Merge pull request #16 from moshejasper/dev

generics & class updates (not reverse compatible in all cases)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: kindisperse
 Title: Simulate and Estimate Close-Kin Dispersal Kernels
-Version: 0.4.2
+Version: 0.4.3
 Authors@R: 
     person(given = "Moshe-Elijah",
            family = "Jasper",

NAMESPACE

@@ -1,7 +1,21 @@
 # Generated by roxygen2: do not edit by hand
 
+export("breedsigma<-")
 export("category<-")
+export("dsigma<-")
+export("filtertype<-")
+export("gravsigma<-")
+export("juvsigma<-")
+export("kerneltype<-")
 export("lifestage<-")
+export("lower<-")
+export("ovisigma<-")
+export("sampledims<-")
+export("samplenum<-")
+export("simdims<-")
+export("simtype<-")
+export("spacing<-")
+export("upper<-")
 export(KinPairSimulation_composite)
 export(KinPairSimulation_simple)
 export(axials)
@@ -13,17 +27,32 @@ export(axials_subtract)
 export(axpermute)
 export(axpermute_standard)
 export(axpermute_subtract)
+export(breedsigma)
 export(category)
 export(distances)
+export(dsigma)
+export(filtertype)
+export(gravsigma)
 export(is.KinPairData)
 export(is.KinPairSimulation)
+export(juvsigma)
+export(kerneltype)
 export(lifestage)
+export(lower)
+export(ovisigma)
 export(run_kindisperse)
 export(sample_kindist)
+export(sampledims)
+export(samplenum)
+export(simdims)
 export(simgraph_data)
 export(simgraph_graph)
+export(simtype)
 export(simulate_kindist_composite)
 export(simulate_kindist_simple)
+export(spacing)
+export(to_tibble)
+export(upper)
 exportClasses(KinPairData)
 exportClasses(KinPairSimulation)
 exportMethods("category<-")
@@ -36,18 +65,22 @@ exportMethods("upper<-")
 exportMethods(breedsigma)
 exportMethods(category)
 exportMethods(distances)
+exportMethods(dsigma)
+exportMethods(filtertype)
 exportMethods(gravsigma)
+exportMethods(initialize)
 exportMethods(juvsigma)
 exportMethods(kerneltype)
 exportMethods(lifestage)
 exportMethods(lower)
 exportMethods(ovisigma)
 exportMethods(sampledims)
 exportMethods(samplenum)
-exportMethods(sigma)
+exportMethods(show)
 exportMethods(simdims)
 exportMethods(simtype)
 exportMethods(spacing)
+exportMethods(to_tibble)
 exportMethods(upper)
 importClassesFrom(tibble,tbl_df)
 importFrom(dplyr,everything)
@@ -82,11 +115,13 @@ importFrom(grid,arrow)
 importFrom(grid,unit)
 importFrom(here,here)
 importFrom(magrittr,"%>%")
+importFrom(methods,initialize)
 importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,setValidity)
+importFrom(methods,show)
 importFrom(methods,validObject)
 importFrom(plotly,ggplotly)
 importFrom(plotly,plotlyOutput)

R/KinPairData.R

@@ -1,128 +1,160 @@
 methods::setOldClass(c("tbl_df", "tbl", "data.frame"))
 
-#' Title
+#' Formal class "KinPairData"
 #'
+#' @description The class \code{KinPairData} is a formal (S4) class for storing kinship and lifespan dispersal information concerning kin pairs.
 #' @slot category character.
 #' @slot lifestage character.
 #' @slot tab tbl_df.
-#'
 #' @return
 #' @export
 #'
-#' @examples
+#'
 KinPairData <- setClass("KinPairData",
                         slots = list(category = "character", lifestage = "character", tab = "tbl_df"))
 
