore.R
@@ -13,7 +13,8 @@
 #' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 #' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-#' bound of the bin.
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #'
 #' @importFrom stats cor na.omit
 #'
@@ -42,6 +43,7 @@
 #'  LDprofile$bin,LDprofile$rsq,LDprofile$sd,X=c(600,1500))
 #'
 #' @export
+#' @seealso \code{\link{create_LDprofile}}
 Zalpha_Zscore<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_rsq, LDprofile_sd, minRandL = 4, minRL = 25, X = NULL){
 
   #Check things are in the correct format
diff --git a/R/Zalpha_all.R b/R/Zalpha_all.R
index 20c6a01..ec55c1c 100644
--- a/R/Zalpha_all.R
+++ b/R/Zalpha_all.R
@@ -11,6 +11,11 @@
 #'   \item For \code{\link{Zalpha_Zscore}} and \code{\link{Zbeta_Zscore}} to be calculated, the parameter \code{LDprofile_sd} must also be supplied.
 #'   \item For \code{\link{Zalpha_BetaCDF}} and \code{\link{Zbeta_BetaCDF}} to be calculated, the parameters \code{LDprofile_Beta_a} and \code{LDprofile_Beta_b} must also be supplied.
 #' }
+#' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
+#' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
+#' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #' For more information about the statistics, please see Jacobs (2016).
 #'
 #' @importFrom stats cor pbeta na.omit
@@ -45,7 +50,7 @@
 #'Zalpha_all(snps$bp_positions,3000,as.matrix(snps[,3:12]))
 #'
 #' @export
-#' @seealso \code{\link{Zalpha}} \code{\link{Zalpha_expected}} \code{\link{Zalpha_rsq_over_expected}} \code{\link{Zalpha_log_rsq_over_expected}} \code{\link{Zalpha_Zscore}} \code{\link{Zalpha_BetaCDF}} \code{\link{Zbeta}} \code{\link{Zbeta_expected}} \code{\link{Zbeta_rsq_over_expected}} \code{\link{Zbeta_log_rsq_over_expected}} \code{\link{Zbeta_Zscore}} \code{\link{Zbeta_BetaCDF}} \code{\link{LR}} \code{\link{L_plus_R}}
+#' @seealso \code{\link{Zalpha}}, \code{\link{Zalpha_expected}}, \code{\link{Zalpha_rsq_over_expected}}, \code{\link{Zalpha_log_rsq_over_expected}}, \code{\link{Zalpha_Zscore}}, \code{\link{Zalpha_BetaCDF}}, \code{\link{Zbeta}}, \code{\link{Zbeta_expected}}, \code{\link{Zbeta_rsq_over_expected}}, \code{\link{Zbeta_log_rsq_over_expected}}, \code{\link{Zbeta_Zscore}}, \code{\link{Zbeta_BetaCDF}}, \code{\link{LR}}, \code{\link{L_plus_R}}, \code{\link{create_LDprofile}}.
 
 Zalpha_all <- function(pos, ws, x=NULL, dist=NULL, LDprofile_bins=NULL, LDprofile_rsq=NULL, LDprofile_sd=NULL, LDprofile_Beta_a=NULL, LDprofile_Beta_b=NULL, minRandL = 4, minRL = 25, X = NULL) {
   #Check things are in the correct format
diff --git a/R/Zalpha_expected.R b/R/Zalpha_expected.R
index 1112fbf..e863366 100644
--- a/R/Zalpha_expected.R
+++ b/R/Zalpha_expected.R
@@ -13,7 +13,8 @@
 #' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 #' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-#' bound of the bin.
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\alpha}^{E[r^2]}}{Zalpha} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -36,7 +37,7 @@
 #' Zalpha_expected(snps$bp_positions,3000,snps$cM_distances,LDprofile$bin,LDprofile$rsq,X=c(600,1500))
 #'
 #' @export
-#'
+#' @seealso \code{\link{create_LDprofile}}
 Zalpha_expected<-function(pos, ws, dist, LDprofile_bins, LDprofile_rsq, minRandL = 4, minRL = 25, X = NULL) {
   #Check things are in the correct format
 
