diff --git a/DESCRIPTION b/DESCRIPTION
index 8374719..50fb07e 100644
--- 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
index c164317..3648a37 100644
--- 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
index c975cc7..bcdf649 100644
--- 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
index b78c59a..4468e77 100644
--- 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
index 88df407..70ad5b5 100644
--- 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
index 38a4c8a..56bb5eb 100644
--- 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
index 15610de..d83fd54 100644
--- 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)
@@ -679,9 +679,13 @@ 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') {
@@ -689,7 +693,10 @@ setMethod(f = 'as.code',
         }
     }
 
-    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)
 }
diff --git a/R/zzz.R b/R/zzz.R
new file mode 100644
index 0000000..e7f4120
--- /dev/null
+++ b/R/zzz.R
@@ -0,0 +1,204 @@
+#' Get struct object help description
+#'
+#' This
+#' function is to help developers including struct objects in their own R
+#' packages, and isnt intended for general use.
+#' Use with roxygen 2 `@eval` tags this function generates a detailed
+#' description of a struct object generated by extracting names,
+#' descriptions etc from slots in a suitable format.
+#'
+#' @param id (character) the name of a struct object to generate documentation for
+#' @return a character string of roxygen formatted documentation for the object
+#' @examples
+#' get_description('example_model')
+#'
+#' @export
+get_description=function(id) {
+
+    # object template
+    M=new_struct(id)
+
+    # title
+    str=paste0('@title ', M$name)
+
+    # get description
+    str=c(str,paste0('@description ',M$description))
+
+    # add inheritance
+    i=.class2(M)
+    w=which(i=='struct_class')
+    str = c(str,
+            '@section ','Inheritance: ',
+            paste0('A `', class(M),
+                   '` object inherits the following `struct` classes: \\cr\\cr'),
+            paste0('`',i[1:w],'()`',collapse = ' \U2B62 '))
+
+
+    # citations
+    cits=citations(M)
+    cits[length(cits)]=NULL
+    for (k in seq_along(cits)) {
+        cit=format(cits[[k]],style='text')
+        str=c(str,paste0('@references ',cit))
+    }
+
+    # get libraries
+    if (length(M$libraries)>0) {
+        str2=paste0('@details ',
+                    'This object makes use of functionality from the following packages:',
+                    '\\itemize{ '
+        )
+        for (k in seq_along(M$libraries)) {
+            str2=paste0(str2,' \\item{\\code{',M$libraries[k],'}}')
+        }
+        str2=paste0(str2,'}')
+        str=c(str,str2)
+    }
+
+    # parameters
+    P=formals(id)
+
+    # for each parameter generate some text
+    D=list()
+    for (k in seq_along(P)) {
+
+        # skip if ellipsis
+        if (names(P)[k]=='...') {
+            D[[k]]= paste0('@param ',names(P)[k],
+                           ' Additional slots and values passed to \\code{struct_class}.')
+            next
+        }
+        #g=param_obj(M,names(P)[k])
+
+        D[[k]]=stringify_params(M,names(P)[k],type='param',val=P[[k]])
+    }
+    str=c(str,D)
+
+    # add outputs and descriptions to value
+    O = output_list(M)
+
+    D=list()
+    for (k in seq_along(O)) {
+        D[[k]]=stringify_params(M,names(O)[k],type='output',val=O[[k]])
+    }
+
+    if (length(D)>0){
+        str=c(str,
+              paste0('@return ','A  \\code{', class(M)[1],'} object with the following \\code{output} slots:' ),
+              '\\tabular{ll}{',
+              D,
+              '}')
+    } else{
+        str=c(str,'@return ','A  \\code{', class(M)[1],'} object. This object has no \\code{output} slots.')
+        if (is(M,'chart')) {
+            str=c(str, 'See \\code{\\link[struct]{chart_plot}} in the \\code{struct} package to plot this chart object.')
+        }
+
+    }
+
+    # basic example
+    eg = '@examples'
+    cd = as.code(M,mode='neat',quiet=TRUE)
+    cd = gsub('[a list]','list()',cd,fixed = TRUE)
+    cd = gsub('[a function]','function(){}',cd,fixed = TRUE)
+    cd = gsub('[a annotation_database]','annotation_database()',cd,fixed = TRUE)
+    cd = gsub('[a logical]','FALSE',cd,fixed = TRUE)
+    cd = gsub('[a data.frame]','data.frame(id=NA)',cd,fixed = TRUE)
+    str=c(str,eg,cd,'')
+
+
+    return(unlist(str))
+}
+
+
+
+# in internal function used by get_desciption
+stringify_params = function(M,P,type='param',val=NULL) {
+
+    # get parameter as an object
+    if (type=='param') {
+        p = param_obj(M,P)
+    } else {
+        p=output_obj(M,P)
+    }
+
+    # if its an entity object then get its description
+    if (is(p,'entity')) {
+        d = p$description
+        # ensure first character is upper case and last character is a fullstop.
