diff --git a/R-libraries/Casal2_22.03.tar.gz b/R-libraries/Casal2_22.03.tar.gz
index 426722aa2..a48cbbf95 100644
Binary files a/R-libraries/Casal2_22.03.tar.gz and b/R-libraries/Casal2_22.03.tar.gz differ
diff --git a/R-libraries/casal2/DESCRIPTION b/R-libraries/casal2/DESCRIPTION
index b607d8c01..cf10f6a00 100644
--- a/R-libraries/casal2/DESCRIPTION
+++ b/R-libraries/casal2/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Casal2
 Title: Casal2 extract package
 Version: 22.03
-Date: 2022-03-02
+Date: 2022-03-15
 Author: Casal2 Development Team
 Description: A set of R functions for extracting and plotting from Casal2 configuration input files, reports, and other associated files.
 Maintainer: Casal2 Development Team <casal2@niwa.co.nz>
diff --git a/R-libraries/casal2/R/ShortHandFunctions.R b/R-libraries/casal2/R/ShortHandFunctions.R
new file mode 100644
index 000000000..5137d7ad3
--- /dev/null
+++ b/R-libraries/casal2/R/ShortHandFunctions.R
@@ -0,0 +1,197 @@
+
+#' @title expand_category_block
+#'
+#' @description
+#' A utility function for expanding short hand syntax in @category blocks in casal2 config files
+#'
+#' @author Craig Marsh
+#' @param categories string of categories
+#' @return a vector of strings
+#' @keywords internal
+#' @examples
+#' \dontrun{
+#' expand_category_block("stock")
+#' expand_category_block("stock.male,female")
+#' expand_category_block("stock.male,female.untagged,1990")
+#' }
+expand_category_block <- function(categories) {
+  expanded_labels = vector();
+  groups = strsplit(categories, split = ".", fixed = TRUE)[[1]]
+  category_list = list()
+  for(i in 1:length(groups)) {
+    if(grepl(groups[i], pattern = ",")) {
+      sub_groups = strsplit(groups[i], split = ",", fixed = TRUE)[[1]]
+      category_list[[i]] = sub_groups
+    } else {
+      category_list[[i]] = groups[i]
+    }
+  }
+  ## now permutate them
+  all_perms <- expand.grid(category_list, stringsAsFactors = FALSE)
+  new_perms = NULL
+  ## need to re-order based on first factor
+  i = 1
+  for(j in 1:length(category_list[[i]])) {
+    ndx = all_perms$Var1 == category_list[[i]][j]
+    new_perms = rbind(new_perms, all_perms[ndx,])
+  }
+  for(i in 1:nrow(new_perms)) {
+    expanded_labels = c(expanded_labels, paste0(new_perms[i,], collapse = "."))
+  }
+  return(expanded_labels)
+}
+
+#' @title expand_category_shorthand
+#'
+#' @description
+#' A utility function for expanding short hand syntax of categories used in subcommands throught casal2 config files
+#'
+#' @author Craig Marsh
+#' @param shorthand_categories shorthand values to expand
+#' @param reference_categories string of categories expanded from the @category block of a config. derived from expand_category_block
+#' @param category_format the format defined in the @categories block
+#' @return a vector of strings
+#' @keywords internal
+#' @examples
+#' \dontrun{
+#' expand_category_shorthand(shorthand_categories ="format=*.EN.*", reference_categories = c("BOP.EN.male"))
+#' expand_category_shorthand(shorthand_categories ="format=*.EN.*", reference_categories = c("BOP.EN.male", "BOP.EN.female"))
+#' expand_category_shorthand(shorthand_categories ="format=*.EN.*", reference_categories = c("BOP.EN.male", "BOP.EN.female", "HAGU.EN.male", "HAGU.EN.female"))
+#' expand_category_shorthand(shorthand_categories ="format = *.EN.+", reference_categories = c("BOP.EN.male", "BOP.EN.female"))
+#' expand_category_shorthand(shorthand_categories ="format = *.EN.+", reference_categories = c("BOP.EN.male", "BOP.EN.female", "HAGU.EN.male", "HAGU.EN.female"))
+#' expand_category_shorthand(shorthand_categories ="*", reference_categories = c("BOP.EN.male", "BOP.EN.female", "HAGU.EN.male", "HAGU.EN.female"))
+#' expand_category_shorthand(shorthand_categories ="stock=BOP", reference_categories = c("BOP.EN.male", "BOP.EN.female", "HAGU.EN.male", "HAGU.EN.female"), category_format = "stock.area.sex")
