update documentation

+ improve get_description + export get_description + update as.code to handle case when iterator has default model object + rebuild documentation
computational-metabolomics · Jan 30, 2024 · aa5922c · aa5922c
1 parent 9a6d86a
commit aa5922c
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Showing 35 changed files with 323 additions and 139 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: struct
 Type: Package
 Title: Statistics in R Using Class-based Templates
-Version: 1.15.2
+Version: 1.15.3
 Authors@R: c(
     person(
         c("Gavin","Rhys"),
@@ -49,7 +49,8 @@ Collate:
     'resampler_class.R'
     'struct.R'
     'struct_templates.R'
-RoxygenNote: 7.1.2
+    'zzz.R'
+RoxygenNote: 7.2.3
 Depends: R (>= 4.0)
 Suggests: 
  testthat,

diff --git a/NAMESPACE b/NAMESPACE
@@ -14,6 +14,7 @@ export("output_value<-")
 export("param_list<-")
 export("param_obj<-")
 export("param_value<-")
+export(.struct_class)
 export(DatasetExperiment)
 export(as.DatasetExperiment)
 export(as.SummarizedExperiment)
@@ -31,6 +32,7 @@ export(enum_stato)
 export(example_chart)
 export(example_iterator)
 export(example_model)
+export(get_description)
 export(iris_DatasetExperiment)
 export(is_output)
 export(is_param)

diff --git a/R/generics.R b/R/generics.R
@@ -230,8 +230,7 @@ setGeneric("output_list<-",function(obj,value)standardGeneric("output_list<-"))
 #'
 #' Returns a list of valid charts for a struct object
 #'
-#' The chart_names method searches chart objects that specify the input object
-#' type as an input.
+#' The chart_names method searches for chart objects associated with the unput object.
 #'
 #' @param obj An object derived from the struct_class object
 #' @param ret A string indicating whether a list of objects ('obj') or a list of chart

diff --git a/R/iterator_class.R b/R/iterator_class.R
@@ -229,7 +229,7 @@ setMethod(f = 'show',
     signature = c('iterator'),
     definition = function(object) {
         callNextMethod()
-        
+
         if (is(models(object),'model_seq')) {
             cat('models:        ','a model_seq with ', length(models(object)),' steps\n',sep='')
         } else {
@@ -251,9 +251,11 @@ setMethod(f = 'as.code',
   definition = function(M,start='M = ',mode='compact',quiet=FALSE) {
     str=.as_code(M,start,mode)
     # get models
-    m=models(M)
-    # if iterator then multiply
-    str=paste0(str,' * \n')
+    m = models(M)
+    # if iterator then multiply, if not default model
+    if (class(m)[1]!='model') {
+        str=paste0(str,' * \n')
+    }
     if (is(m,'model_seq') & length(m) > 1) {
       if (mode=='expanded') {
         str=paste0(str,paste0(paste0(rep(' ',nchar(start)),collapse=''),'(\n'))
@@ -266,14 +268,14 @@ setMethod(f = 'as.code',
       }
 
       str=paste0(str,')')
-    } else {
+    } else if (class(m)[1]!='model') {
       str=paste0(str,as.code(m,start=paste0(rep(' ',nchar(start)),collapse=''),mode,quiet=TRUE))
     }
-    
+
     if (!quiet){
         cat(str)
     }
-    
+
     invisible(str)
   }
 )
@@ -288,7 +290,7 @@ setMethod(f = 'as.code',
   .DollarNames.struct_class(x,pattern)
 }
 
-#' @export 
+#' @export
 #' @rdname autocompletion
 setMethod('.DollarNames','iterator',.DollarNames.iterator)
 
diff --git a/R/output_class.R b/R/output_class.R
@@ -1,6 +1,6 @@
 #' @include generics.R struct_class.R
 #'
-#' @describeIn output_obj
+#' @rdname output_obj
 #' @export
 setMethod(f = "output_obj",
     signature = c("struct_class","character"),
@@ -10,7 +10,7 @@ setMethod(f = "output_obj",
     }
 )
 
-#' @describeIn output_obj
+#' @rdname output_obj
 #' @export
 #' @return the modified object
 setMethod(f = "output_obj<-",
@@ -24,7 +24,7 @@ setMethod(f = "output_obj<-",
     }
 )
 
-#' @describeIn is_output
+#' @rdname is_output
 #' @export
 setMethod(f = "is_output",
     signature = c("struct_class"),
@@ -38,7 +38,7 @@ setMethod(f = "is_output",
     }
 )
 
-#' @describeIn output_ids
+#' @rdname output_ids
 #' @export
 setMethod(f = "output_ids",
     signature = c("struct_class"),
@@ -62,7 +62,7 @@ setMethod(f = "output_ids",
     }
 )
 
-#' @describeIn output_name
+#' @rdname output_name
 #' @export
 setMethod(f = "output_name",
     signature = c("struct_class",'character'),
@@ -79,7 +79,7 @@ setMethod(f = "output_name",
     }
 )
 