+        d=unlist(lapply(d,function(x){
+            # first is upper
+            substr(x,1,1) = toupper(substr(x,1,1))
+            # last is .
+            if (substr(x,nchar(x),nchar(x)) != '.') {
+                x=paste0(x,'.')
+            }
+            return(x)
+        }))
+
+        # if d has more than one entry and is a named vector then...
+        if (length(d)>1) {
+            # if it has names then
+            if (!is.null(names(d))) {
+                # create a named list
+                it_list='\\itemize{ '
+                for (j in seq_along(d)) {
+                    it_list=paste0(it_list,'\\item{\\code{"',names(d)[j],'"}: ',d[j],'}')
+                }
+            } else {
+                # no names so use a bulleted list
+                it_list='\\itemize{'
+                for (j in seq_along(d)) {
+                    it_list=paste0(it_list,'\\item{',d[j],'}')
+                }
+            }
+
+            # add list
+            it_list=paste0(it_list,'}')
+            d=paste0(p$name,'. Allowed values are limited to the following: ',it_list)
+        }
+
+        # add the allowed types
+        t = p$type
+
+    } else {
+        # if not an entity then there is no description
+        d = ''
+        t=class(val)[[1]]
+    }
+    # collapse if more than 1
+    t=paste0(t,collapse=', ')
+    # enclose in brackets
+    t=paste0('(',t,') ')
+    # add to description
+    d=paste0(t,d)
+
+    # if the parameter has a default, then add on the text.
+    if ( (!is(val,'name')) & type=='param'){
+        d=paste0(d, ' The default is ')
+        if (length(val)>1 & !is.call(val)) {
+            d=paste0(d,'\\code{',capture.output(val)[1],'}.')
+        } else {
+            if (is.null(val)) {
+                d=paste0(d,'\\code{NULL}.')
+            } else if (is(val,'character')) {
+                d=paste0(d,'\\code{"',val,'"}.')
+            } else if (is.function(val) | is.call(val)) {
+                d=paste0(d,'\\code{',gsub('}','\\}',
+                                          paste0(trimws(deparse(val)),collapse='')),'}.')
+                #d=paste0(d,'\\code{some_function()}.')
+            } else {
+
+                d=paste0(d,'\\code{',val,'}.\\cr')
+            }
+        }
+    } else {
+        # no default is provided
+    }
+    if (type=='param') {
+        OUT=paste0('@', type, ' ', P, ' ', d)
+    } else {
+        OUT=paste0('\\code{',P,'} \\tab          ',d,' \\cr')
+    }
+}
+
diff --git a/man/as.DatasetExperiment.Rd b/man/as.DatasetExperiment.Rd
index aa40113..68f52b3 100644
--- a/man/as.DatasetExperiment.Rd
+++ b/man/as.DatasetExperiment.Rd
@@ -13,7 +13,7 @@ as.DatasetExperiment(obj)
 a DatasetExperiment object
 }
 \description{
-Converts a SummarizedExperiment to DatasetExperiment. The assay data is 
+Converts a SummarizedExperiment to DatasetExperiment. The assay data is
 transposed, and colData and rowData switched to match. struct specific
 slots such as "name" and "description" are extracted from the metaData.
 }
diff --git a/man/as.SummarizedExperiment.Rd b/man/as.SummarizedExperiment.Rd
index 33da13c..51a8019 100644
--- a/man/as.SummarizedExperiment.Rd
+++ b/man/as.SummarizedExperiment.Rd
@@ -13,7 +13,7 @@ as.SummarizedExperiment(obj)
 a SummarizedExperiment object
 }
 \description{
-Converts a DatasetExperiment to SummarizedExperiment. The assay data is 
+Converts a DatasetExperiment to SummarizedExperiment. The assay data is
 transposed, and colData and rowData switched to match. struct specific
 slots such as "name" and "description" are stored in the metaData.
 }
diff --git a/man/cash-set-struct_class-method.Rd b/man/cash-set-struct_class-method.Rd
index d351a68..604d527 100644
--- a/man/cash-set-struct_class-method.Rd
+++ b/man/cash-set-struct_class-method.Rd
@@ -17,7 +17,7 @@
 Parameter/output value
 }
 \description{
-Dollar syntax can be used to as a shortcut for getting/setting input parameter 
+Dollar syntax can be used to as a shortcut for getting/setting input parameter
 and output values for struct objects.
 }
 \examples{
diff --git a/man/cash-struct_class-method.Rd b/man/cash-struct_class-method.Rd
index 7d61a5c..51e2b72 100644
--- a/man/cash-struct_class-method.Rd
+++ b/man/cash-struct_class-method.Rd
@@ -15,7 +15,7 @@
 Parameter/output value
 }
 \description{
-Dollar syntax can be used to as a shortcut for getting/setting input parameter 
+Dollar syntax can be used to as a shortcut for getting/setting input parameter
 and output values for struct objects.
 }
 \examples{
diff --git a/man/chart_names.Rd b/man/chart_names.Rd
index 852f903..dd5eedf 100644
--- a/man/chart_names.Rd
+++ b/man/chart_names.Rd
@@ -12,7 +12,7 @@ chart_names(obj, ret = "char")
 \arguments{
 \item{obj}{An object derived from the struct_class object}
 