+#' }
+expand_category_shorthand <- function(shorthand_categories, reference_categories, category_format = NULL) {
+  expanded_categories = vector();
+  formats = NULL
+  if(!is.null(category_format)) {
+    formats = strsplit(category_format, ".", fixed = T)[[1]]
+  }
+  broken_ref_vals = Reduce(rbind, strsplit(reference_categories, ".", fixed = T))
+  if(is.null(dim(broken_ref_vals))) {
+    broken_ref_vals = matrix(broken_ref_vals, nrow =1)
+  }
+  # strip whitespace
+  shorthand_categories_no_space = gsub(" ", "", shorthand_categories, fixed = TRUE)
+  expanded_categories = shorthand_categories_no_space
+  # if format strip that out
+  format_found = grepl(shorthand_categories_no_space, pattern = "format=", fixed = TRUE)
+  if(format_found) {
+    shorthand_categories_no_space = gsub("format=", "", shorthand_categories_no_space, fixed = TRUE)
+  }
+  # if other shorthand
+  format_found = grepl(shorthand_categories_no_space, pattern = "=", fixed = TRUE)
+  if(format_found) {
+    expanded_categories = NULL
+    temp_formats = strsplit(shorthand_categories_no_space, "=", fixed = T)[[1]]
+    cat_ndx = which(formats == temp_formats[1])
+    ref_ndx = broken_ref_vals[,cat_ndx] == temp_formats[2]
+    these_categories = broken_ref_vals[ref_ndx, ]
+    for(i in 1:nrow(these_categories)) {
+      expanded_categories = c(expanded_categories, paste0(these_categories[i,], collapse = "."))
+    }
+  }
+
+
+  ## now should be only category labels, periods ('.'), astrix, or +
+  rep_syntax = grepl(shorthand_categories_no_space, pattern = "*", fixed = TRUE)
+  category_list = list();
+  if(rep_syntax) {
+    if(shorthand_categories_no_space == "*") {
+      # return all categories
+      expanded_categories = reference_categories
+    } else {
+      ## need to repeat some category levels
+      broken_vals = strsplit(shorthand_categories_no_space, ".", fixed = T)[[1]]
+      for(i in 1:length(broken_vals)) {
+        if(broken_vals[i] == "*") {
+          category_list[[i]] = unique(broken_ref_vals[,i])
+        } else {
+          category_list[[i]] = broken_vals[i]
+        }
+      }
+      ## now permutate them
+      all_perms <- expand.grid(category_list, stringsAsFactors = FALSE)
+      for(i in 1:nrow(all_perms)) {
+        expanded_categories = c(expanded_categories, paste0(all_perms[i,], collapse = "."))
+      }
+    }
+  }
+  return(expanded_categories)
+}
+
+#' @title expand_shorthand_syntax
+#'
+#' @description
+#' A utility function for expanding short hand syntax for based on - format=*.EN.*, label*5, and + syntax
+#'
+#' @author Craig Marsh
+#' @param syntax string of the syntax to expand
+#' @return a vector of strings
+#' @keywords internal
+#' @examples
+#' \dontrun{
+#' # currently can handle these shorthand
+#' expand_shorthand_syntax(syntax = "age_length")
+#' expand_shorthand_syntax(syntax = "age_length * 8")
+#' expand_shorthand_syntax(syntax ="age_length*8")
+#' expand_shorthand_syntax(syntax ="age_length_BP*4 age_length_EN*4")
+#' expand_shorthand_syntax(syntax = "1990:2000")
+#' expand_shorthand_syntax(syntax ="age_length_BP*4,age_length_EN*4")
+#' expand_shorthand_syntax(syntax ="0.75*3")
+#' expand_shorthand_syntax(syntax ="0.75 * 3 ")
+#' # cant deal with
+#' expand_shorthand_syntax(syntax ="0.75*3 0.75*3")
+#' }
+expand_shorthand_syntax <- function(syntax) {
+  syntax = paste(syntax, collapse = "")
+  ## strip whitespace out of syntax to make it easier
+  syntax_no_space = gsub(" ", "", syntax, fixed = TRUE)
+  # we wont deal with  ',' so strip them out to
+  syntax_no_space = gsub(",", "", syntax_no_space, fixed = TRUE)
+
+  rep_syntax = grepl(syntax_no_space, pattern = "*", fixed = TRUE)
+  colon_syntax = grepl(syntax_no_space, pattern = ":", fixed = TRUE)
+
+  ## deal with repeat labels
+  repeated_values = vector();
+  if(rep_syntax) {
+    ## simple expansion
