Commit f67ffe3e authored by Konrad Zych's avatar Konrad Zych
Browse files

bufgfix in few examples

parent 11adf3d4
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Package: SIAMCAT
Type: Package
Title: Statistical Inference of Associations between Microbial Communities And host phenoTypes
Version: 0.99.0
Version: 0.99.1
Author: Georg Zeller [aut,cre], Jakob Wirbel[aut], Konrad Zych [aut], Nicolai Karcher[ctb] and Kersten Breuer[ctb]
Authors@R: c(person("Georg", "Zeller", role = c("aut", "cre"), email = "zeller@embl.de", comment = c(ORCID = "0000-0003-1429-7485")),
person("Konrad", "Zych", role = c("aut", "cre"), email = "konrad.zych@embl.de", comment = c(ORCID = "0000-0001-7426-0516")),
......@@ -27,7 +27,8 @@ Imports:
PRROC,
RColorBrewer,
stats,
utils
utils,
methods
License: GPL-3
Encoding: UTF-8
LazyData: true
......
......@@ -37,6 +37,7 @@ exportClasses(model_list)
exportClasses(siamcat)
import(LiblineaR)
import(glmnet, except = "auc")
import(methods)
import(mlr)
import(phyloseq)
importFrom(PRROC,pr.curve)
......
#' @import phyloseq mlr LiblineaR
#' @import phyloseq mlr LiblineaR methods
#' @rawNamespace import(glmnet, except = "auc")
#' @importFrom grDevices col2rgb colorRampPalette dev.off gray pdf rgb
#' @importFrom graphics abline arrows axis barplot box strheight strwidth
......
......@@ -92,7 +92,7 @@ is.component.class = function(x,class){
#' @export
#' @examples
#' data(siamcat_example)
#' siamcat_example <- reset.features(siamcat)
#' siamcat_example <- reset.features(siamcat_example)
reset.features <- function(siamcat){
siamcat@phyloseq@otu_table <- siamcat@orig_feat
return(siamcat)
......@@ -103,11 +103,11 @@ reset.features <- function(siamcat){
#' @name get.features
#' @description Function to access features in siamcat@phylose@otu_table
#' @param siamcat an object of class \link{siamcat-class}
#' @return Features as \link[phyloseq]{otu_table} object
#' @return Features as \link[phyloseq]{otu_table-class} object
#' @export
#' @examples
#' data(siamcat_example)
#' feat <- get.features(siamcat)
#' feat <- get.features(siamcat_example)
get.features <- function(siamcat){
return(siamcat@phyloseq@otu_table)
}
......@@ -121,7 +121,7 @@ get.features <- function(siamcat){
#' @export
#' @examples
#' data(siamcat_example)
#' phyloseq <- get.phyloseq(siamcat)
#' phyloseq <- get.phyloseq(siamcat_example)
get.phyloseq <- function(siamcat){
return(siamcat@phyloseq)
}
......@@ -135,7 +135,7 @@ get.phyloseq <- function(siamcat){
#' @export
#' @examples
#' data(siamcat_example)
#' feat <- get.features.matrix(siamcat)
#' feat <- get.features.matrix(siamcat_example)
get.features.matrix <- function(siamcat){
return(matrix(siamcat@phyloseq@otu_table,nrow=nrow(siamcat@phyloseq@otu_table), ncol=ncol(siamcat@phyloseq@otu_table),
dimnames = list(rownames(siamcat@phyloseq@otu_table), colnames(siamcat@phyloseq@otu_table))))
......@@ -150,7 +150,7 @@ get.features.matrix <- function(siamcat){
#' @export
#' @examples
#' data(siamcat_example)
#' model_list <- get.model_list(siamcat)
#' model_list <- get.model_list(siamcat_example)
get.model_list <- function(siamcat){
return(siamcat@model_list)
}
......@@ -158,12 +158,12 @@ get.model_list <- function(siamcat){
#' @title get.model.type
#' @name get.model.type
#' @description Function to access features in siamcat@model_list@model.type
#' @param siamcat an object of class \link{siamcat-class}t
#' @param siamcat an object of class \link{siamcat-class}
#' @return Character string specifing the name of the method used to construct the model.
