doc: mergelcMethod-related generic docs with other signatures (#147)

R/generics.R

@@ -1,21 +1,3 @@
-#' @name latrend-generics
-#' @title Method- and model-specific generics defined by the latrend package
-#' @description List of S4 generic methods which have no general use other than supporting
-#' functions with signatures of `lcMethod` or `lcModel`.
-#' @param object The object.
-#' @param method The method.
-#' @param data `data.frame`.
-#' @param newdata `data.frame` of newdata.
-#' @param name Metric name.
-#' @param envir `environment`.
-#' @param what Parameter.
-#' @param cluster Cluster name.
-#' @param verbose [R.utils::Verbose].
-#' @param ... Arguments.
-#' @keywords internal
-NULL
-
-
 # nClusters ####
 #' @export
 #' @name nClusters
@@ -127,8 +109,9 @@ setGeneric('clusterTrajectories', function(object, ...) {
 
 # compose ####
 #' @export
-#' @name latrend-generics
-setGeneric('compose', def = function(method, envir, ...) {
+#' @name compose
+#' @param ... Not used.
+setGeneric('compose', function(method, envir, ...) {
   newmethod <- standardGeneric('compose')
 
   assert_that(
@@ -246,7 +229,9 @@ setGeneric('estimationTime', function(object, unit = 'secs', ...) {
 
 # fit ####
 #' @export
-#' @name latrend-generics
+#' @name fit
+#' @param ... Not used.
+#' @return The fitted object, inheriting from `lcModel`.
 setGeneric('fit', function(method, data, envir, verbose, ...) {
   dateStart = Sys.time()
   start = .tic()
@@ -544,7 +529,8 @@ setGeneric('plotTrajectories', function(object, ...) standardGeneric('plotTrajec
 
 # postFit ####
 #' @export
-#' @name latrend-generics
+#' @name postFit
+#' @param ... Not used.
 setGeneric('postFit', function(method, data, model, envir, verbose, ...) {
   model <- standardGeneric('postFit')
 
@@ -761,7 +747,9 @@ setGeneric('predictPostprob', function(object, newdata = NULL, ...) {
 
 # prepareData ####
 #' @export
-#' @name latrend-generics
+#' @name prepareData
+#' @param ... Not used.
+#' @return An `environment`.
 setGeneric('prepareData', function(method, data, verbose, ...) {
   envir <- standardGeneric('prepareData')
   assert_that(
@@ -778,8 +766,8 @@ setGeneric('prepareData', function(method, data, verbose, ...) {
 
 # preFit ####
 #' @export
-#' @name latrend-generics
-#' @aliases preFit-method
+#' @name preFit
+#' @param ... Not used.
 setGeneric('preFit', function(method, data, envir, verbose, ...) {
   modelEnv <- standardGeneric('preFit')
   assert_that(
@@ -945,7 +933,10 @@ setGeneric('trajectoryAssignments', function(object, ...) {
 
 # validate ####
 #' @export
-#' @name latrend-generics
+#' @name validate
+#' @param ... Not used.
+#' @return Either `TRUE` if all validation checks passed,
+#' or a `scalar character` containing a description of the failed validation checks.
 setGeneric('validate', function(method, data, envir, ...) {
   validationResult <- standardGeneric('validate')
 

R/method.R

@@ -487,7 +487,7 @@ as.data.frame.lcMethod = function(x, ..., eval = TRUE, nullValue = NA, envir = N
 
 #. compose ####
 #' @export
-#' @name compose
+#' @rdname compose
 #' @aliases compose,lcMethod-method
 #' @title `lcMethod` estimation step: compose an lcMethod object
 #' @description Note: this function should not be called directly, as it is part of the `lcMethod` [estimation procedure][lcMethod-estimation].
@@ -519,7 +519,7 @@ setMethod('compose', 'lcMethod', function(method, envir = NULL) {
 
 # . fit ####
 #' @export
-#' @name fit
+#' @rdname fit
 #' @aliases fit,lcMethod-method
 #' @title `lcMethod` estimation step: logic for fitting the method to the processed data
 #' @description Note: this function should not be called directly, as it is part of the `lcMethod` [estimation procedure][lcMethod-estimation].
@@ -528,7 +528,6 @@ setMethod('compose', 'lcMethod', function(method, envir = NULL) {
 #' The `fit()` function of the `lcMethod` object estimates the model with the evaluated method specification, processed training data, and prepared environment.
 #' @inheritParams preFit
 #' @param envir The `environment` containing variables generated by [prepareData()] and [preFit()].
-#' @return The fitted object inheriting from `lcModel`.
 #' @section Implementation:
 #' This method should be implemented for all `lcMethod` subclasses.
 #'
@@ -813,7 +812,7 @@ setMethod('names', 'lcMethod', function(x) {
 