+    rep_components = strsplit(syntax_no_space, split = "*", fixed = TRUE)[[1]]
+    convert_vals = suppressWarnings(as.numeric(rep_components))
+    if(all(!is.na(convert_vals))) {
+      ## all numbers so must be 0.45 * 2
+      #   pairs = length(rep_components) / 2
+      if(length(rep_components) != 2)
+        stop("unknown syntax")
+      repeated_values = rep(convert_vals[1], convert_vals[2])
+    } else {
+      # Numbers and words
+      for(i in 1:length(rep_components)) {
+        # no numbers
+        if(gsub("[^\\d]+", "", rep_components[i], perl=TRUE) == "") {
+          ## simple case "label"
+          value = rep_components[i]
+        } else if(gsub("[^\\d]+", "", rep_components[i], perl=TRUE) != "" & (nchar(gsub("[^\\d]+", "", rep_components[i], perl=TRUE)) != nchar(rep_components[i]))) {
+          ## has numbers and words...
+          ## get number
+          rep_num = as.numeric(gsub("[^\\d]+", "", rep_components[i], perl=TRUE))
+          repeated_values = c(repeated_values, rep(value, rep_num))
+          ## get the other word
+          value = gsub('[[:digit:]]+', '', rep_components[i])
+        } else {
+          ## just number repeat value by this number
+          repeated_values = c(repeated_values, rep(value, as.numeric(gsub("[^\\d]+", "", rep_components[i], perl=TRUE))))
+        }
+      }
+    }
+  } else if(colon_syntax) {
+    ## assumes only numbers lowerval:upperval
+    seq_components = strsplit(syntax_no_space, split = ":", fixed = TRUE)[[1]]
+    repeated_values = as.numeric(seq_components[1]):as.numeric(seq_components[2])
+  } else {
+    repeated_values = syntax
+  }
+  return(repeated_values)
+}
diff --git a/R-libraries/casal2/R/extract.csl2.file.R b/R-libraries/casal2/R/extract.csl2.file.R
index 943c10efe..cb2f702ee 100644
--- a/R-libraries/casal2/R/extract.csl2.file.R
+++ b/R-libraries/casal2/R/extract.csl2.file.R
@@ -63,7 +63,6 @@
   ## this will be the default label if no user defined label is specified
   for (i in 1:length(file)) {
     temp <- string.to.vector.of.words(file[i])
-    check_inputs <- check_short_hand(temp)
     ## expand numeric shorthand
     #if (any(check_inputs$numeric) && (substr(Command, 1, 3) != "est") | (substr(Command, 1, 3) != "par")) {
       #vals <- eval(parse(text = temp[check_inputs$numeric]))
@@ -101,8 +100,24 @@
     }
     ## Check if it is a valid type/subcommand
     if (type == "vector") {
-      ## deal with a vector subcommand
-      ans[[Command]][[temp[1]]] <- list("value" = temp[-1])
+      new_string = temp[1]
+      ## if category or parameter subcommand skip expand short hand for * and : 
+      if(grepl(temp[1], pattern = "categor", fixed = TRUE) | grepl(temp[1], pattern = "parameter", fixed = TRUE)) {
+        new_string = temp
+      } else {
+        ## check white space hasn't split it up already
+        second_values = NULL
+        if(any(temp[2:length(temp)] == "*")) {
+          second_values = paste(temp[2:length(temp)], collapse = "")
+        } else {
+          second_values = temp[2:length(temp)]
+        }
+        ## deal with : shorthand
+        for (j in 1:length(second_values)) {
+          new_string <- c(new_string, expand_shorthand_syntax(second_values[j]))
+        }
+      }
+      ans[[Command]][[new_string[1]]] <- list("value" = new_string[-1])
     } else if ((type == "table_label") || in_table) {
       ## deal with a table input. the biggest pain in ithe ass
       in_table <- TRUE
diff --git a/R-libraries/casal2/R/generate.starting.pars.R b/R-libraries/casal2/R/generate.starting.pars.R
index 16d4f1dda..0cd2dcecb 100644
--- a/R-libraries/casal2/R/generate.starting.pars.R
+++ b/R-libraries/casal2/R/generate.starting.pars.R
@@ -3,18 +3,20 @@
 #' This function reads a Casal2 estimation configuration file and returns a par file. Where each parameter is drawn from the prior defined in an @estimate block.
