docs: fix S3 method exports

philips-software · Jan 12, 2024 · 2db0782 · 2db0782
1 parent c802e3f
commit 2db0782
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Showing 11 changed files with 144 additions and 84 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,33 +1,26 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method("[",lcModels)
-S3method(as.data.frame,lcMethod)
+S3method(R.utils::evaluate,lcMethod)
 S3method(as.data.frame,lcMethods)
 S3method(as.data.frame,lcModels)
-S3method(as.list,lcMethod)
 S3method(as.list,lcModels)
-S3method(coef,lcModel)
+S3method(base::as.character,lcMetaMethod)
+S3method(base::as.character,lcMethod)
+S3method(base::as.data.frame,lcMethod)
+S3method(base::as.list,lcMethod)
+S3method(base::merge,formula)
+S3method(base::print,lcMethod)
 S3method(coef,lcModelCrimCV)
 S3method(coef,lcModelFlexmix)
 S3method(coef,lcModelFunFEM)
 S3method(coef,lcModelLMKM)
-S3method(coef,lcModelMixAK_GLMM)
 S3method(coef,lcModelMixTVEM)
 S3method(coef,lcModelMixtoolsGMM)
-S3method(deviance,lcModel)
-S3method(deviance,lcModelMixAK_GLMM)
-S3method(df.residual,lcModel)
-S3method(evaluate,lcMethod)
 S3method(fitted,lcApproxModel)
-S3method(fitted,lcModel)
 S3method(fitted,lcModelFlexmix)
 S3method(fitted,lcModelFunFEM)
 S3method(fitted,lcModelLcmmGMM)
-S3method(formula,lcMethod)
-S3method(formula,lcModel)
-S3method(getCall,lcMetaMethod)
-S3method(getCall,lcMethod)
-S3method(getCall,lcModel)
 S3method(logLik,lcModel)
 S3method(logLik,lcModelCrimCV)
 S3method(logLik,lcModelFlexmix)
@@ -41,25 +34,39 @@ S3method(logLik,lcModelMixtoolsRM)
 S3method(max,lcModels)
 S3method(min,lcModels)
 S3method(model.data,lcModel)
-S3method(model.frame,lcModel)
 S3method(model.matrix,lcModelLcmmGMM)
-S3method(nobs,lcModel)
 S3method(nobs,lcModelLcmmGMM)
-S3method(predict,lcModel)
 S3method(predict,lcModelMixTVEM)
-S3method(print,lcMethod)
 S3method(print,lcModels)
-S3method(residuals,lcModel)
-S3method(sigma,lcModel)
 S3method(sigma,lcModelLcmmGMM)
 S3method(sigma,lcModelMixTVEM)
 S3method(sigma,lcModelMixtoolsGMM)
+S3method(stats::coef,GLMM_MCMC)
+S3method(stats::coef,lcModel)
+S3method(stats::coef,lcModelMixAK_GLMM)
+S3method(stats::coef,lcModelMixAK_GLMMlist)
+S3method(stats::deviance,GLMM_MCMC)
+S3method(stats::deviance,lcModel)
+S3method(stats::deviance,lcModelMixAK_GLMM)
+S3method(stats::deviance,lcModelMixAK_GLMMlist)
+S3method(stats::df.residual,lcModel)
+S3method(stats::fitted,lcModel)
+S3method(stats::formula,lcMethod)
+S3method(stats::formula,lcModel)
+S3method(stats::getCall,lcMetaMethod)
+S3method(stats::getCall,lcMethod)
+S3method(stats::getCall,lcModel)
+S3method(stats::model.frame,lcModel)
+S3method(stats::nobs,lcModel)
+S3method(stats::predict,lcModel)
+S3method(stats::residuals,lcModel)
+S3method(stats::sigma,lcModel)
+S3method(stats::time,lcModel)
+S3method(stats::update,lcMetaMethod)
+S3method(stats::update,lcModel)
 S3method(subset,lcModels)
 S3method(summary,lcModel)
-S3method(time,lcModel)
-S3method(update,lcMetaMethod)
 S3method(update,lcMethod)
-S3method(update,lcModel)
 export("clusterNames<-")
 export(APPA)
 export(OCC)
@@ -262,13 +269,6 @@ importFrom(stats,getCall)
 importFrom(stats,logLik)
 importFrom(stats,mahalanobis)
 importFrom(stats,model.frame)
-importFrom(stats,model.matrix)
-importFrom(stats,nobs)
-importFrom(stats,predict)
-importFrom(stats,residuals)
-importFrom(stats,sigma)
-importFrom(stats,time)
-importFrom(stats,update)
 importFrom(stats,weighted.mean)
 importFrom(utils,capture.output)
 importFrom(utils,combn)

