improve as.code

Author: grlloyd

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: struct
 Type: Package
 Title: Statistics in R Using Class-based Templates
-Version: 1.7.0
+Version: 1.7.1
 Authors@R: c(
     person(
         c("Gavin","Rhys"),
@@ -49,7 +49,7 @@ Collate:
     'resampler_class.R'
     'struct.R'
     'struct_templates.R'
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Depends: R (>= 4.0)
 Suggests: 
  testthat,

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(.DollarNames,DatasetExperiment)
 S3method(.DollarNames,chart)
 S3method(.DollarNames,iterator)
 S3method(.DollarNames,metric)

NEWS

@@ -1,3 +1,7 @@
+Changes 1.7.1
++ fix as.code generic
++ improve as.code for all objects
+
 Changes in 1.5.3
 + fix variable_meta assignment
 

R/DatasetExperiment_class.R

@@ -233,3 +233,18 @@ setMethod(f = "export_xlsx",
   }
 )
 
+#' @export
+#' @rdname autocompletion
+#' @method .DollarNames DatasetExperiment
+.DollarNames.DatasetExperiment <- function(x, pattern = "") {
+    IN = c('data', 'sample_meta','variable_meta','name','description','type',
+        'libraries','citations','ontology')
+    return(IN)
+}
+
+#' @export 
+#' @rdname autocompletion
+setMethod('.DollarNames','DatasetExperiment',.DollarNames.DatasetExperiment)
+
+
+

R/chart_class.R

@@ -53,7 +53,7 @@ setMethod(f = "show",
     }
 )
 
-# autocompletion, return sample_meta column names
+# autocompletion
 #' @export
 #' @rdname autocompletion
 #' @method .DollarNames chart
@@ -63,4 +63,5 @@ setMethod(f = "show",
 
 #' @export 
 #' @rdname autocompletion
-setMethod('.DollarNames','chart',.DollarNames.chart)
+setMethod('.DollarNames','chart',.DollarNames.chart)
+

R/generics.R

@@ -611,14 +611,15 @@ setGeneric("as.DatasetExperiment",function(obj)standardGeneric("as.DatasetExperi
 #' @param start text prepended to the code. Default is "M = "
 #' @param mode "compact" will use the least amount of lines, "expanded" will
 #' put each object and input on a new line. "neat" will produce an output
-#' somewhere between "compact" and "extended".
+#' somewhere between "compact" and "expanded".
+#' @param quiet TRUE or FALSE to print code to console
 #' @return A string of code to reproduce the input object.
 #' @export
 #' @rdname as.code
 #' @examples 
 #' M = example_model(value_1 = 10)
 #' as.code(M)
-setGeneric('as.code',function(M,start='M = ',mode='compact')standrdGeneric("as.code"))
+setGeneric('as.code',function(M,start='M = ',mode='compact',quiet=FALSE)standardGeneric("as.code"))
 
 #' convert to data.frame
 #'

R/iterator_class.R

@@ -248,7 +248,7 @@ setMethod(f = 'show',
 #' @return a string of code to reproduce the iterator
 setMethod(f = 'as.code',
   signature = c('iterator'),
-  definition = function(M,start='M = ',mode='compact') {
+  definition = function(M,start='M = ',mode='compact',quiet=FALSE) {
     str=.as_code(M,start,mode)
     # get models
     m=models(M)
@@ -257,20 +257,24 @@ setMethod(f = 'as.code',
     if (is(m,'model_seq') & length(m) > 1) {
       if (mode=='expanded') {
         str=paste0(str,paste0(paste0(rep(' ',nchar(start)),collapse=''),'(\n'))
-        str=paste0(str,as.code(m,start=paste0(paste0(rep(' ',nchar(start)+2),collapse='')),mode))
+        str=paste0(str,as.code(m,start=paste0(paste0(rep(' ',nchar(start)+2),collapse='')),mode,quiet=TRUE))
       } else {
-        str=paste0(str,as.code(m,start=paste0(paste0(rep(' ',nchar(start)),collapse=''),'('),mode))
+        str=paste0(str,as.code(m,start=paste0(paste0(rep(' ',nchar(start)),collapse=''),'('),mode,quiet=TRUE))
       }
       if (mode != 'compact') {
         str=paste0(str,'\n',paste0(rep(' ',nchar(start)),collapse=''))
       }
 
       str=paste0(str,')')
     } else {
-      str=paste0(str,as.code(m,start=paste0(rep(' ',nchar(start)),collapse=''),mode))
+      str=paste0(str,as.code(m,start=paste0(rep(' ',nchar(start)),collapse=''),mode,quiet=TRUE))
     }
 