 #'
 #' @author Craig Marsh
-#' @param Estimation_csl2_file the name of the configuration file containing the @estimate blocks.
+#' @param estimation_csl2_file the name of the configuration file containing the @estimate blocks.
 #' @param path Optionally, the path to the file
-#' @param N the number of random samples you want.
+#' @param n_sim the number of random samples you want.
 #' @param par_file_name = the filename of the file created 
 #' @param all_uniform = logical if TRUE draw from a uniform between bounds regardless of prior distribution
+#' @param quiet Optional, supresses printing statements
 #' @param fileEncoding Optional, allows the R-library to read in files that have been encoded in alternative UTF formats, see the manual for the error message that would indicate when to use this switch.
+
 #' @return a file named 'parms.out' in the path directory
 #' @export
 #'
 
-'generate.starting.pars' = function(path = "", Estimation_csl2_file = "Estimation.csl2", N = 10, par_file_name = "starting_pars.out", all_uniform = FALSE, fileEncoding = "") {
-  estimate_config = extract.csl2.file(file = Estimation_csl2_file, path = path, fileEncoding = fileEncoding);
+generate.starting.pars <- function(path = "", estimation_csl2_file = "Estimation.csl2", n_sim = 10, par_file_name = "starting_pars.out", all_uniform = FALSE, fileEncoding = "", quiet = T) {
+  estimate_config = extract.csl2.file(file = estimation_csl2_file, path = path, fileEncoding = fileEncoding, quiet = quiet);
   ## pull out the estimates only, they are the only components interested in at the moment
   estimate_ndx = grepl(pattern = "estimate\\[", x = names(estimate_config))
   estimate_block_labels = names(estimate_config)[estimate_ndx]
@@ -37,67 +39,7 @@
     if (!this_estimate$type %in% allowed_types) {
       stop(paste0("Sorry, we haven't coded a random number generator for the distribution of type ", this_estimate$type, " we currently only have the following types ", paste(allowed_types, collapse = ", ")))
     }
-    #########################################
-    ## Check priors don't related to EstimateTransformations?
-    ## these will need to be taken care of
-    deal_with_transformations = FALSE;
-    skip_parameter = FALSE
-    ## this gets tricky we need to iterate over the estimate_transfomration blocks so we can see if there is another parameter involved?  
-    if (!is.null(this_estimate$prior_applies_to_transform) && (this_estimate$prior_applies_to_transform$value == "TRUE" || this_estimate$prior_applies_to_transform$value == "t" || this_estimate$prior_applies_to_transform$value == "true")) {
-      ## Check to see if we haven't already found this parameter in a previous transformation
-      if (length(names(conditional_parameters)) > 0) {
-        for (previous_trans in names(conditional_parameters)) {
-          previous_transformation = get(previous_trans, conditional_parameters)
-          if (previous_transformation$other_label == Label) {
-            ## this parameter has been associated with a previous transformatin block.
