Chipping away at cran check warnings #38

DESCRIPTION

@@ -4,13 +4,12 @@ Title: <short description here>
 Version: 0.1.0
 Date: 2014-02-16
 BugReports: https://github.com/GotelliLab/EcoSimR/issues
-Authors@R: c(person("Nick", "Gotelli", role = c("aut", "cre"),
+Authors@R: c(person("Nick", "Gotelli", role = c("aut"),
     email = "ngotelli@uvm.edu"),
-    person("Edmund", "Hart", role = "aut",
+    person("Edmund", "Hart", role = c("aut","cre"),
     email = "edmund.m.hart@gmail.com"),
-    person("Aaron", "Ellison", role = c("aut","cre"),
+    person("Aaron", "Ellison", role = c("aut"),
     email = "aellison@fas.harvard.edu") )
-Maintainer: Edmund Hart <edmund.m.hart@gmail.com>
 LazyLoad: yes
 LazyData: yes
 Description: <longer description here>

NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(plot,coocnullmod)
 S3method(plot,nichenullmod)
+S3method(plot,sizenullmod)
 S3method(summary,coocnullmod)
 S3method(summary,nichenullmod)
 S3method(summary,sizenullmod)

R/coccurrence_null.R

@@ -70,6 +70,7 @@ cooc_null_model <- function(speciesData, algo = "sim1", metric = "c_score", nRep
 
 #' Generic function for calculating null model summary statistics
 #' @description Takes as input a list of Null.Model.Out, with Obs, Sim, Elapsed Time, and Time Stamp values
+#' @param object the null model object to print a summary.
 #' @export
 
 summary.coocnullmod <- function(object,...)
@@ -111,8 +112,11 @@ summary.coocnullmod <- function(object,...)
 
 
 
-#' Null Model Plot function
-#' @description Generic function for plotting a histogram of simulated values Takes as input a list of Null.Model.Out, with Obs and Sim values
+#' Co-Occurrence Model Plot function
+#' @description Plot co-occurrence null model object.
+#' @param x the null model to plot
+#' @param type the type of null plot to make.  See details for more information
+#' @details the valid types for size are "hist" to show a histogram and "size" to show a sample size null model.
 #' @export
 
 

R/niche_overlap_null.R

@@ -40,6 +40,7 @@ niche_null_model <- function(speciesData, algo = "ra3", metric = "pianka", nReps
 
 #' Generic function for calculating null model summary statistics
 #' @description Takes as input a list of Null.Model.Out, with Obs, Sim, Elapsed Time, and Time Stamp values
+#' @param object the null model object to print a summary of. 
 #' @export
 
 summary.nichenullmod <- function(object,...)
@@ -83,8 +84,11 @@ summary.nichenullmod <- function(object,...)
 
 
 
-#' Null Model Plot function
+#' Niche Null Model Plot function
 #' @description Generic function for plotting a histogram of simulated values Takes as input a list of Null.Model.Out, with Obs and Sim values
+#' @param x the null model to plot
+#' @param type the type of null plot to make.  See details for more information
+#' @details the valid types for size are "hist" to show a histogram and "niche" to show a sample draw from the null model.
 #' @export
 
 

R/sim9fast.R

@@ -1,5 +1,6 @@
 #' Sim9.fast function
-#' @description Special implementation of sequential swap algorithm
+#' @description Special implementation of sequential swap algorithm.
+
 #' @export
 
 

R/sizeratio_null.R

@@ -54,6 +54,7 @@ size_null_model <- function(speciesData, algo = "size_uniform", metric = "var_ra
 
 #' Generic function for calculating null model summary statistics
 #' @description Takes as input a list of Null.Model.Out, with Obs, Sim, Elapsed Time, and Time Stamp values
+#' @param object the null model object to print a summary of. 
 #' @export
 
 summary.sizenullmod <- function(object,...)
@@ -95,9 +96,16 @@ summary.sizenullmod <- function(object,...)
 }
 