diff --git a/R/formula.R b/R/formula.R
@@ -2,6 +2,7 @@ is.formula = function(x) {
   inherits(x, 'formula')
 }
 
+
 hasResponse = function(f) {
   if (is.formula(f)) {
     tt = terms(f)
@@ -11,6 +12,7 @@ hasResponse = function(f) {
   attr(tt, 'response') != 0
 }
 
+
 hasIntercept = function(f) {
   if (is.formula(f)) {
     tt = terms(f)
@@ -20,10 +22,12 @@ hasIntercept = function(f) {
   attr(tt, 'intercept') != 0
 }
 
+
 hasSingleResponse = function(f) {
   hasResponse(f) && length(getResponse(f)) == 1
 }
 
+
 getResponse = function(f) {
   if (hasResponse(f)) {
     update(f, . ~ 1) %>% all.vars()
@@ -33,22 +37,26 @@ getResponse = function(f) {
   }
 }
 
+
 getREterms = function(f) {
   .loadOptionalPackage('lme4')
   terms = lme4::findbars(f)
 }
 
+
 REtermAsFormula = function(term) {
   assert_that(is.call(term))
   assert_that(!is.formula(term))
   as.character(term)[2] %>% reformulate
 }
 
+
 getREGroupName = function(term) {
   assert_that(is.call(term))
   as.character(term)[3]
 }
 
+
 getCovariates = function(f) {
   if(is.null(f)) {
     character()
@@ -57,14 +65,17 @@ getCovariates = function(f) {
   }
 }
 
+
 hasCovariates = function(f) {
   length(getCovariates(f)) > 0
 }
 
+
 hasRE = function(f) {
   length(getREterms(f)) > 0
 }
 
+
 addInteraction = function(f, var) {
   assert_that(is.formula(f))
   assert_that(is.character(var))
@@ -91,6 +102,8 @@ addInteraction = function(f, var) {
   }
 }
 
+
+#' @exportS3Method base::merge
 merge.formula = function(x, y, ...) {
   assert_that(is.formula(x))
   assert_that(is.formula(y))
@@ -115,6 +128,7 @@ merge.formula = function(x, y, ...) {
   }
 }
 
+
 dropResponse = function(f) {
   if (hasResponse(f)) {
     update(f, NULL ~ .)
@@ -123,6 +137,7 @@ dropResponse = function(f) {
   }
 }
 
+
 dropIntercept = function(f) {
   if (hasIntercept(f)) {
     update(f, ~ .+-1)
@@ -131,6 +146,7 @@ dropIntercept = function(f) {
   }
 }
 
+
 #' @noRd
 #' @importFrom stats drop.terms
 #' @title Drop random-effects component from a formula
@@ -184,6 +200,7 @@ getSpecialTerms = function(f, special) {
     vapply(deparse, FUN.VALUE = '')
 }
 
+
 #' @noRd
 #' @title Get special terms as formula
 #' @details An intercept is added unless the formula contains a special removing it, e.g. time(0)
@@ -203,6 +220,7 @@ getSpecialFormula = function(f, special) {
   }
 }
 
+
 dropSpecial = function(f, special) {
   assert_that(is.scalar(special))
   tt = terms(f, specials = special)

diff --git a/R/meta-method.R b/R/meta-method.R
@@ -19,6 +19,8 @@ setClass(
   slots = c(method = 'lcMethod')
 )
 