-\item{ret}{A string indicating whether a list of objects ('obj') or a list of chart 
+\item{ret}{A string indicating whether a list of objects ('obj') or a list of chart
 names ('char') is returned. 'char' is default.}
 }
 \value{
@@ -22,14 +22,8 @@ list of chart names, or a list of chart objects
 Returns a list of valid charts for a struct object
 }
 \details{
-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.
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{struct_class}: 
-}}
-
 \examples{
 M = example_model()
 chart_names(M) # 'example_chart'
diff --git a/man/chart_plot.Rd b/man/chart_plot.Rd
index 5985a21..206e226 100644
--- a/man/chart_plot.Rd
+++ b/man/chart_plot.Rd
@@ -23,14 +23,14 @@ a plot object
 Plots a chart object
 }
 \details{
-The optional optional inputs depend on the input object/chart, but might 
+The optional optional inputs depend on the input object/chart, but might
 include an additional dataset object or a second model object, for example.
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{obj = chart,dobj = ANY}: 
-}}
+\item \code{chart_plot(obj = chart, dobj = ANY)}: 
 
+}}
 \examples{
 C = example_chart()
 chart_plot(C,iris_DatasetExperiment())
diff --git a/man/get_description.Rd b/man/get_description.Rd
new file mode 100644
index 0000000..c9db88e
--- /dev/null
+++ b/man/get_description.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{get_description}
+\alias{get_description}
+\title{Get struct object help description}
+\usage{
+get_description(id)
+}
+\arguments{
+\item{id}{(character) the name of a struct object to generate documentation for}
+}
+\value{
+a character string of roxygen formatted documentation for the object
+}
+\description{
+This
+function is to help developers including struct objects in their own R
+packages, and isnt intended for general use.
+Use with roxygen 2 `@eval` tags this function generates a detailed
+description of a struct object generated by extracting names,
+descriptions etc from slots in a suitable format.
+}
+\examples{
+get_description('example_model')
+
+}
diff --git a/man/is_output.Rd b/man/is_output.Rd
index 8c30d74..a14d6a5 100644
--- a/man/is_output.Rd
+++ b/man/is_output.Rd
@@ -20,11 +20,6 @@ TRUE if output name is valid, FALSE if not
 \description{
 Verify that the name of a output is valid for an object
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{struct_class}: 
-}}
-
 \examples{
 M = example_model()
 is_output(M,'result_1') # TRUE
diff --git a/man/is_param.Rd b/man/is_param.Rd
index baba22c..9d531ad 100644
--- a/man/is_param.Rd
+++ b/man/is_param.Rd
@@ -20,11 +20,6 @@ TRUE if parameter name is valid, FALSE if not
 \description{
 Verify that the input name is a valid input parameter for an object
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{struct_class}: 
-}}
-
 \examples{
 M = example_model()
 is_param(M,'value_1') # TRUE
diff --git a/man/model.Rd b/man/model.Rd
index cf5024e..7c9b116 100644
--- a/man/model.Rd
+++ b/man/model.Rd
@@ -16,7 +16,9 @@
 model(
   predicted = character(0),
   seq_in = "data",
-  seq_fcn = function(x) {     return(x) },
+  seq_fcn = function(x) {
+     return(x)
+ },
   ...
 )
 
