bump to 0.6.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: calmr
 Title: Canonical Associative Learning Models and their Representations
-Version: 0.6.0
+Version: 0.6.1
 Authors@R: 
     person("Victor", "Navarro", , "[email protected]", role = c("aut", "cre"))
 Description: Implementations of canonical associative learning models, with tools to run experiment simulations, estimate model parameters, and compare model representations. Experiments and results are represented using S4 classes and methods.

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("parameters<-")
 export(calmr_model_graph)
 export(calmr_model_plot)
 export(calmr_verbosity)
@@ -14,7 +13,6 @@ export(get_parameters)
 export(make_experiment)
 export(model_outputs)
 export(parameter_info)
-export(parse)
 export(parse_design)
 export(patch_graphs)
 export(patch_plots)
@@ -26,19 +24,17 @@ export(supported_families)
 export(supported_models)
 export(supported_optimizers)
 export(supported_plots)
-export(trials)
 exportClasses(CalmrDesign)
 exportClasses(CalmrExperiment)
+exportClasses(CalmrExperimentResult)
 exportClasses(CalmrFit)
-exportClasses(CalmrModel)
 exportClasses(CalmrRSA)
 exportClasses(CalmrResult)
 exportMethods("parameters<-")
 exportMethods(AIC)
 exportMethods(BIC)
 exportMethods(NLL)
 exportMethods(aggregate)
-exportMethods(augment)
 exportMethods(design)
 exportMethods(experiences)
 exportMethods(graph)

NEWS.md

@@ -1,3 +1,7 @@
+# calmr 0.6.1
+* Added `outputs` argument to `run_experiment()`, `parse()`, and `aggregate()`, allowing the user to parse/aggregate only some model outputs.
+* Documentation corrections for CRAN resubmission.
+
 # calmr 0.6.0
 * Added dependency on `data.table` resulting in great speedups for large experiments.
 * Replaced dependency on `cowplot` with dependency on `patchwork`.

R/HD2022.R

@@ -108,7 +108,7 @@ HD2022 <- function(v = NULL, # nolint: object_name_linter.
     vs = vs,
     rs = rs,
     as = as,
-    acts = list(combvs = combvs, chainvs = chainvs)
+    heidi_acts = list(combvs = combvs, chainvs = chainvs)
   )
   results
 }

R/HDI2020.R

@@ -97,7 +97,7 @@ HDI2020 <- function(v = NULL, # nolint: object_name_linter.
     vs = vs,
     rs = rs,
     as = as,
-    acts = list(combvs = combvs, chainvs = chainvs)
+    heidi_acts = list(combvs = combvs, chainvs = chainvs)
   )
   results
 }

R/anccr_helpers.R

@@ -1,5 +1,5 @@
 #' Set reward parameters for ANCCR model
-#' @param parameters A list of parameters, as returned by `get_parameters`
+#' @param parameters A list of parameters, as returned by [get_parameters()]
 #' @param rewards A character vector specifying the reward stimuli.
 #' Default = `c("US")`
 #' @return A list of parameters

R/assertions.R

@@ -106,3 +106,26 @@ is_experiment <- function(object) {
 is_design <- function(object) {
   inherits(object, "CalmrDesign")
 }
+
+#' Sanitize model outputs
+#' @param os Given outputs. Character vector
+#' @param m A model name
+#' @return A character vector
+#' @note If os is not NULL, cuts extraneous outputs.
+#' @noRd
+.sanitize_outputs <- function(os, m) {
+  moutputs <- model_outputs(m)
+  if (is.null(os)) {
+    return(moutputs)
+  }
+  # extra parameters
+  extra <- setdiff(os, moutputs)
+  throw_warn <- length(extra) > 0
+  os <- os[!(os %in% extra)]
+  # final parameters
+  if (!length(os)) {
+    stop("Ended with zero outputs after sanitization. Check your outputs.")
+  }
+  if (throw_warn) warning("Found unsupported outputs. Trimming...")
+  os
+}

R/calmr_verbosity.R

@@ -5,7 +5,7 @@
 #' This is just a convenience function.
 #' @export
 #' @return The list of progressr handlers (invisibly).
-#' @note See package `progressr` for further details.
+#' @note See package 'progressr' for further details.
 calmr_verbosity <- function(verbose) {
   if (verbose) {
     progressr::handlers("progress")

R/class_design.R

@@ -1,4 +1,4 @@
-#' S4 class for Calmr designs
+#' S4 class for calmr designs
 #'
 #' @section Slots:
 #' \describe{
@@ -18,8 +18,16 @@ methods::setClass(
   ),
   prototype(augmented = FALSE)
 )
+
 #' CalmrDesign methods
+#' @description S4 methods for `CalmrDesign` class.
+#' @param object A `CalmrDesign` object
+#' @name CalmrDesign-methods
+NULL
+#> NULL
+
 #' @export
+#' @return `show()` returns NULL (invisibly).
 #' @rdname CalmrDesign-methods
 methods::setMethod(
   "show", "CalmrDesign",
@@ -35,27 +43,26 @@ methods::setMethod(
   }
 )
 
-#' @rdname CalmrDesign-methods
+#' @noRd
 methods::setGeneric(
   "mapping",
   function(object) methods::standardGeneric("mapping") # nocov
 )
-#' CalmrDesign methods
-#' @description Methods mapping, and trials, are extractor functions.
-#' @param object A CalmrDesign, as returned by parse_design
 #' @export
+#' @aliases mapping
+#' @return `mapping()` returns a list with trial mappings.
 #' @rdname CalmrDesign-methods
 methods::setMethod(
   "mapping", "CalmrDesign",
   function(object) object@mapping
 )
-#' @export
-#' @rdname CalmrDesign-methods
+#' @noRd
 methods::setGeneric(
   "trials",
   function(object) methods::standardGeneric("trials") # nocov
 )
 #' @export
+#' @return `trials()` returns NULL (invisibly).
 #' @rdname CalmrDesign-methods
 methods::setMethod(
   "trials", "CalmrDesign",
@@ -91,8 +98,7 @@ methods::setGeneric(
 #' @param ... Additional parameters depending on the model.
 #' @rdname CalmrDesign-methods
 #' @aliases augment
-#' @order 1
-#' @export
+#' @noRd
 methods::setMethod("augment", "CalmrDesign", function(object, model, ...) {
   if (model %in% c("ANCCR")) {
     # creates eventlogs