 
+
+#' plot a size null model
+#' @description plot a variety of size null models
+#' @param x the null model to plot
+#' @param type the type of null plot to make.  See details for more information
+#' @details the valid types for size are "hist" to show a histogram and "size" to show a sample size null model.
+#' @export
+
 plot.sizenullmod <- function(x, type = "hist",...)
 {
-cat("in here")
 nullmodObj <- x
 if(type == "hist"){
   par(mfrow=c(1,1))

man/plot.coocnullmod.Rd

@@ -1,11 +1,19 @@
 % Generated by roxygen2 (4.0.2): do not edit by hand
 \name{plot.coocnullmod}
 \alias{plot.coocnullmod}
-\title{Null Model Plot function}
+\title{Co-Occurrence Model Plot function}
 \usage{
 \method{plot}{coocnullmod}(x, type = "hist", ...)
 }
+\arguments{
+\item{x}{the null model to plot}
+
+\item{type}{the type of null plot to make.  See details for more information}
+}
 \description{
-Generic function for plotting a histogram of simulated values Takes as input a list of Null.Model.Out, with Obs and Sim values
+Plot co-occurrence null model object.
+}
+\details{
+the valid types for size are "hist" to show a histogram and "size" to show a sample size null model.
 }
 

man/plot.nichenullmod.Rd

@@ -1,11 +1,19 @@
 % Generated by roxygen2 (4.0.2): do not edit by hand
 \name{plot.nichenullmod}
 \alias{plot.nichenullmod}
-\title{Null Model Plot function}
+\title{Niche Null Model Plot function}
 \usage{
 \method{plot}{nichenullmod}(x, type = "hist", ...)
 }
+\arguments{
+\item{x}{the null model to plot}
+
+\item{type}{the type of null plot to make.  See details for more information}
+}
 \description{
 Generic function for plotting a histogram of simulated values Takes as input a list of Null.Model.Out, with Obs and Sim values
 }
+\details{
+the valid types for size are "hist" to show a histogram and "niche" to show a sample draw from the null model.
+}
 

man/plot.sizenullmod.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{plot.sizenullmod}
+\alias{plot.sizenullmod}
+\title{plot a size null model}
+\usage{
+\method{plot}{sizenullmod}(x, type = "hist", ...)
+}
+\arguments{
+\item{x}{the null model to plot}
+
+\item{type}{the type of null plot to make.  See details for more information}
+}
+\description{
+plot a variety of size null models
+}
+\details{
+the valid types for size are "hist" to show a histogram and "size" to show a sample size null model.
+}
+

man/sim9.Rd

@@ -7,6 +7,6 @@ sim9(speciesData, algo, metric, nReps = 1000, rowNames = TRUE,
   saveSeed = FALSE, burn_in = 0)
 }
 \description{
-Special implementation of sequential swap algorithm
+Special implementation of sequential swap algorithm.
 }
 

man/summary.coocnullmod.Rd

@@ -5,6 +5,9 @@
 \usage{
 \method{summary}{coocnullmod}(object, ...)
 }
+\arguments{
+\item{object}{the null model object to print a summary.}
+}
 \description{
 Takes as input a list of Null.Model.Out, with Obs, Sim, Elapsed Time, and Time Stamp values
 }

man/summary.nichenullmod.Rd

@@ -5,6 +5,9 @@
 \usage{
 \method{summary}{nichenullmod}(object, ...)
 }
+\arguments{
+\item{object}{the null model object to print a summary of.}
+}
 \description{
 Takes as input a list of Null.Model.Out, with Obs, Sim, Elapsed Time, and Time Stamp values
 }

man/summary.sizenullmod.Rd

@@ -5,6 +5,9 @@
 \usage{
 \method{summary}{sizenullmod}(object, ...)
 }
+\arguments{
+\item{object}{the null model object to print a summary of.}
+}
 \description{
 Takes as input a list of Null.Model.Out, with Obs, Sim, Elapsed Time, and Time Stamp values
 }