diff --git a/R/Zalpha_log_rsq_over_expected.R b/R/Zalpha_log_rsq_over_expected.R
index 9548804..bde2f5c 100644
--- a/R/Zalpha_log_rsq_over_expected.R
+++ b/R/Zalpha_log_rsq_over_expected.R
@@ -13,7 +13,8 @@
 #' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 #' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-#' bound of the bin.
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #'
 #' @importFrom stats cor na.omit
 #'
@@ -41,6 +42,7 @@
 #'  LDprofile$bin,LDprofile$rsq,X=c(600,1500))
 #'
 #' @export
+#' @seealso \code{\link{create_LDprofile}}
 Zalpha_log_rsq_over_expected<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_rsq, minRandL = 4, minRL = 25, X = NULL){
 
   #Check things are in the correct format
diff --git a/R/Zalpha_rsq_over_expected.R b/R/Zalpha_rsq_over_expected.R
index 732c03b..56672a3 100644
--- a/R/Zalpha_rsq_over_expected.R
+++ b/R/Zalpha_rsq_over_expected.R
@@ -13,7 +13,8 @@
 #' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 #' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-#' bound of the bin.
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #'
 #' @importFrom stats cor na.omit
 #'
@@ -41,6 +42,7 @@
 #'  LDprofile$bin,LDprofile$rsq,X=c(600,1500))
 #'
 #' @export
+#' @seealso \code{\link{create_LDprofile}}
 Zalpha_rsq_over_expected<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_rsq, minRandL = 4, minRL = 25, X = NULL){
 
   #Check things are in the correct format
diff --git a/R/Zbeta_BetaCDF.R b/R/Zbeta_BetaCDF.R
index 3be71e6..c378482 100644
--- a/R/Zbeta_BetaCDF.R
+++ b/R/Zbeta_BetaCDF.R
@@ -14,7 +14,8 @@
 #' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 #' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-#' bound of the bin.
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #'
 #' @importFrom stats cor pbeta na.omit
 #'
@@ -43,6 +44,7 @@
 #'  LDprofile$bin,LDprofile$Beta_a,LDprofile$Beta_b,X=c(600,1500))
 #'
 #' @export
+#' @seealso \code{\link{create_LDprofile}}
 Zbeta_BetaCDF<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_Beta_a, LDprofile_Beta_b, minRandL = 4, minRL = 25, X = NULL){
 
   #Check things are in the correct format
diff --git a/R/Zbeta_Zscore.R b/R/Zbeta_Zscore.R
index 9c4031c..e2795dd 100644
--- a/R/Zbeta_Zscore.R
+++ b/R/Zbeta_Zscore.R
@@ -13,7 +13,8 @@
 #' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 #' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-#' bound of the bin.
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #'
 #' @importFrom stats cor na.omit
 #'
@@ -42,6 +43,7 @@
 #'  LDprofile$bin,LDprofile$rsq,LDprofile$sd,X=c(600,1500))
 #'
 #' @export
+#' @seealso \code{\link{create_LDprofile}}
 Zbeta_Zscore<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_rsq, LDprofile_sd, minRandL = 4, minRL = 25, X = NULL){
 
   #Check things are in the correct format
diff --git a/R/Zbeta_expected.R b/R/Zbeta_expected.R
index 05bde70..76776da 100644
--- a/R/Zbeta_expected.R
+++ b/R/Zbeta_expected.R
@@ -13,7 +13,8 @@
 #' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 #' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-#' bound of the bin.
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\beta}^{E[r^2]}}{Zbeta} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -36,7 +37,7 @@
 #' Zbeta_expected(snps$bp_positions,3000,snps$cM_distances,LDprofile$bin,LDprofile$rsq,X=c(600,1500))
 #'
 #' @export
-#'
+#' @seealso \code{\link{create_LDprofile}}
 Zbeta_expected<-function(pos, ws, dist, LDprofile_bins, LDprofile_rsq, minRandL = 4, minRL = 25, X = NULL) {
   #Check things are in the correct format
 