+
+#' @exportS3Method base::as.character
 as.character.lcMetaMethod = function(x, ...) {
   c(
     sprintf('%s encapsulating:', class(x)[1]),
@@ -28,7 +30,8 @@ as.character.lcMetaMethod = function(x, ...) {
   )
 }
 
-#' @export
+
+#' @exportS3Method stats::getCall
 getCall.lcMetaMethod = function(x, ...) {
   do.call(
     call,
@@ -42,6 +45,7 @@ getCall.lcMetaMethod = function(x, ...) {
   )
 }
 
+
 #' @export
 #' @rdname interface-metaMethods
 setMethod('compose', 'lcMetaMethod', function(method, envir = NULL) {
@@ -50,6 +54,7 @@ setMethod('compose', 'lcMetaMethod', function(method, envir = NULL) {
   newMethod
 })
 
+
 #' @export
 #' @rdname interface-metaMethods
 setMethod('getLcMethod', 'lcMetaMethod', function(object, ...) {
@@ -60,57 +65,76 @@ setMethod('getLcMethod', 'lcMetaMethod', function(object, ...) {
   object@method
 })
 
+
 #' @export
 #' @rdname interface-metaMethods
-setMethod('getName', 'lcMetaMethod', function(object, ...) getName(getLcMethod(object), ...))
+setMethod('getName', 'lcMetaMethod',
+  function(object, ...) getName(getLcMethod(object), ...)
+)
+
 
 #' @export
 #' @rdname interface-metaMethods
-setMethod('getShortName', 'lcMetaMethod', function(object, ...) getShortName(getLcMethod(object), ...))
+setMethod('getShortName', 'lcMetaMethod',
+  function(object, ...) getShortName(getLcMethod(object), ...)
+)
+
 
 #' @export
 #' @rdname interface-metaMethods
 setMethod('idVariable', 'lcMetaMethod', function(object, ...) idVariable(getLcMethod(object), ...))
 
+
 #' @export
 #' @rdname interface-metaMethods
 setMethod('preFit', 'lcMetaMethod', function(method, data, envir, verbose) {
   preFit(getLcMethod(method), data = data, envir = envir, verbose = verbose)
 })
 
+
 #' @export
 #' @rdname interface-metaMethods
 setMethod('prepareData', 'lcMetaMethod', function(method, data, verbose) {
   prepareData(getLcMethod(method), data = data, verbose = verbose)
 })
 
+
 #' @export
 #' @rdname interface-metaMethods
 setMethod('fit', 'lcMetaMethod', function(method, data, envir, verbose) {
   fit(getLcMethod(method), data = data, envir = envir, verbose = verbose)
 })
 
+
 #' @export
 #' @rdname interface-metaMethods
 setMethod('postFit', 'lcMetaMethod', function(method, data, model, envir, verbose) {
   postFit(getLcMethod(method), data = data, model = model, envir = envir, verbose = verbose)
 })
 
+
 #' @export
 #' @rdname interface-metaMethods
-setMethod('responseVariable', 'lcMetaMethod', function(object, ...) responseVariable(getLcMethod(object), ...))
+setMethod('responseVariable', 'lcMetaMethod',
+  function(object, ...) responseVariable(getLcMethod(object), ...)
+)
+
 
 #' @export
 #' @rdname interface-metaMethods
-setMethod('timeVariable', 'lcMetaMethod', function(object, ...) timeVariable(getLcMethod(object), ...))
+setMethod('timeVariable', 'lcMetaMethod',
+  function(object, ...) timeVariable(getLcMethod(object), ...)
+)
+
 
 #' @export
 #' @rdname interface-metaMethods
 setMethod('validate', 'lcMetaMethod', function(method, data, envir = NULL, ...) {
   validate(getLcMethod(method), data = data, envir = envir, ...)
 })
 
-#' @export
+
+#' @exportS3Method stats::update
 #' @rdname interface-metaMethods
 #' @inheritParams update.lcMethod
 update.lcMetaMethod = function(object, ...) {