-            skip_parameter = TRUE;
-          }
-        }
-      }
-      if (!skip_parameter) {
-        estimate_transformation_ndx = grepl(pattern = "estimate_transformation", x = names(estimate_config))
-        if (any(estimate_transformation_ndx)) {
-          for (trans in 1:sum(estimate_transformation_ndx)) {
-            this_trans = get(names(estimate_config)[estimate_transformation_ndx][trans], estimate_config)
-            if (this_trans$type$value == "average_difference") {
-              if (this_trans$estimate_label$value == Label) {
-                conditional_parameters[[Label]]$other_label = this_trans$difference_estimate$value
-                conditional_parameters[[Label]]$type = "average_difference"
-                conditional_parameters[[Label]]$first_estimate = "true"
-              } else if (this_trans$difference_estimate$value == Label) {
-                conditional_parameters[[Label]]$other_label = this_trans$estimate_label$value
-                conditional_parameters[[Label]]$type = "average_difference"
-                conditional_parameters[[Label]]$first_estimate = "false"
-              }
-            } else if (this_trans$type$value == "log_sum") {
-              if (this_trans$estimate_label$value == Label) {
-                conditional_parameters[[Label]]$other_label = this_trans$second_estimate$value
-                conditional_parameters[[Label]]$type = "log_sum"
-                conditional_parameters[[Label]]$first_estimate = "true"
-              } else if (this_trans$second_estimate$value == Label) {
-                conditional_parameters[[Label]]$other_label = this_trans$estimate_label$value
-                conditional_parameters[[Label]]$type = "log_sum"
-                conditional_parameters[[Label]]$first_estimate = "false"
-              }
-            } else if (this_trans$type$value == "orthogonal") {
-              if (this_trans$estimate_label$value == Label) {
-                conditional_parameters[[Label]]$other_label = this_trans$second_estimate$value
-                conditional_parameters[[Label]]$first_estimate = "true"
-                conditional_parameters[[Label]]$type = "orthogonal"
-              } else if (this_trans$second_estimate$value == Label) {
-                conditional_parameters[[Label]]$other_label = this_trans$estimate_label$value
-                conditional_parameters[[Label]]$type = "orthogonal"
-                conditional_parameters[[Label]]$first_estimate = "false"
-              }
-            } else if (this_trans$type$value == "simplex") {
-              if (this_trans$estimate_label$value == Label) {
-                stop("This code cannot deal with the simplex transformation?")
-              }
-            }
-          }
-        }
-      }
-    }
+    
     ## check if this parameter needs to be split out into multiple parameters
     start_nd = as.numeric(regexpr(pattern = "\\{", text = this_estimate$parameter$value))
     end_nd = as.numeric(regexpr(pattern = "\\}", text = this_estimate$parameter$value))
@@ -123,19 +65,19 @@
       param_labels = c(param_labels, this_estimate$parameter$value)
       ## Now simulate data.
       values = NULL;
-      if (this_estimate$type == "uniform" || all_uniform) {
-        values = runif(n = N, min = as.numeric(this_estimate$lower_bound$value), max = as.numeric(this_estimate$upper_bound$value))
-      } else if (this_estimate$type == "uniform_log") {
-        values = exp(runif(n = N, min = log(as.numeric(this_estimate$lower_bound$value)), max = log(as.numeric(this_estimate$upper_bound$value))))
-      } else if (this_estimate$type == "normal") {
+      if (this_estimate$type$value == "uniform" || all_uniform) {
+        values = runif(n = n_sim, min = as.numeric(this_estimate$lower_bound$value), max = as.numeric(this_estimate$upper_bound$value))
+      } else if (this_estimate$type$value == "uniform_log") {
+        values = exp(runif(n = n_sim, min = log(as.numeric(this_estimate$lower_bound$value)), max = log(as.numeric(this_estimate$upper_bound$value))))
+      } else if (this_estimate$type$value == "normal") {
         std_dev = as.numeric(this_estimate$mu$value) * as.numeric(this_estimate$cv$value)
-        values = rnorm(n = N, mean = as.numeric(this_estimate$mu$value), sd = std_dev)
+        values = rnorm(n = n_sim, mean = as.numeric(this_estimate$mu$value), sd = std_dev)
       } else if (this_estimate$type == "lognormal") {
-        values = Rlnorm(n = N, mu = as.numeric(this_estimate$mu$value), cv = as.numeric(this_estimate$cv$value))
+        values = Rlnorm(n = n_sim, mu = as.numeric(this_estimate$mu$value), cv = as.numeric(this_estimate$cv$value))
       } else if (this_estimate$type == "normal_by_stdev") {
-        values = rnorm(n = N, mean = as.numeric(this_estimate$mu$value), sd = as.numeric(this_estimate$sigma$value))
+        values = rnorm(n = n_sim, mean = as.numeric(this_estimate$mu$value), sd = as.numeric(this_estimate$sigma$value))