 
 # . preFit ####
-#' @name preFit
+#' @rdname preFit
 #' @aliases preFit,lcMethod-method
 #' @title `lcMethod` estimation step: method preparation logic
 #' @description Note: this function should not be called directly, as it is part of the `lcMethod` [estimation procedure][lcMethod-estimation].
@@ -879,7 +878,7 @@ setMethod('prepareData', 'lcMethod', function(method, data, verbose) {
 
 
 # . postFit ####
-#' @name postFit
+#' @rdname postFit
 #' @aliases postFit,lcMethod-method
 #' @title `lcMethod` estimation step: logic for post-processing the fitted lcModel
 #' @description Note: this function should not be called directly, as it is part of the `lcMethod` [estimation procedure][lcMethod-estimation].
@@ -1171,7 +1170,7 @@ setMethod('timeVariable', 'lcMethod', function(object, ...) object$time)
 
 #. validate ####
 #' @export
-#' @name validate
+#' @rdname validate
 #' @aliases validate,lcMethod-method
 #' @title `lcMethod` estimation step: method argument validation logic
 #' @description Note: this function should not be called directly, as it is part of the `lcMethod` [estimation procedure][lcMethod-estimation].
@@ -1191,8 +1190,6 @@ setMethod('timeVariable', 'lcMethod', function(object, ...) object$time)
 #' @param method An object inheriting from `lcMethod` with all its arguments having been evaluated and finalized.
 #' @param data A `data.frame` representing the transformed training data.
 #' @param ... Not used.
-#' @return Either `TRUE` if all validation checks passed,
-#' or a `character` containing a description of the failed validation checks.
 #' @inheritSection lcMethod-estimation Estimation procedure
 #' @section Implementation:
 #' An example implementation checking for the existence of specific arguments and type:

R/models.R

@@ -238,19 +238,20 @@ setMethod('externalMetric', c('lcModels', 'missing'),
 setMethod('externalMetric', c('lcModels', 'character'),
   function(object, object2 = 'adjustedRand') {
     .externalMetricDist.lcModels(object, name = object2)
-})
+  }
+)
 
 
 #' @export
-#' @name externalMetric
+#' @rdname externalMetric
 #' @aliases externalMetric,lcModels,lcModels-method
 #' @return For `externalMetric(lcModels, lcModel)`: A named `numeric` vector or `data.frame`
 #' containing the computed model metrics.
 setMethod('externalMetric', c('lcModels', 'lcModel'), .externalMetric.lcModels)
 
 
 #' @export
-#' @name externalMetric
+#' @rdname externalMetric
 #' @aliases externalMetric,list,lcModel-method
 #' @inheritParams metric
 #' @return For `externalMetric(list, lcModel)`: A named `numeric` vector or `data.frame`
@@ -259,7 +260,8 @@ setMethod('externalMetric', c('list', 'lcModel'),
   function(object, object2, name, drop = TRUE) {
     models = as.lcModels(object)
     .externalMetric.lcModels(models, object2, name, drop = drop)
-})
+  }
+)
 
 
 .metric.lcModels = function(object, name, drop = TRUE) {
@@ -300,11 +302,13 @@ setMethod('metric', 'list', function(object, name, drop = TRUE) {
   .metric.lcModels(as.lcModels(object), name, drop = drop)
 })
 
+
 #' @export
 #' @rdname metric
 #' @return For `metric(lcModels)`: A `data.frame` with a metric per column.
 setMethod('metric', 'lcModels', .metric.lcModels)
 
+
 #' @export
 #' @title Select the lcModel with the lowest metric value
 #' @inheritSection lcModels-class Functionality
@@ -341,6 +345,7 @@ min.lcModels = function(x, name, ...) {
   }
 }
 
+
 #' @export
 #' @title Select the lcModel with the highest metric value
 #' @inheritSection lcModels-class Functionality
@@ -524,6 +529,7 @@ plotMetric = function(
   p
 }
 
+
 #' @export
 #' @title Subsetting a lcModels list based on method arguments
 #' @inheritSection lcModels-class Functionality
@@ -568,6 +574,7 @@ subset.lcModels = function(x, subset, drop = FALSE, ...) {
   }
 }
 
+
 #' @export
 #' @title Print lcModels list concisely
 #' @inheritSection lcModels-class Functionality