Updated documentation

man/fgetl.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fgetl.R
+% Please edit documentation in R/fgetl-fopen.R
 \name{fgetl}
 \alias{fgetl}
 \title{Read line from file, removing newline characters}

man/fopen.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fgetl.R
+% Please edit documentation in R/fgetl-fopen.R
 \name{fopen}
 \alias{fopen}
 \title{Open file}

man/linkage.Rd

@@ -7,7 +7,7 @@
 linkage(Y, method = "co")
 }
 \arguments{
-\item{Y}{data}
+\item{Y}{matrix}
 
 \item{method}{either 'si', 'av', 'co' 'ce' or 'wa'}
 }
@@ -19,4 +19,9 @@ Z = LINKAGE(Y) creates a hierarchical cluster tree, using the single
 linkage algorithm.  The input Y is a distance matrix such as is generated by
 PDIST. Y may also be a more general dissimilarity matrix conforming to the
 output format of PDIST.
+
+Z = linkage(X) returns a matrix Z that encodes a tree containing hierarchical clusters of the rows of the input data matrix X.
+}
+\note{
+This is also a base Matlab function. The reason why the source code is also present here is unclear.
 }

man/lueNimi.Rd

@@ -13,5 +13,5 @@ lueNimi(line)
 nimi
 }
 \description{
-Reads the line name
+Returns the part of the line from the beginning that is before the comma. Useful for returning the name of a GenePop area
 }

man/min_MATLAB.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/min.R
+\name{min_MATLAB}
+\alias{min_MATLAB}
+\title{Minimum (MATLAB version)}
+\usage{
+min_MATLAB(X, indices = TRUE)
+}
+\arguments{
+\item{X}{matrix}
+
+\item{indices}{return indices?}
+}
+\value{
+Either a list or a vector
+}
+\description{
+Finds the minimum value for each column of a matrix, potentially returning the indices instead
+}
+\author{
+Waldir Leoncio
+}

man/rivinSisaltamienMjonojenLkm.Rd

@@ -13,5 +13,5 @@ rivinSisaltamienMjonojenLkm(line)
 count
 }
 \description{
-Number of M queues
+Returns the number of queues contained in the line. There must be a space between the queues.
 }

man/testaaGenePopData.Rd

@@ -9,6 +9,12 @@ testaaGenePopData(tiedostonNimi)
 \arguments{
 \item{tiedostonNimi}{Filename}
 }
+\value{
+kunnossa (binary "ok" condition value) == 0 if the data is not valid genePop data. Otherwise, kunnossa == 1.
+}
 \description{
 Tests GenePop data
 }
+\details{
+GenePop data are textfiles that follow the GenePop format. This function checks if such file is properly formatted as GenePop.
+}

man/testaaPop.Rd

@@ -10,7 +10,7 @@ testaaPop(rivi)
 \item{rivi}{Line}
 }
 \value{
-pal
+pal = 1 if the line starts with one of the following
 }
 \description{
 Test a line in the population