#' @export
#' @examples
#' data(siamcat_example)
#' get.model.type(siamcat)
#' get.model.type(siamcat_example)
get.model.type <- function(siamcat){
return(model.type=siamcat@model_list@model.type)
}
......@@ -172,12 +172,12 @@ get.model.type <- function(siamcat){
#' @title get.models
#' @name get.models
#' @description Function to access models in siamcat@model_list@models
#' @param siamcat an object of class \link{siamcat-class}t
#' @param siamcat an object of class \link{siamcat-class}
#' @return List of models
#' @export
#' @examples
#' data(siamcat_example)
#' models <- get.models(siamcat)
#' models <- get.models(siamcat_example)
get.models <- function(siamcat){
return(siamcat@model_list@models)
}
......@@ -190,7 +190,7 @@ get.models <- function(siamcat){
#' @export
#' @examples
#' data(siamcat_example)
#' eval_data <- get.eval_data(siamcat)
#' eval_data <- get.eval_data(siamcat_example)
get.eval_data <- function(siamcat){
return(siamcat@eval_data)
}
......@@ -200,11 +200,11 @@ get.eval_data <- function(siamcat){
#' @description Function to access prediction matrix in siamcat@pred_matrix
#' siamcat@orig_feat in an object of class \link{siamcat-class}
#' @param siamcat an object of class \link{siamcat-class}t
#' @return Prediction matrix as \link{pred_matrix-class} object
#' @return Prediction matrix
#' @export
#' @examples
#' data(siamcat_example)
#' pred_matrix <- get.pred_matrix(siamcat)
#' pred_matrix <- get.pred_matrix(siamcat_example)
get.pred_matrix <- function(siamcat){
return(siamcat@pred_matrix)
}
......@@ -218,7 +218,7 @@ get.pred_matrix <- function(siamcat){
#' @export
#' @examples
#' data(siamcat_example)
#' label <- get.label.label(siamcat)
#' label <- get.label.label(siamcat_example)
get.label.label <- function(siamcat){
return(siamcat@label@label)
}
......@@ -232,21 +232,21 @@ get.label.label <- function(siamcat){
#' @export
#' @examples
#' data(siamcat_example)
#' label <- get.label(siamcat)
#' label <- get.label(siamcat_example)
get.label <- function(siamcat){
return(siamcat@label)
}
#' Access labels in siamcat@label
#' @title get.label
#' @name get.label
#' @title get.label.list
#' @name get.label.list
#' @description Function to access labels in siamcat@label
#' @param siamcat an object of class \link{siamcat-class}
#' @return Label object converted to a list
#' @export
#' @examples
#' data(siamcat_example)
#' label <- get.label.list(siamcat)
#' label <- get.label.list(siamcat_example)
get.label.list <- function(siamcat){
return(list(label = siamcat@label@label, header = siamcat@label@header,
info=siamcat@label@info, positive.lab=siamcat@label@positive.lab,
......@@ -256,15 +256,15 @@ get.label.list <- function(siamcat){
}
#' Access label info in siamcat@label@info
#' @title get.label
#' @name get.label
#' @title get.label.info
#' @name get.label.info
#' @description Function to access label info in siamcat@label@info
#' @param siamcat an object of class \link{siamcat-class}
#' @return List of label informations
#' @export
#' @examples
#' data(siamcat_example)
#' label_info <- get.label.info(siamcat)
#' label_info <- get.label.info(siamcat_example)
get.label.info <- function(siamcat){
return(siamcat@label@info)
}
......