       } else if (this_estimate$type == "normal_log") {
-        values = exp(rnorm(n = N, mean = as.numeric(this_estimate$mu$value), sd = as.numeric(this_estimate$sigma$value)))
+        values = exp(rnorm(n = n_sim, mean = as.numeric(this_estimate$mu$value), sd = as.numeric(this_estimate$sigma$value)))
       }
       ## set to bounds if generated past them
       values[values < as.numeric(this_estimate$lower_bound$value)] = as.numeric(this_estimate$lower_bound$value)
@@ -164,7 +106,7 @@
       ## Now simulate data for each param      
       if (this_estimate$type == "uniform" || all_uniform) {
         for (param in 1:n_params) {
-          values = runif(n = N, min = as.numeric(this_estimate$lower_bound$value[param]), max = as.numeric(this_estimate$upper_bound$value[param]))
+          values = runif(n_sim = n_sim, min = as.numeric(this_estimate$lower_bound$value[param]), max = as.numeric(this_estimate$upper_bound$value[param]))
           ## check within bounds
           values[values < as.numeric(this_estimate$lower_bound$value[param])] = as.numeric(this_estimate$lower_bound$value[param])
           values[values > as.numeric(this_estimate$upper_bound$value[param])] = as.numeric(this_estimate$upper_bound$value[param])
@@ -172,7 +114,7 @@
         }
       } else if (this_estimate$type == "uniform_log") {
         for (param in 1:n_params) {
-          values = exp(runif(n = N, min = log(as.numeric(this_estimate$lower_bound$value[param])), max = log(as.numeric(this_estimate$upper_bound$value[param]))))
+          values = exp(runif(n_sim = n_sim, min = log(as.numeric(this_estimate$lower_bound$value[param])), max = log(as.numeric(this_estimate$upper_bound$value[param]))))
           ## check within bounds
           values[values < as.numeric(this_estimate$lower_bound$value[param])] = as.numeric(this_estimate$lower_bound$value[param])
           values[values > as.numeric(this_estimate$upper_bound$value[param])] = as.numeric(this_estimate$upper_bound$value[param])
@@ -192,7 +134,7 @@
         std_dev = as.numeric(this_estimate$mu$value) * as.numeric(this_estimate$cv$value)
 
         for (param in 1:n_params) {
-          values = rnorm(n = N, mean = as.numeric(this_estimate$mu$value[param]), sd = std_dev[param])
+          values = rnorm(n_sim = n_sim, mean = as.numeric(this_estimate$mu$value[param]), sd = std_dev[param])
           ## check within bounds
           values[values < as.numeric(this_estimate$lower_bound$value[param])] = as.numeric(this_estimate$lower_bound$value[param])
           values[values > as.numeric(this_estimate$upper_bound$value[param])] = as.numeric(this_estimate$upper_bound$value[param])
@@ -210,7 +152,7 @@
           this_estimate$cv$value = rep(left_value, n_params)
         }
         for (param in 1:n_params) {
-          values = Rlnorm(n = N, mu = as.numeric(this_estimate$mu$value[param]), cv = as.numeric(this_estimate$cv$value[param]))
+          values = Rlnorm(n = n_sim, mu = as.numeric(this_estimate$mu$value[param]), cv = as.numeric(this_estimate$cv$value[param]))
           ## check within bounds
           values[values < as.numeric(this_estimate$lower_bound$value[param])] = as.numeric(this_estimate$lower_bound$value[param])
           values[values > as.numeric(this_estimate$upper_bound$value[param])] = as.numeric(this_estimate$upper_bound$value[param])
@@ -228,7 +170,7 @@
           this_estimate$sigma$value = rep(left_value, n_params)
         }
         for (param in 1:n_params) {
-          values = rnorm(n = N, mean = as.numeric(this_estimate$mu$value[param]), sd = as.numeric(this_estimate$sigma$value[param]))
+          values = rnorm(n_sim = n_sim, mean = as.numeric(this_estimate$mu$value[param]), sd = as.numeric(this_estimate$sigma$value[param]))
           ## check within bounds
           values[values < as.numeric(this_estimate$lower_bound$value[param])] = as.numeric(this_estimate$lower_bound$value[param])
           values[values > as.numeric(this_estimate$upper_bound$value[param])] = as.numeric(this_estimate$upper_bound$value[param])
@@ -246,7 +188,7 @@
           this_estimate$sigma$value = rep(left_value, n_params)
         }
         for (param in 1:n_params) {
-          values = exp(rnorm(n = N, mean = as.numeric(this_estimate$mu$value), sd = as.numeric(this_estimate$sigma$value)))
+          values = exp(rnorm(n_sim = n_sim, mean = as.numeric(this_estimate$mu$value), sd = as.numeric(this_estimate$sigma$value)))
           ## check within bounds
           values[values < as.numeric(this_estimate$lower_bound$value[param])] = as.numeric(this_estimate$lower_bound$value[param])
           values[values > as.numeric(this_estimate$upper_bound$value[param])] = as.numeric(this_estimate$upper_bound$value[param])
@@ -257,45 +199,12 @@
     }
   }
   colnames(param_values) = value_labels;
-  ## Deal with transformations if any of the priors are described for the transformed space.