@@ -41,10 +43,10 @@ model(
 \arguments{
 \item{predicted}{The name of an output slot to return when using \code{predicted()} (see details)}
 
-\item{seq_in}{the name of an output slot to connect with the "predicted" output 
+\item{seq_in}{the name of an output slot to connect with the "predicted" output
 of another model (see details)}
 
-\item{seq_fcn}{a function to apply to seq_in before inputting into the next model. 
+\item{seq_fcn}{a function to apply to seq_in before inputting into the next model.
 Typically used to extract a single column, or convert from factor to char etc.}
 
 \item{...}{named slots and their values.}
@@ -66,9 +68,9 @@ dataset dataset object with the reverse model applied
 
 the predicted output, as specified by predicted_name
 
-the id of the input parameter to be replaced by the \code{predicted} 
-output of the previous model in a model sequence. Reserved keyword 'data' 
-means that the input data used by \code{model_train}, \code{model_apply} etc is used. 
+the id of the input parameter to be replaced by the \code{predicted}
+output of the previous model in a model sequence. Reserved keyword 'data'
+means that the input data used by \code{model_train}, \code{model_apply} etc is used.
 \code{seq_in = 'data'} is the default setting.
 
 the modified model object
@@ -93,11 +95,11 @@ into the next model in a sequence as the data for that model.
 
 \section{\code{seq_in} slot}{
 
-In a sequence of models (see model_seq) the "predicted" slot is connected to the 
+In a sequence of models (see model_seq) the "predicted" slot is connected to the
 DatasetExperiment input of the next model. \code{seq_in} can be used to control
 flow and connect the "predicted" output to the input parameter of the next model.
-Default is the keyword 'data', and can otherwise be replaced by any input slot 
-from the model. The slot \code{seq_fcn} can be used to apply a transformation to 
+Default is the keyword 'data', and can otherwise be replaced by any input slot
+from the model. The slot \code{seq_fcn} can be used to apply a transformation to
 the output before it is used as an input. This allows you to e.g. convert between types,
 extract a single column from a data.frame etc.
 }
diff --git a/man/model_apply.Rd b/man/model_apply.Rd
index 9ac3087..74c4e7a 100644
--- a/man/model_apply.Rd
+++ b/man/model_apply.Rd
@@ -4,12 +4,14 @@
 \alias{model_apply}
 \title{Apply a model}
 \usage{
-model_apply(M, D)
+model_apply(M, D, ...)
 }
 \arguments{
 \item{M}{a `method` object}
 
 \item{D}{another object used by the first}
+
+\item{...}{other optional inputs}
 }
 \value{
 Returns a modified method object
diff --git a/man/model_reverse.Rd b/man/model_reverse.Rd
index f195c1b..5c7a9d1 100644
--- a/man/model_reverse.Rd
+++ b/man/model_reverse.Rd
@@ -4,12 +4,14 @@
 \alias{model_reverse}
 \title{Reverse preprocessing}
 \usage{
-model_reverse(M, D)
+model_reverse(M, D, ...)
 }
 \arguments{
 \item{M}{a model object}
 
