rdecision 1.3.0

• Added rhub workflow to git repository.
• Increased minimum version of R in DESCRIPTION to 3.6.0 to be consistent with functions str2lang and hcl.colors which require it, and added backport linter to list of linters to identify whether the minimum version of R is required to be changed in future builds.
• Added packages rmarkdown and igraph to VignetteBuilder field of DESCRIPTION because these are required to build the vignettes.
• Changed internal functions abortif and abortifnot to use base R rather then rlang. Replaced legacy calls to rlang::abort in classes with calls to abortif or abortifnot.
• Added utility discount rate argument to LeafNode class, and modified method QALY in LeafNode to calculate QALYs gained, assuming present value of future utility under a continuous discount assumption. Revised documentation of DecisionTree and LeafNode to clarify the timing assumptions used by rdecision in decision tree modelling (that all costs are incurred at time t = 0, and that QALYs are gained over the time horizons defined in the leaf nodes).
• Added citation to O’Mahony et al (2015) to HIV vignette, and SemiMarkovModel and DecisionTree documentation.
• Calling methods set_cost and set_utility in class MarkovState without an argument is trapped as an error.
• Calling method set_cost in class Transition without an argument is trapped as an error.
• Arguments index and ref in the tornado method of DecisionTree may now each be expressed as a single Action edge, rather than a list of action edges, if there is one decision node in the tree. As many decision problems are a choice between two strategies, this is a common usage of tornado, and will lead to more compact code. Method is_strategy also modified to permit compact notation of index and reference strategies.
• Decision tree drawing algorithm improved to place leaf node labels to the right of the symbol, and to accurately calculate margin sizes required to accommodate symbols and labels efficiently. Node and edge grid drawing functions moved to classes for those objects.
• Added package qualifier for function dev.size in grDevices, and functions abline, axis, rect, strwidth and text in package graphics.
• Moved code to plot a tornado diagram into ’utils.Rto make it available for creating such diagrams given any input source (e.g., Markov models), rather than restricting its use toModVar`s in decision trees.
• Added vignette SM00, a narrative explanation of replicating Sonnenberg and Beck’s three-state model of people having a prosthetic heart valve. Removed dependency of the package readme file on test-model-Lifestyle.R and test-model-PHV.R, and revised, simplified and corrected the readme file.
• Removed dependency on external file for vignette DT00 by direct inclusion of model code from test-model-Lifestyle.R. Test expectations replaced by stopifnot assertions to ensure that the vignette model results agree with published values. Replaced calls to knitr::kable with base R table output for purled output.
• Removed dependency on external file for vignette DT01 by direct inclusion of model code from test-model-Sumatriptan.R. Test expectations replaced by stopifnot assertions to ensure that the vignette model results agree with published values. Replaced calls to knitr::kable with base R table output for purled output.
• Removed dependency on external file for vignette DT03 by direct inclusion of model code from test-model-ShaleGas.R. Test expectations replaced by stopifnot assertions to ensure that the vignette model results agree with published values. Replaced calls to knitr::kable with base R table output for purled output.
• Removed dependency on external file for vignette GT01 by direct inclusion of model code from test-model-BurgerRun.R. Test expectations replaced by stopifnot assertions to ensure that the vignette model results agree with published values. Replaced calls to knitr::kable with base R table output for purled output.
• Removed dependency on external R files from vignette SM02-TKR by direct inclusion of model code from test-model-SM02.R. Test expectations replaced by stopifnot assertions in the vignette to ensure that vignette model results agree with published values. Removed test-model-SM02.R from testthat folder. Replaced calls to pander and knitr::kable with base R table output so that tables and plots are displayed when purled code is executed using source with echo.
• Removed dependency on external R files from vignette DT02-Tegaderm by direct inclusion of model code from test-model-Tegaderm.R. Test expectations replaced by stopifnot assertions in the vignette to ensure that vignette model results agree with published values. Removed test-model-Tegaderm.R from testthat folder and added extra tests to test-DecisionTree. Replaced calls to pander and knitr::kable with base R table output so that tables and plots are displayed when purled code is executed using source with echo.
• Removed dependency on external R files from vignette SM01-HIV by direct inclusion of model code from test-model-AZT.R. Test expectations replaced by stopifnot assertions in the vignette to ensure that vignette model results agree with published values. Removed test-model-AZT.R from testthat folder. This is because some package build and check environments break during vignette building if the vignette R markdown refers to external scripts.
• Moved function gbp from vutils.R (in vignettes) to utils.R, and removed vutils.R. This function is now available to the package, and vignettes no longer need to refer to it in an external file. Removed functions gv2png and placeholder which are no longer required due to use of igraph for drawing models.
• Removed suggested package dependency on DiagrammeR and added a suggested package dependency on igraph. Diagrams of Markov models in package vignettes and readme file are now drawn with package igraph. Extra code is required to produce desired appearance, compared with using GraphViz, but the resultant image files are compact and can be generated without the need for a command line tool.
• Removed argument expressions from modvar_table in classes DecisionTree and SemiMarkovModel. This is because operands of expressions are included in the table, and it makes no sense to exclude expression model variables which depend on those operands.
• Modified modvars function in various classes to use vectorization. Added to base classes Node and Edge to avoid type checks.
• Removed name attributes from internal representation of node and edge lists provided directly or indirectly to class Graph. This was causing errors under certain circumstances when creating graphs with named lists, e.g., g <- Graph(V = list(a = nodea, b = nodeb), E = list(e = edgee)) because internal graph logic tests using identical gave false negatives.
  
