diff --git a/.Rhistory b/.Rhistory
new file mode 100644
index 0000000..e69de29
diff --git a/R-plotter.r b/R-plotter.r
index ed8c037..9157b79 100644
--- a/R-plotter.r
+++ b/R-plotter.r
@@ -1,17 +1,14 @@
-rm(list = ls()) 
-library(ggplot2) #Needs ggplot2 - run install.packages(ggplot2) if not already installed !!
-
 cols <- hcl.colors(30, "Spectral")
 
 Ne = 10000 #Quantities needed to recale time back into years before present 
 g = 5
 
-ImpT <- t(read.table("D:/MCMC4WF-ThetaZero/ImpT.txt", quote = "\"", comment.char = "")) #Input location of file ImpT.txt here! 
+ImpT <- t(read.table("D:/ImpT.txt", quote = "\"", comment.char = "")) #Input location of file ImpT.txt here! 
 ImpT <-(((ImpT * 2 * Ne * g) - 20000)) #Converting from diffusion time to years before present
-ImpHT <-(t(read.table("D:/MCMC4WF-ThetaZero/HorseTrajectories.txt", quote = "\"", comment.char = ""))) #Input location of file ImpHT.txt here!
-OGT <-t(read.table("D:/MCMC4WF-ThetaZero/OGT.txt", quote = "\"", comment.char = "")) #Input location of file OGT.txt here! 
+ImpHT <-(t(read.table("D:/HorseTrajectories.txt", quote = "\"", comment.char = ""))) #Input location of file ImpHT.txt here!
+OGT <-t(read.table("D:/OGT.txt", quote = "\"", comment.char = "")) #Input location of file OGT.txt here! 
 OGT <-(((OGT * 2 * Ne * g) - 20000)) #Converting from diffusion time to years before present
-OGHT <-(t(read.table("D:/MCMC4WF-ThetaZero/OGHT.txt", quote = "\"", comment.char = ""))) #Input location of file OGHT.txt here
+OGHT <-(t(read.table("D:/OGHT.txt", quote = "\"", comment.char = ""))) #Input location of file OGHT.txt here
 
 setEPS()
 postscript(file = "horseTrajectories.eps") #Selection of figure format
diff --git a/README.md b/README.md
index d0bece3..fab3ba5 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 #EWF
 
-An efficient simulator for exact Wright-Fisher diffusion and diffusion bridge paths, accounting for a wide class of selective regimes (genic, diploid and arbitrary polynomial selection), and the presence/absence of mutation.
+An efficient simulator for exact Wright-Fisher diffusion and diffusion bridge paths, accounting for a wide class of selective regimes (genic, diploid and arbitrary polynomial selection), and the presence/absence of mutation. Please consult the _UserManual.pdf_ for all details with regards to installing dependencies, setting the correct linker flags, running the program and configuring the program input.
 
 *Dependencies*
 
diff --git a/UserManual.pdf b/UserManual.pdf
new file mode 100644
index 0000000..133662e
Binary files /dev/null and b/UserManual.pdf differ
diff --git a/config.cfg b/config.cfg
index 867ec7a..3836ee9 100644
--- a/config.cfg
+++ b/config.cfg
@@ -26,7 +26,7 @@ sigma_entry = 0.0;
 #reduces to genic selection!
 dominance_entry = 0.5;
 
-#Degree of polynomial for selection coefficient.Current implementation should 
+#Degree of polynomial for selection coefficient+1.Current implementation should 
 #be able to deal with any degree polynomials, but has only been tested for 
 #degree smaller than 25! Use higher degree polynomials at your own discretion!
 polyDeg_entry = 6;
diff --git a/configHorseCoat.cfg b/configHorseCoat.cfg
index ff0690a..7c56c8f 100644
--- a/configHorseCoat.cfg
+++ b/configHorseCoat.cfg
@@ -33,7 +33,7 @@ Ne_entry = 10000;
 #Dominance parameter h in the case of diploid selection
 dominance_entry = 0.5;
 
-#Degree of polynomial for selection coefficient.
+#Degree of polynomial for selection coefficient+1.
 polyDeg_entry = 6;
 
 #Entries for polynomial selection coefficient in increasing order of power.