......@@ -20,5 +20,5 @@ Access evaluation data in siamcat@eval_data
}
\examples{
data(siamcat_example)
eval_data <- get.eval_data(siamcat)
eval_data <- get.eval_data(siamcat_example)
}
......@@ -10,7 +10,7 @@ get.features(siamcat)
\item{siamcat}{an object of class \link{siamcat-class}}
}
\value{
Features as \link[phyloseq]{otu_table} object
Features as \link[phyloseq]{otu_table-class} object
}
\description{
Function to access features in siamcat@phylose@otu_table
......@@ -20,5 +20,5 @@ Access features in siamcat@phylose@otu_table
}
\examples{
data(siamcat_example)
feat <- get.features(siamcat)
feat <- get.features(siamcat_example)
}
......@@ -20,5 +20,5 @@ Access features in siamcat@phylose@otu_table
}
\examples{
data(siamcat_example)
feat <- get.features.matrix(siamcat)
feat <- get.features.matrix(siamcat_example)
}
......@@ -2,51 +2,23 @@
% Please edit documentation in R/siamcat_class_methods.R
\name{get.label}
\alias{get.label}
\alias{get.label}
\alias{get.label.list}
\alias{get.label}
\alias{get.label.info}
\title{get.label}
\usage{
get.label(siamcat)
get.label.list(siamcat)
get.label.info(siamcat)
}
\arguments{
\item{siamcat}{an object of class \link{siamcat-class}}
\item{siamcat}{an object of class \link{siamcat-class}}
\item{siamcat}{an object of class \link{siamcat-class}}
}
\value{
an object of class \link{label-class}
Label object converted to a list
List of label informations
}
\description{
Function to access labels in siamcat@label
Function to access labels in siamcat@label
Function to access label info in siamcat@label@info
}
\details{
Access label object in siamcat@label
Access labels in siamcat@label
Access label info in siamcat@label@info
}
\examples{
data(siamcat_example)
label <- get.label(siamcat)
data(siamcat_example)
label <- get.label.list(siamcat)
data(siamcat_example)
label_info <- get.label.info(siamcat)
label <- get.label(siamcat_example)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/siamcat_class_methods.R
\name{get.label.info}
\alias{get.label.info}
\title{get.label.info}
\usage{
get.label.info(siamcat)
}
\arguments{
\item{siamcat}{an object of class \link{siamcat-class}}
}
\value{
List of label informations
}
\description{
Function to access label info in siamcat@label@info
}
\details{
Access label info in siamcat@label@info
}
\examples{
data(siamcat_example)
label_info <- get.label.info(siamcat_example)
}
......@@ -20,5 +20,5 @@ Access labels in siamcat@label@label
}
\examples{
data(siamcat_example)
label <- get.label.label(siamcat)
label <- get.label.label(siamcat_example)
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/siamcat_class_methods.R
\name{get.label.list}
\alias{get.label.list}
\title{get.label.list}
\usage{
get.label.list(siamcat)
}
\arguments{
\item{siamcat}{an object of class \link{siamcat-class}}
}
\value{
Label object converted to a list
}
\description{
Function to access labels in siamcat@label
}
\details{
Access labels in siamcat@label
}
\examples{
data(siamcat_example)
label <- get.label.list(siamcat_example)
}
......@@ -7,7 +7,7 @@
get.model.type(siamcat)
}
\arguments{
\item{siamcat}{an object of class \link{siamcat-class}t}
\item{siamcat}{an object of class \link{siamcat-class}}
}
\value{
Character string specifing the name of the method used to construct the model.
......@@ -20,5 +20,5 @@ Access model type in siamcat@model_list@model.type
}
\examples{
data(siamcat_example)
get.model.type(siamcat)
get.model.type(siamcat_example)
}
......@@ -20,5 +20,5 @@ Access features in siamcat@phylose@otu_table
}
\examples{
data(siamcat_example)
model_list <- get.model_list(siamcat)
model_list <- get.model_list(siamcat_example)
}
......@@ -7,7 +7,7 @@
get.models(siamcat)
}
\arguments{
\item{siamcat}{an object of class \link{siamcat-class}t}
\item{siamcat}{an object of class \link{siamcat-class}}
}
\value{
List of models
......@@ -20,5 +20,5 @@ Access models in siamcat@model_list@models
}
\examples{
data(siamcat_example)
models <- get.models(siamcat)
models <- get.models(siamcat_example)
}
......@@ -16,9 +16,9 @@ Object of class \link[phyloseq]{phyloseq-class}
Function to access phyloseq object in siamcat@phylose
}
\details{
Access phyloseq object in siamcat@phylose
Access phyloseq object in siamcat@phyloseq
}
\examples{
data(siamcat_example)
phyloseq <- get.phyloseq(siamcat)
phyloseq <- get.phyloseq(siamcat_example)
}
......@@ -10,7 +10,7 @@ get.pred_matrix(siamcat)
\item{siamcat}{an object of class \link{siamcat-class}t}
}
\value{
Prediction matrix as \link{pred_matrix-class} object
Prediction matrix
}
\description{
Function to access prediction matrix in siamcat@pred_matrix
......@@ -21,5 +21,5 @@ Access Prediction matrix in siamcat@pred_matrix
}
\examples{
data(siamcat_example)
pred_matrix <- get.pred_matrix(siamcat)
pred_matrix <- get.pred_matrix(siamcat_example)
}
......@@ -21,5 +21,5 @@ Reset features in siamcat@phylose@otu_table to those in siamcat@orig_feat
}
\examples{
data(siamcat_example)
siamcat_example <- reset.features(siamcat)
siamcat_example <- reset.features(siamcat_example)
}
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