-  if (length(names(conditional_parameters)) > 0) {
-    for (previous_trans in names(conditional_parameters)) {
-      previous_transformation = get(previous_trans, conditional_parameters)
-      if (previous_transformation$type == "average_difference") {
-        ## get the correct columns from the values matrix to transform
-        X2 = param_values[, previous_transformation$other_label]
-        X1 = param_values[, previous_trans]
-        param1 = X1 + (X2 / 2)
-        param2 = X1 - (X2 / 2)
-        ## override values
-        param_values[, previous_transformation$other_label] = param2
-        param_values[, previous_trans] = param1
-      } else if (previous_transformation$type == "log_sum") {
-        ## get the correct columns from the values matrix to transform
-        X2 = param_values[, previous_transformation$other_label]
-        X1 = param_values[, previous_trans]
-        total = exp(X1);
-        param1 = total * X2
-        param2 = total * (1 - X2)
-        param_values[, previous_transformation$other_label] = param2
-        param_values[, previous_trans] = param1
-      } else if (previous_transformation$type == "orthogonal") {
-        ## get the correct columns from the values matrix to transform
-        X2 = param_values[, previous_transformation$other_label]
-        X1 = param_values[, previous_trans]
-        param1 = sqrt(X1 * X2);
-        param2 = sqrt(X1 / X2);
-        param_values[, previous_transformation$other_label] = param2
-        param_values[, previous_trans] = param1
-      }
-    }
-  }
   ## write the file.
   filename = make.filename(path = path, file = par_file_name)
   cat(param_labels, file = filename, sep = " ", fill = F, labels = NULL, append = F)
   cat("\n", file = filename, sep = " ", fill = F, labels = NULL, append = T)
-  for (i in 1:N) {
+  for (i in 1:n_sim) {
     cat(param_values[i,], file = filename, sep = " ", fill = F, labels = NULL, append = T)
     cat("\n", file = filename, sep = " ", fill = F, labels = NULL, append = T)
   }
-}
\ No newline at end of file
+}
diff --git a/R-libraries/casal2/man/expand_category_block.Rd b/R-libraries/casal2/man/expand_category_block.Rd
new file mode 100644
index 000000000..06ec72e30
--- /dev/null
+++ b/R-libraries/casal2/man/expand_category_block.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ShortHandFunctions.R
+\name{expand_category_block}
+\alias{expand_category_block}
+\title{expand_category_block}
+\usage{
+expand_category_block(categories)
+}
+\arguments{
+\item{categories}{string of categories}
+}
+\value{
+a vector of strings
+}
+\description{
+A utility function for expanding short hand syntax in @category blocks in casal2 config files
+}
+\examples{
+\dontrun{
+expand_category_block("stock")
+expand_category_block("stock.male,female")
+expand_category_block("stock.male,female.untagged,1990")
+}
+}
+\author{
+Craig Marsh
+}
+\keyword{internal}
diff --git a/R-libraries/casal2/man/expand_category_shorthand.Rd b/R-libraries/casal2/man/expand_category_shorthand.Rd
new file mode 100644
index 000000000..a454ab45d
--- /dev/null
+++ b/R-libraries/casal2/man/expand_category_shorthand.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ShortHandFunctions.R
+\name{expand_category_shorthand}
+\alias{expand_category_shorthand}
+\title{expand_category_shorthand}
+\usage{
+expand_category_shorthand(
+  shorthand_categories,
+  reference_categories,
+  category_format = NULL
+)
+}
+\arguments{
+\item{shorthand_categories}{shorthand values to expand}
+
+\item{reference_categories}{string of categories expanded from the @category block of a config. derived from expand_category_block}
+
+\item{category_format}{the format defined in the @categories block}
+}
+\value{
+a vector of strings
+}
+\description{
+A utility function for expanding short hand syntax of categories used in subcommands throught casal2 config files