diff --git a/R/Zbeta_log_rsq_over_expected.R b/R/Zbeta_log_rsq_over_expected.R
index 4293b5c..d5640bb 100644
--- a/R/Zbeta_log_rsq_over_expected.R
+++ b/R/Zbeta_log_rsq_over_expected.R
@@ -13,7 +13,8 @@
 #' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 #' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-#' bound of the bin.
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #'
 #' @importFrom stats cor na.omit
 #'
@@ -41,6 +42,7 @@
 #'  LDprofile$bin,LDprofile$rsq,X=c(600,1500))
 #'
 #' @export
+#' @seealso \code{\link{create_LDprofile}}
 Zbeta_log_rsq_over_expected<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_rsq, minRandL = 4, minRL = 25, X = NULL){
 
   #Check things are in the correct format
diff --git a/R/Zbeta_rsq_over_expected.R b/R/Zbeta_rsq_over_expected.R
index b779188..e0cc7fe 100644
--- a/R/Zbeta_rsq_over_expected.R
+++ b/R/Zbeta_rsq_over_expected.R
@@ -13,7 +13,8 @@
 #' The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 #' real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-#' bound of the bin.
+#' bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+#' using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 #'
 #' @importFrom stats cor na.omit
 #'
@@ -41,6 +42,7 @@
 #'  LDprofile$bin,LDprofile$rsq,X=c(600,1500))
 #'
 #' @export
+#' @seealso \code{\link{create_LDprofile}}
 Zbeta_rsq_over_expected<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_rsq, minRandL = 4, minRL = 25, X = NULL){
 