-#' Title
+
+######### GENERICS and METHODS#############
+
+#' Extract KinPairData to tibble (generic)
 #'
-#' @param x
+#' @param x object of class \code{KinPairData}
+#'
+#' @return tibble (class \code{tbl_df})
+#' @export
+#'
+#'
+setGeneric("to_tibble", function(x) standardGeneric("to_tibble"))
+
+#'
+#'
+#' @param KinPairData
 #'
 #' @return
 #' @export
 #'
-#' @examples
+#' @describeIn KinPairData extract to tibble
+setMethod("to_tibble", "KinPairData", function(x) x@tab)
+
+#' Access or assign kin category (generic for KinPairData class)
+#'
+#' @param x object with relevant method
+#'
+#' @return \code{character}. Kinship category of object
+#' @export
+#'
 setGeneric("category", function(x) standardGeneric("category"))
-#' Title
 #'
-#' @param x
-#' @param value
+#' @rdname category
+#' @param x object with relevant method
+#' @param value new value to assign
 #'
-#' @return
+#' @return returns modified object
 #' @export
 #'
-#' @examples
+#'
 setGeneric("category<-", function(x, value) standardGeneric("category<-"))
-#' Title
+#' Access or assign lifestage (generic for KinPairData class)
 #'
-#' @param x
+#' @param x object with relevant method
 #'
 #' @return
 #' @export
 #'
-#' @examples
+#'
 setGeneric("lifestage", function(x) standardGeneric("lifestage"))
-#' Title
 #'
-#' @param x
-#' @param value
+#' @rdname lifestage
+#' @param x object with relevant method
+#' @param value new value to assign
 #'
 #' @return
 #' @export
 #'
-#' @examples
+#'
 setGeneric("lifestage<-", function(x, value) standardGeneric("lifestage<-"))
 
-#' Access distances (generic for KinPairData Class)
+#' Access distances (generic for KinPairData class)
 #'
 #' @param x Object of Class KinPairData
 #'
 #' @return Returns a numeric vector of kin separation distances
 #' @export
 #'
-#' @examples
+#'
 setGeneric("distances", function(x) standardGeneric("distances"))
 
 
-#' Title
+
+
 #'
-#' @param KinPairData
+#'
+#' @param KinPairData object of class \code{KinPairData}
 #'
 #' @return
 #' @export
 #'
-#' @examples
+#' @describeIn KinPairData access distances
 setMethod("distances", "KinPairData", function(x) x@tab$distance)
 
-#' Access or assign KinPairData kin category
-#' @name category
-#' @param KinPairData
+#'
+#'
+#' @param KinPairData object of class \code{KinPairData}
 #'
 #' @return
 #' @export
 #'
-#' @examples
+#' @describeIn KinPairData access kin category
 setMethod("category", "KinPairData", function(x) x@category)
 
 #'
-#' @rdname category
-#' @param KinPairData
+#'
+#' @param KinPairData object of class \code{KinPairData}
 #'
 #' @return
 #' @export
 #'
-#' @examples
+#' @describeIn KinPairData assign kin category
 setMethod("category<-", "KinPairData", function(x, value){
   x@category <- value
   validObject(x)
   x
 })
 
 
-#' Access or assign KinPairData lifestage
-#' @name lifestage
+#'
+#'
 #' @param KinPairData
 #'
 #' @return
 #' @export
 #'
-#' @examples
+#' @describeIn KinPairData access lifestage
 setMethod("lifestage", "KinPairData", function(x) x@lifestage)
 
 #'
 #'
-#' @rdname lifestage
+#'
 #' @param KinPairData
 #'
 #' @return
 #' @export
 #'
-#' @examples
+#' @describeIn KinPairData assign lifestage
 setMethod("lifestage<-", "KinPairData", function(x, value){
   x@lifestage <- value
   validObject(x)
   x
 })
 
+#'
+#'
+#' @param KinPairData
+#'
+#' @return
+#' @export
+#'
+#' @describeIn KinPairData standard print method
 setMethod(
   "show",
   "KinPairData",
@@ -139,6 +171,14 @@ setMethod(
 
 # Constructor method of KinPairData
 
+#' Title
+#'
+#' @param KinPairData
+#'
+#' @return
+#' @export
+#'
+#' @describeIn KinPairData initialize method
 setMethod("initialize", "KinPairData",
           function(.Object,
           data,
@@ -199,6 +239,7 @@ setMethod("initialize", "KinPairData",
 }
 )
 
+
 setValidity("KinPairData", function(object){
   if (! object@category %in% c("UN", "PO", "GG", "GGG", "FS", "AV", "GAV", "1C", "1C1", "2C", "HS", "HAV", "HGAV", "H1C", "H1C1", "H2C")) {
     "@category must be one of UN PO GG GGG FS AV GAV 1C 1C1 2C HS HAV HGAV H1C H1C1 H2C"
@@ -214,10 +255,10 @@ setValidity("KinPairData", function(object){
 #'
 #' @param x object to be checked
 #'
-#' @return Returns TRUE if of class KinPairData, FALSE if not.
+#' @return Returns TRUE if of class \code{KinPairData}, FALSE if not.
 #' @export
 #'
-#' @examples
+#'
 is.KinPairData <- function(x){
   "KinPairData" %in% is(x)
 }