fix in read.dna and change in write.dna

[ape.git] / man / parafit.Rd

diff --git a/man/parafit.Rd b/man/parafit.Rd
index 6cb16ac835b61fccf3df3fb46b72f1a9d02d4c1a..9a1c1560eba792b2ff31d62587c02da79cc6f9de 100644 (file)
--- a/man/parafit.Rd
+++ b/man/parafit.Rd
@@ -11,8 +11,8 @@ Function \code{\link{parafit}} tests the hypothesis of coevolution between a cla
 The method, which is described in detail in Legendre et al. (2002), requires some estimates of the phylogenetic trees or phylogenetic distances, and also a description of the host-parasite associations (H-P links) observed in nature.
 }
 \usage{
-parafit(host.D, para.D ,HP ,nperm=999, test.links=FALSE, seed=NULL,
-correction="none", silent=FALSE)
+parafit(host.D, para.D, HP, nperm = 999, test.links = FALSE,
+        seed = NULL, correction = "none", silent = FALSE)
 }
 
 \arguments{
@@ -24,7 +24,7 @@ correction="none", silent=FALSE)
   \item{test.links }{ \code{test.links = TRUE} will test the significance of individual host-parasite links. Default: \code{test.links = FALSE}. }
   \item{seed }{ \code{seed = NULL} (default): a seed is chosen at random by the function. That seed is used as the starting point for all tests of significance, i.e. the global H-P test and the tests of individual H-P links if they are requested. Users can select a seed of their choice by giving any integer value to \code{seed}, for example \code{seed = -123456}. Running the function again with the same seed value will produce the exact same test results. }
   \item{correction}{ Correction methods for negative eigenvalues (details below): \code{correction="lingoes"} and \code{correction="cailliez"}. Default value: \code{"none"}.  }
-  \item{silent}{ Informative messages and the time to compute the tests will not be written to the R console if silent=TRUE. Useful when the function is called by a numerical simulation function. }
+  \item{silent}{ Informative messages and the time to compute the tests will not be written to the \R console if silent=TRUE. Useful when the function is called by a numerical simulation function. }
 }
 
 \details{