 \item{D}{a dataset object}
+
+\item{...}{other optional inputs}
 }
 \value{
 Returns a modified dataset object
diff --git a/man/new_struct.Rd b/man/new_struct.Rd
index 2bd9771..a0be209 100644
--- a/man/new_struct.Rd
+++ b/man/new_struct.Rd
@@ -15,10 +15,10 @@ new_struct(class, ...)
 An object derived from struct_class
 }
 \description{
-This function creates a newly allocated object from the class identified by 
-the first argument. It works almost identically to \code{new} but is specific 
-to objects from the \pkg{struct} package and ensures that \code{entity} slots have 
-their values assigned correctly. This function is usually called by class 
+This function creates a newly allocated object from the class identified by
+the first argument. It works almost identically to \code{new} but is specific
+to objects from the \pkg{struct} package and ensures that \code{entity} slots have
+their values assigned correctly. This function is usually called by class
 constructors and not used directly.
 }
 \examples{
diff --git a/man/ontology.Rd b/man/ontology.Rd
index dffccee..8131981 100644
--- a/man/ontology.Rd
+++ b/man/ontology.Rd
@@ -35,7 +35,7 @@ ontology_list(terms = list())
 \arguments{
 \item{obj}{a struct object}
 
-\item{cache}{a named list of ontology_terms for offline use. Terms from the cache are search 
+\item{cache}{a named list of ontology_terms for offline use. Terms from the cache are search
 based on the name of the list items matching the ontology id. If cache=NULL then the OLS API is used to lookup terms.}
 
 \item{id}{(character) The ontology term id e.g. 'STATO:0000555'}
diff --git a/man/output_ids.Rd b/man/output_ids.Rd
index e02088a..d134d16 100644
--- a/man/output_ids.Rd
+++ b/man/output_ids.Rd
@@ -18,11 +18,6 @@ list of output ids
 \description{
 return a list of valid output ids for an object
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{struct_class}: 
-}}
-
 \examples{
 M = example_model()
 output_ids(M)
diff --git a/man/output_list.Rd b/man/output_list.Rd
index d761c85..1131923 100644
--- a/man/output_list.Rd
+++ b/man/output_list.Rd
@@ -28,13 +28,6 @@ struct object
 \description{
 get/set a named list of outputs and their current value for an object
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{struct_class}: 
-
-\item \code{obj = struct_class,value = list}: 
-}}
-
 \examples{
 M = example_model()
 L = output_list(M)
diff --git a/man/output_name.Rd b/man/output_name.Rd
index f7d9168..8cddd97 100644
--- a/man/output_name.Rd
+++ b/man/output_name.Rd
@@ -20,11 +20,6 @@ name of output
 \description{
 return a the name for a output, if available
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{obj = struct_class,name = character}: 
-}}
-
 \examples{
 M = example_model()
 output_name(M,'result_1')
diff --git a/man/output_obj.Rd b/man/output_obj.Rd
index 44caa4e..e11b6eb 100644
--- a/man/output_obj.Rd
+++ b/man/output_obj.Rd
@@ -33,13 +33,6 @@ the modified object
 \description{
 Gets or sets the object of an output e.g. to an entity() object.
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{obj = struct_class,name = character}: 
-
-\item \code{obj = struct_class,name = character}: 
-}}
-
 \examples{
 # get the output as an object
 M = example_model()
diff --git a/man/output_value.Rd b/man/output_value.Rd
index 0394e80..c170e2c 100644
--- a/man/output_value.Rd
+++ b/man/output_value.Rd
@@ -30,13 +30,6 @@ struct object
 \description{
 get/set the values for an output_
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{obj = struct_class,name = character}: 
-
-\item \code{obj = struct_class,name = character}: 
-}}
-
 \examples{
 M = example_model()
 output_value(M,'result_1')
diff --git a/man/param_ids.Rd b/man/param_ids.Rd
index 0b84833..58317c9 100644
--- a/man/param_ids.Rd
+++ b/man/param_ids.Rd
@@ -18,11 +18,6 @@ list of parameter ids
 \description{
 return a list of valid parameter ids for an object
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{struct_class}: 
-}}
-
 \examples{
 M = example_model()
 param_ids(M)
diff --git a/man/param_list.Rd b/man/param_list.Rd
index 6597734..8b03198 100644
--- a/man/param_list.Rd
+++ b/man/param_list.Rd
@@ -26,13 +26,6 @@ A named list of parameters names and corresponding values
 \description{
 get/set a named list of parameters and thier current value for an object
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{struct_class}: 
-
-\item \code{obj = struct_class,value = list}: 
-}}
-
 \examples{
 M = example_model()
 L = param_list(M)
diff --git a/man/param_name.Rd b/man/param_name.Rd
index 2e9c669..4fd1e87 100644
--- a/man/param_name.Rd
+++ b/man/param_name.Rd
@@ -20,11 +20,6 @@ name of parameter
 \description{
 Returns the name for a parameter, if available
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{obj = struct_class,name = character}: 
-}}
-
 \examples{
 M = example_model()
 param_name(M,'value_1')
diff --git a/man/param_value.Rd b/man/param_value.Rd
index 66fc97f..07a74ed 100644
--- a/man/param_value.Rd
+++ b/man/param_value.Rd
@@ -28,13 +28,6 @@ Value of parameter
 \description{
 get/set the values for a parameter.
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{obj = struct_class,name = character}: 
-
-\item \code{obj = struct_class,name = character}: 
-}}
-
 \examples{
 M = example_model()
 param_value(M,'value_1')
diff --git a/man/predict.Rd b/man/predict.Rd
index 7e2cfe5..8cc41bc 100644
--- a/man/predict.Rd
+++ b/man/predict.Rd
@@ -4,12 +4,14 @@
 \alias{model_predict}
 \title{Model prediction}
 \usage{
-model_predict(M, D)
+model_predict(M, D, ...)
 }
 \arguments{
 \item{M}{a model object}
 