• Added methods as_gml to classes Graph and Digraph for exporting of graphs in the Graph Modelling Language (GML). Graph representations written in this format can be imported to other packages, such as igraph to permit modification of nodes, edges and their attributes.
• Added parameters rankdir, width and height to function as_DOT in Graph for consistency with function of the same name in Digraph. Removed requirement for all nodes to have labels before using them by identifying nodes with their ID, and using the label attribute in the file.

rdecision 1.2.1

• Added fields URL and BugReports to DESCRIPTION file, linking to GitHub repository.
• Added method set_utility to class MarkovState to allow setting dynamically.
• Added get_cycle to class SemiMarkovModel to query the current cycle number.
• Added get_tcycle to class SemiMarkovModel to query the cycle duration.
• Added argument hcc.QALY to methods for cycling in class SemiMarkovModel. The hcc arguments control whether half cycle correction is applied to the values written to the Markov trace but do not affect the value of the end-cycle population passed to the next cycle, or when the state populations are queried. The new argument permits half cycle correction to be applied independently to the trace values of state populations, costs and QALYs, which can be useful if, for example, it is desired to display end-cycle populations with mid-cycle costs and utilities.
• Revised method draw of class DecisionTree to avoid unintentional clipping of node labels. Modified algorithm to make better use of unit conversions that are implicit in package grid and to ensure that symbols for nodes retain the correct aspect ratio when drawn in plot windows that are not square.
• Reaction edges have a default conditional probability of 0.
• Added a test to method evaluate in class DecisionTree to check that the sum of probabilities for each strategy is one, for each run. Confirmed that the check operates correctly when the conditional probabilities of traversing an edge are scalars or ModVars.
• Added facility to set the probability of at most one reaction edge from each chance node in a decision tree to NA. The missing value is replaced at each evaluation of the tree by a value which ensures that the sum of probabilities for all reaction edges leaving the node sums to unity. This avoids the need to create expression model variables to represent 1 - p where p is sampled from a Beta distribution, for example. Revised the Tegaderm vignette to demonstrate this feature.
• Disallowed use of some reserved words for decision node labels when added to a decision tree because they would conflict with column titles used during decision tree evaluation.
• Added checks to Action and Reaction to disallow values of NA for cost and benefit.
• Added set_interval to LeafNode to allow dynamic setting. Disallowed a utility of NA.