   #Check things are in the correct format
diff --git a/man/Zalpha_BetaCDF.Rd b/man/Zalpha_BetaCDF.Rd
index 4547af6..994bd43 100644
--- a/man/Zalpha_BetaCDF.Rd
+++ b/man/Zalpha_BetaCDF.Rd
@@ -55,7 +55,8 @@ the estimated a and b parameters from the LD profile.
 The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-bound of the bin.
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 }
 \examples{
 ## load the snps and LDprofile example datasets
@@ -72,3 +73,6 @@ Zalpha_BetaCDF(snps$bp_positions,3000,as.matrix(snps[,3:12]),snps$cM_distances,
 \references{
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
+\seealso{
+\code{\link{create_LDprofile}}
+}
diff --git a/man/Zalpha_Zscore.Rd b/man/Zalpha_Zscore.Rd
index ec27b08..8c21c01 100644
--- a/man/Zalpha_Zscore.Rd
+++ b/man/Zalpha_Zscore.Rd
@@ -54,7 +54,8 @@ the squared correlation between a pair of SNPs, \eqn{E[r^2]}{E[r^2]} is equal to
 The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-bound of the bin.
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 }
 \examples{
 ## load the snps and LDprofile example datasets
@@ -71,3 +72,6 @@ Zalpha_Zscore(snps$bp_positions,3000,as.matrix(snps[,3:12]),snps$cM_distances,
 \references{
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
+\seealso{
+\code{\link{create_LDprofile}}
+}
diff --git a/man/Zalpha_all.Rd b/man/Zalpha_all.Rd
index 2a57189..0a30d00 100644
--- a/man/Zalpha_all.Rd
+++ b/man/Zalpha_all.Rd
@@ -59,6 +59,11 @@ This includes the statistics: \code{\link{Zalpha_expected}}, \code{\link{Zalpha_
   \item For \code{\link{Zalpha_Zscore}} and \code{\link{Zbeta_Zscore}} to be calculated, the parameter \code{LDprofile_sd} must also be supplied.
   \item For \code{\link{Zalpha_BetaCDF}} and \code{\link{Zbeta_BetaCDF}} to be calculated, the parameters \code{LDprofile_Beta_a} and \code{LDprofile_Beta_b} must also be supplied.
 }
+The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
+real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
+profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 For more information about the statistics, please see Jacobs (2016).
 }
 \examples{
@@ -80,5 +85,5 @@ Zalpha_all(snps$bp_positions,3000,as.matrix(snps[,3:12]))
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
 \seealso{
-\code{\link{Zalpha}} \code{\link{Zalpha_expected}} \code{\link{Zalpha_rsq_over_expected}} \code{\link{Zalpha_log_rsq_over_expected}} \code{\link{Zalpha_Zscore}} \code{\link{Zalpha_BetaCDF}} \code{\link{Zbeta}} \code{\link{Zbeta_expected}} \code{\link{Zbeta_rsq_over_expected}} \code{\link{Zbeta_log_rsq_over_expected}} \code{\link{Zbeta_Zscore}} \code{\link{Zbeta_BetaCDF}} \code{\link{LR}} \code{\link{L_plus_R}}
+\code{\link{Zalpha}}, \code{\link{Zalpha_expected}}, \code{\link{Zalpha_rsq_over_expected}}, \code{\link{Zalpha_log_rsq_over_expected}}, \code{\link{Zalpha_Zscore}}, \code{\link{Zalpha_BetaCDF}}, \code{\link{Zbeta}}, \code{\link{Zbeta_expected}}, \code{\link{Zbeta_rsq_over_expected}}, \code{\link{Zbeta_log_rsq_over_expected}}, \code{\link{Zbeta_Zscore}}, \code{\link{Zbeta_BetaCDF}}, \code{\link{LR}}, \code{\link{L_plus_R}}, \code{\link{create_LDprofile}}.
 }
diff --git a/man/Zalpha_expected.Rd b/man/Zalpha_expected.Rd
index b2a8ca9..04316d4 100644
--- a/man/Zalpha_expected.Rd
+++ b/man/Zalpha_expected.Rd
@@ -48,7 +48,8 @@ and \eqn{E[r^2]}{E[r^2]} is equal to the expected squared correlation between a
 The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-bound of the bin.
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 }
 \examples{
 ## load the snps and LDprofile example datasets
@@ -63,3 +64,6 @@ Zalpha_expected(snps$bp_positions,3000,snps$cM_distances,LDprofile$bin,LDprofile
 \references{
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
+\seealso{
+\code{\link{create_LDprofile}}
+}
diff --git a/man/Zalpha_log_rsq_over_expected.Rd b/man/Zalpha_log_rsq_over_expected.Rd
index 8ef0f96..ecf83f6 100644
--- a/man/Zalpha_log_rsq_over_expected.Rd
+++ b/man/Zalpha_log_rsq_over_expected.Rd
@@ -51,7 +51,8 @@ the squared correlation between a pair of SNPs, and \eqn{E[r^2]}{E[r^2]} is equa
 The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-bound of the bin.
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 }
 \examples{
 ## load the snps and LDprofile example datasets
@@ -68,3 +69,6 @@ Zalpha_log_rsq_over_expected(snps$bp_positions,3000,as.matrix(snps[,3:12]),snps$
 \references{
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
+\seealso{
+\code{\link{create_LDprofile}}