 \item{D}{a dataset object}
+
+\item{...}{other optional inputs}
 }
 \value{
 Returns a modified model object
diff --git a/man/seq_in.Rd b/man/seq_in.Rd
index 70e23ec..effa2a5 100644
--- a/man/seq_in.Rd
+++ b/man/seq_in.Rd
@@ -16,14 +16,14 @@ seq_in(M) <- value
 }
 \value{
 \describe{
-\item{\code{seq_in}}{returns the name of the input parameter replaced 
+\item{\code{seq_in}}{returns the name of the input parameter replaced
 when used in a model sequence}
-\item{\code{seq_in<-}}{sets the name of the input parameter replaced 
+\item{\code{seq_in<-}}{sets the name of the input parameter replaced
 when used in a model sequence}
 }
 }
 \description{
-get/set the input parameter replaced by the output of the previous model in 
+get/set the input parameter replaced by the output of the previous model in
 a model sequence. Default is "data" which passes the output as the data input
 for methods such as \code{model_train} and \code{model_apply}.
 }
diff --git a/man/struct_class-class.Rd b/man/struct_class-class.Rd
index 0e566d7..bd05f00 100644
--- a/man/struct_class-class.Rd
+++ b/man/struct_class-class.Rd
@@ -15,9 +15,9 @@ and not intended for direct use. It defines slots and methods common to all
 }
 \section{Public slots}{
 
-Public slots can be accessed using shorthand $ notation and are intended for 
+Public slots can be accessed using shorthand $ notation and are intended for
 users building workflows.
- 
+
 \describe{
   \item{\code{name}}{\code{character()} A short descriptive name of the struct object}
   \item{\code{description}}{\code{character()} A longer description of the struct object and what it does}
@@ -31,7 +31,7 @@ users building workflows.
 \section{Private slots}{
 
 Private slots are not readily accessible to users and are intended for developers
-creating their own struct objects. Any slot not listed within `.params` or 
+creating their own struct objects. Any slot not listed within `.params` or
 `.outputs` is considered a private slot.
 
 \describe{
diff --git a/man/train.Rd b/man/train.Rd
index e3e085e..8faa5fe 100644
--- a/man/train.Rd
+++ b/man/train.Rd
@@ -4,12 +4,14 @@
 \alias{model_train}
 \title{Train a model}
 \usage{
-model_train(M, D)
+model_train(M, D, ...)
 }
 \arguments{
 \item{M}{a model object}
 
 \item{D}{a dataset object}
+
+\item{...}{other optional inputs}
 }
 \value{
 Returns a modified model object