-    return(str)
+    if (!quiet){
+        cat(str)
+    }
+    
+    invisible(str)
   }
 )
 

R/model_class.R

@@ -232,90 +232,7 @@ setMethod(f = "show",
 )
 
 
-#' @rdname as.code
-#' @export
-#' @examples
-#' M = example_model()
-#' as.code(M)
-#' @return a string of code to reproduce the model
-setMethod(f = 'as.code',
-    signature = c('model'),
-    definition = function(M,start = 'M = ',mode = 'compact') {
-        .as_code(M,start,mode)
-    }
-)
-
-
 
-.as_code = function(M,start='M = ',mode = 'compact') {
-    
-    if (!(mode %in% c('compact','neat','expanded','full'))) {
-        stop(paste0('unknown option "', mode , '" for as.code()'))
-    }
-    str=start
-    # model object name
-    str=paste0(str,class(M)[1],'(')
-    
-    # parameters
-    P = param_ids(M)
-    
-    # add seq_in if not equal to data
-    if (is(M,'model')) {
-        if (M@seq_in != 'data' | mode=='full') {
-        P=c(P,'seq_in')
-        }
-    }
-    # add predicted if its not the default
-    if (is(M,'model')) {
-        N=new_struct(class(M)[1])
-        if (length(predicted_name(N))==0) {
-            N@predicted='cake'
-        }
-            
-        if  (predicted_name(N) != predicted_name(M) | mode=='full') {
-            P=c(P,'predicted')
-        }
-    }
-    
-    if (mode != "compact") {
-        str=paste0(str,'\n')
-        indent=nchar(start)+2
-    } else {
-        indent=(nchar(start)+1)+nchar(class(M)[1])
-    }
-    
-    for (p in seq_len(length(P))) {
-        if (p>1 | mode!="compact") {
-            str=paste0(str,paste0(rep(' ',indent),collapse=''))
-        } 
-        
-        if (P[p]=='seq_in') {
-            str=paste0(str,P[p], ' = "', seq_in(M), '"')
-        } else if (P[p]=='predicted') {
-            str=paste0(str,P[p], ' = "', predicted_name(M), '"')
-        } else if (is(param_value(M,P[p]),'character')) {
-            str=paste0(str,P[p], ' = "', as.character(param_value(M,P[p])), '"')
-        } else {
-            str=paste0(str,P[p], ' = ', as.character(param_value(M,P[p])))
-        }
-        
-        
-        if (p==length(P)) {
-            if (mode=='expanded') {
-                str=paste0(str,'\n',paste0(rep(' ',indent-2),collapse=''))
-            }
-            
-            
-            str=paste0(str,')')
-            
-            
-        } else {
-            str=paste0(str,',\n')
-        }
-    }
-    
-    return(str)
-}
 
 # autocompletion, return sample_meta column names
 #' @export

R/model_list_class.R

@@ -329,18 +329,23 @@ setMethod(f = "model_apply",
 #' @return a string of code to reproduce the model sequence
 setMethod(f = 'as.code',
     signature = c('model_seq'),
-    definition = function(M,start='M = ',mode='compact') {
+    definition = function(M,start='M = ',mode='compact',quiet=FALSE) {
         str=''
         for (i in seq_len(length(M))) {
             if (i==1) {
-                str=paste0(str,as.code(M[i],start=start,mode=mode))
+                str=paste0(str,as.code(M[i],start=start,mode=mode,quiet=TRUE))
             } else {
-                str=paste0(str,as.code(M[i],start=paste0(rep(' ',nchar(start)),collapse=''),mode))
+                str=paste0(str,as.code(M[i],start=paste0(rep(' ',nchar(start)),collapse=''),mode,quiet=TRUE))
             }
             if (i<length(M)) {
                 str=paste0(str,' +\n')
             }
         }
-        return(str)
+        
+        if (!quiet) {
+            cat(str)
+        }
+        
+        invisible(str)
     }
 )