-#' @describeIn output_list
+#' @rdname output_list
 #' @export
 setMethod(f = 'output_list',
     signature = c('struct_class'),
@@ -93,7 +93,7 @@ setMethod(f = 'output_list',
     }
 )
 
-#' @describeIn output_list
+#' @rdname output_list
 #' @export
 setMethod(f = 'output_list<-',
     signature = c('struct_class','list'),
@@ -106,7 +106,7 @@ setMethod(f = 'output_list<-',
     }
 )
 
-#' @describeIn output_value
+#' @rdname output_value
 #' @export
 setMethod(f = "output_value",
     signature = c("struct_class","character"),
@@ -125,7 +125,7 @@ setMethod(f = "output_value",
 )
 
 
-#' @describeIn output_value
+#' @rdname output_value
 #' @export
 setMethod(f = "output_value<-",
     signature = c("struct_class","character"),

diff --git a/R/parameter_class.R b/R/parameter_class.R
@@ -25,7 +25,7 @@ setMethod(f = "param_obj",
 
 
 #' @export
-#' @describeIn is_param
+#' @rdname is_param
 setMethod(f = "is_param",
     signature = c("struct_class"),
     definition = function(obj,name) {
@@ -39,7 +39,7 @@ setMethod(f = "is_param",
 )
 
 #' @export
-#' @describeIn param_ids
+#' @rdname param_ids
 setMethod(f = "param_ids",
     signature = c("struct_class"),
     definition = function(obj) {
@@ -65,7 +65,7 @@ setMethod(f = "param_ids",
 
 
 #' @export
-#' @describeIn param_name
+#' @rdname param_name
 setMethod(f = "param_name",
     signature = c("struct_class",'character'),
     definition = function(obj,name) {
@@ -82,7 +82,7 @@ setMethod(f = "param_name",
 )
 
 #' @export
-#' @describeIn param_list
+#' @rdname param_list
 setMethod(f = 'param_list',
     signature = c('struct_class'),
     definition = function(obj) {
@@ -96,7 +96,7 @@ setMethod(f = 'param_list',
 )
 
 #' @export
-#' @describeIn param_list
+#' @rdname param_list
 setMethod(f = 'param_list<-',
     signature = c('struct_class','list'),
     definition = function(obj,value) {
@@ -109,7 +109,7 @@ setMethod(f = 'param_list<-',
 )
 
 #' @export
-#' @describeIn param_value
+#' @rdname param_value
 setMethod(f = "param_value",
     signature = c("struct_class","character"),
     definition = function(obj,name) {
@@ -128,7 +128,7 @@ setMethod(f = "param_value",
 )
 
 #' @export
-#' @describeIn param_value
+#' @rdname param_value
 setMethod(f = "param_value<-",
     signature = c("struct_class","character","ANY"),
     definition = function(obj,name,value) {

diff --git a/R/struct_class.R b/R/struct_class.R
@@ -226,8 +226,8 @@ setMethod(f = "$<-",
     }
 )
 
-#' @describeIn chart_names
 #' @export
+#' @rdname chart_names
 setMethod(f = "chart_names",
     signature = c("struct_class"),
     definition = function(obj,ret = 'char') {
@@ -647,7 +647,7 @@ setMethod('.DollarNames','struct_class',.DollarNames.struct_class)
 setMethod(f = 'as.code',
     signature = c('struct_class'),
     definition = function(M,start = 'M = ',mode = 'compact',quiet=FALSE) {
-        str=.as_code(M,start,mode)
+        str=struct:::.as_code(M,start,mode)
 
         if (!quiet) {
             cat(str)
@@ -664,9 +664,9 @@ setMethod(f = 'as.code',
     if (!(mode %in% c('compact','neat','expanded','full'))) {
         stop(paste0('unknown option "', mode , '" for as.code()'))
     }
-    str=start
+    str = start
     # model object name
-    str=paste0(str,class(M)[1],'(')
+    str = paste0(str,class(M)[1],'(')
 
     # parameters
     P = param_ids(M)
@@ -679,17 +679,24 @@ setMethod(f = 'as.code',
     }
     # add predicted if its not the default
     if (is(M,'model')) {
-        N=new_struct(class(M)[1])
+        N = new_struct(class(M)[1])
+
         if (length(predicted_name(N))==0) {
-            N@predicted='cake'
+            N@predicted='not specified'
+        }
+        if (length(predicted_name(M))==0) {
+            M@predicted='not specified'
         }
 
         if  (predicted_name(N) != predicted_name(M) | mode=='full') {
             P=c(P,'predicted')
         }
     }
 
-    if (mode != "compact") {
+    if ((mode=='neat' | mode=='expanded') & length(P)==0) {
+        str=paste0(str)
+        indent=nchar(start)+2
+    } else if (mode != "compact") {
         str=paste0(str,'\n')
         indent=nchar(start)+2
     } else {
@@ -753,5 +760,9 @@ setMethod(f = 'as.code',
         }
     }
 
+    if (length(P)==0) {
+        str=paste0(str,')')
+    }
+
    return(str)
 }