+}
+\examples{
+\dontrun{
+expand_category_shorthand(shorthand_categories ="format=*.EN.*", reference_categories = c("BOP.EN.male"))
+expand_category_shorthand(shorthand_categories ="format=*.EN.*", reference_categories = c("BOP.EN.male", "BOP.EN.female"))
+expand_category_shorthand(shorthand_categories ="format=*.EN.*", reference_categories = c("BOP.EN.male", "BOP.EN.female", "HAGU.EN.male", "HAGU.EN.female"))
+expand_category_shorthand(shorthand_categories ="format = *.EN.+", reference_categories = c("BOP.EN.male", "BOP.EN.female"))
+expand_category_shorthand(shorthand_categories ="format = *.EN.+", reference_categories = c("BOP.EN.male", "BOP.EN.female", "HAGU.EN.male", "HAGU.EN.female"))
+expand_category_shorthand(shorthand_categories ="*", reference_categories = c("BOP.EN.male", "BOP.EN.female", "HAGU.EN.male", "HAGU.EN.female"))
+expand_category_shorthand(shorthand_categories ="stock=BOP", reference_categories = c("BOP.EN.male", "BOP.EN.female", "HAGU.EN.male", "HAGU.EN.female"), category_format = "stock.area.sex")
+}
+}
+\author{
+Craig Marsh
+}
+\keyword{internal}
diff --git a/R-libraries/casal2/man/expand_shorthand_syntax.Rd b/R-libraries/casal2/man/expand_shorthand_syntax.Rd
new file mode 100644
index 000000000..c79711684
--- /dev/null
+++ b/R-libraries/casal2/man/expand_shorthand_syntax.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ShortHandFunctions.R
+\name{expand_shorthand_syntax}
+\alias{expand_shorthand_syntax}
+\title{expand_shorthand_syntax}
+\usage{
+expand_shorthand_syntax(syntax)
+}
+\arguments{
+\item{syntax}{string of the syntax to expand}
+}
+\value{
+a vector of strings
+}
+\description{
+A utility function for expanding short hand syntax for based on - format=*.EN.*, label*5, and + syntax
+}
+\examples{
+\dontrun{
+# currently can handle these shorthand
+expand_shorthand_syntax(syntax = "age_length")
+expand_shorthand_syntax(syntax = "age_length * 8")
+expand_shorthand_syntax(syntax ="age_length*8")
+expand_shorthand_syntax(syntax ="age_length_BP*4 age_length_EN*4")
+expand_shorthand_syntax(syntax = "1990:2000")
+expand_shorthand_syntax(syntax ="age_length_BP*4,age_length_EN*4")
+expand_shorthand_syntax(syntax ="0.75*3")
+expand_shorthand_syntax(syntax ="0.75 * 3 ")
+# cant deal with
+expand_shorthand_syntax(syntax ="0.75*3 0.75*3")
+}
+}
+\author{
+Craig Marsh
+}
+\keyword{internal}
diff --git a/R-libraries/casal2/man/generate.starting.pars.Rd b/R-libraries/casal2/man/generate.starting.pars.Rd
index a2aee3cbd..243e369c5 100644
--- a/R-libraries/casal2/man/generate.starting.pars.Rd
+++ b/R-libraries/casal2/man/generate.starting.pars.Rd
@@ -6,25 +6,28 @@
 \usage{
 generate.starting.pars(
   path = "",
-  Estimation_csl2_file = "Estimation.csl2",
-  N = 10,
+  estimation_csl2_file = "Estimation.csl2",
+  n_sim = 10,
   par_file_name = "starting_pars.out",
   all_uniform = FALSE,
-  fileEncoding = ""
+  fileEncoding = "",
+  quiet = T
 )
 }
 \arguments{
 \item{path}{Optionally, the path to the file}
 
-\item{Estimation_csl2_file}{the name of the configuration file containing the @estimate blocks.}
+\item{estimation_csl2_file}{the name of the configuration file containing the @estimate blocks.}
 
-\item{N}{the number of random samples you want.}
+\item{n_sim}{the number of random samples you want.}
 
 \item{par_file_name}{= the filename of the file created}
 
 \item{all_uniform}{= logical if TRUE draw from a uniform between bounds regardless of prior distribution}
 
 \item{fileEncoding}{Optional, allows the R-library to read in files that have been encoded in alternative UTF formats, see the manual for the error message that would indicate when to use this switch.}
+
+\item{quiet}{Optional, supresses printing statements}
 }
 \value{
 a file named 'parms.out' in the path directory