+}
diff --git a/man/Zalpha_rsq_over_expected.Rd b/man/Zalpha_rsq_over_expected.Rd
index 97ecd31..4043174 100644
--- a/man/Zalpha_rsq_over_expected.Rd
+++ b/man/Zalpha_rsq_over_expected.Rd
@@ -51,7 +51,8 @@ the squared correlation between a pair of SNPs, and \eqn{E[r^2]}{E[r^2]} is equa
 The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-bound of the bin.
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 }
 \examples{
 ## load the snps and LDprofile example datasets
@@ -68,3 +69,6 @@ Zalpha_rsq_over_expected(snps$bp_positions,3000,as.matrix(snps[,3:12]),snps$cM_d
 \references{
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
+\seealso{
+\code{\link{create_LDprofile}}
+}
diff --git a/man/Zbeta_BetaCDF.Rd b/man/Zbeta_BetaCDF.Rd
index c0fc55f..df3bfb8 100644
--- a/man/Zbeta_BetaCDF.Rd
+++ b/man/Zbeta_BetaCDF.Rd
@@ -55,7 +55,8 @@ the estimated a and b parameters from the LD profile.
 The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-bound of the bin.
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 }
 \examples{
 ## load the snps and LDprofile example datasets
@@ -72,3 +73,6 @@ Zbeta_BetaCDF(snps$bp_positions,3000,as.matrix(snps[,3:12]),snps$cM_distances,
 \references{
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
+\seealso{
+\code{\link{create_LDprofile}}
+}
diff --git a/man/Zbeta_Zscore.Rd b/man/Zbeta_Zscore.Rd
index 91bc7a5..647ccb8 100644
--- a/man/Zbeta_Zscore.Rd
+++ b/man/Zbeta_Zscore.Rd
@@ -54,7 +54,8 @@ the squared correlation between a pair of SNPs, \eqn{E[r^2]}{E[r^2]} is equal to
 The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-bound of the bin.
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 }
 \examples{
 ## load the snps and LDprofile example datasets
@@ -71,3 +72,6 @@ Zbeta_Zscore(snps$bp_positions,3000,as.matrix(snps[,3:12]),snps$cM_distances,
 \references{
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
+\seealso{
+\code{\link{create_LDprofile}}
+}
diff --git a/man/Zbeta_expected.Rd b/man/Zbeta_expected.Rd
index 7cdfd59..ffa8030 100644
--- a/man/Zbeta_expected.Rd
+++ b/man/Zbeta_expected.Rd
@@ -48,7 +48,8 @@ and \eqn{E[r^2]}{E[r^2]} is equal to the expected squared correlation between a
 The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-bound of the bin.
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 }
 \examples{
 ## load the snps and LDprofile example datasets
@@ -63,3 +64,6 @@ Zbeta_expected(snps$bp_positions,3000,snps$cM_distances,LDprofile$bin,LDprofile$
 \references{
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
+\seealso{
+\code{\link{create_LDprofile}}
+}
diff --git a/man/Zbeta_log_rsq_over_expected.Rd b/man/Zbeta_log_rsq_over_expected.Rd
index 6513c73..07cfb9e 100644
--- a/man/Zbeta_log_rsq_over_expected.Rd
+++ b/man/Zbeta_log_rsq_over_expected.Rd
@@ -51,7 +51,8 @@ the squared correlation between a pair of SNPs, and \eqn{E[r^2]}{E[r^2]} is equa
 The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-bound of the bin.
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 }
 \examples{
 ## load the snps and LDprofile example datasets
@@ -68,3 +69,6 @@ Zbeta_log_rsq_over_expected(snps$bp_positions,3000,as.matrix(snps[,3:12]),snps$c
 \references{
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
+\seealso{
+\code{\link{create_LDprofile}}
+}
diff --git a/man/Zbeta_rsq_over_expected.Rd b/man/Zbeta_rsq_over_expected.Rd
index 6fc3ef9..10f250a 100644
--- a/man/Zbeta_rsq_over_expected.Rd
+++ b/man/Zbeta_rsq_over_expected.Rd
@@ -51,7 +51,8 @@ the squared correlation between a pair of SNPs, and \eqn{E[r^2]}{E[r^2]} is equa
 The LD profile describes the expected correlation between SNPs at a given genetic distance, generated using simulations or
 real data. Care should be taken to utilise an LD profile that is representative of the population in question. The LD
 profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
-bound of the bin.
+bound of the bin. Ideally, an LD profile would be generated using data from a null population with no selection, however one can be generated
+using this data. See the \code{\link{create_LDprofile}} function for more information on how to create an LD profile.
 }
 \examples{
 ## load the snps and LDprofile example datasets
@@ -68,3 +69,6 @@ Zbeta_rsq_over_expected(snps$bp_positions,3000,as.matrix(snps[,3:12]),snps$cM_di
 \references{
 Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
 }
+\seealso{
+\code{\link{create_LDprofile}}
+}
-- 
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