rdecision 1.2.0

• Updated citation for ProbOnto in LogNormModVar and LogNormDistribution to reference the article in BioInformatics.
• Updated URLs for GraphViz and codecov.
• Escaped brackets in Rd method documentation that are not Rd macros.
• Tidied up image file names and badges used by README.md.
• Placed code for the shale gas example in a separate script with test expectations and referenced it from the vignette to avoid code duplication in the package.
• Placed code for the New Scientist digraph puzzle in a separate script with test expectations, and referenced it from the vignette, to avoid code duplication in the package.
• Placed code for Sonnenberg and Beck’s canonical prosthetic heart valve example in a separate model script with test expectations. Referenced it in the second README example, to avoid code duplication in the package.
• Changed README decision tree code (“lifestyle” example) to reference code in a separate script (the same code used for the decision tree tutorial).
• Placed decision tree tutorial vignette code in a separate script with test_that expectations, and referenced code from the vignette’s markdown. This avoided duplication of code between the vignette and test code.
• Added method set_utility to LeafNode.
• Changed evaluate method of DecisionTree to ensure that the components of strategy labels are ordered by the lexicographical order of node labels. For example, if there is a decision node labelled d1 with emanating action edges d1a and d1b, and a decision node labelled d2 with emanating action edges d2a and d2b, the set of strategy labels is {d1a_d2a, d1a_d2b, d1b_d2a, d1b_d2b}, not {d2a_d1a, d2a_d1b, d2b_d1a, d2b_d1b}, even if node d1 has a greater index than node d2.
• Changed evaluate_walks method of DecisionTree to return the index of the leaf node for each path as the row name of the numeric matrix. Formerly it was coerced into a real value and saved in the matrix in a column called Leaf.
• Changed reset function of SemiMarkovModel to default to zero population in each state. Previously the first state was allocated 1000 people, but if vertexes were reordered, the first state is not the same as the first one provided, leading to unexpected behaviour.
• Changed postree method of Arborescence to use lexicographic order of node labels to define sibling order. Changed local array indexing to use [[]] and fixed unintentional use of array slicing under some circumstances.
• Replaced calls to par in the tornado plot section of DecisionTree with calls to withr::with_par. This avoids the need to change the global plot defaults. Package withr added to dependency list.
• Placed Tegaderm model vignette code in a separate script with test_that expectations, and referenced code from the vignette’s markdown. This reduced duplication of code between vignette and test harness.
• Added functions vertex_label and edge_label to Graph to support checked iteration of lists of nodes and edges when retrieving labels.
• Vectorized functions edge_index, edge_at and has_edge in Graph.
• Vectorized functions vertex_index, vertex_at and has_vertex in Graph.
• Added functions arrow_source and arrow_target to Digraph to support checked iteration of lists of arrows to retrieve their source or target nodes.
• Placed code for the Sumatriptan vignette into a single script with tests, (test-model-Sumatriptan.R), to avoid replicating code in test scripts.
• Added set_cost, set_benefit and set_probability to class Reaction to allow dynamic setting of costs, benefits and probabilities in decision trees without the need to rebuild the model.
• Added set_cost and set_benefit to class Action to allow dynamic setting of costs and benefits in decision trees without the need to rebuild the model.
• Created vutils.R in folder vignettes as a home for helper functions used in vignette building.
• Optimised cycling speed in SemiMarkovModel by creating private methods to manage the kernel operations of cycling the population and tallying the costs and benefits. Approx factor of 10 improvement in speed, which is helpful with PSA.
• Clarified the role of hcc.pop and hcc.cost in function cycle of SemiMarkovModel. Removed the requirement for hcc.pop to be TRUE if hcc.cost is TRUE (i.e., the corrections are applied independently).
• Combined code for Chancellor model of combination therapy for HIV into a single script with tests (test-model-AZT.R), taking code from the SM01-HIV vignette and the SemiMarkovModel test script. Non-test chunks are referenced by the vignette to avoid repetition. Edited and clarified the vignette and added PSA (as per Briggs example 4.7). Used DiagrammeR to create Markov model diagram.
• Added vignette for total knee replacement, a semi Markov model with PSA, replicating Dong and Buxton, 2006. R code is taken from chunks in a test_that context, thus avoiding repetition of code between the vignette and the test case.
• Code chunks in vignettes which are entirely presentational are marked as “purl = FALSE” to remove them from the R scripts that are generated at vignette build.
• Added arguments rankdir, width and height in Digraph::as_DOT to permit the drawing direction and size of canvas to be adjusted in the dot syntax.
• Changed the first argument in utility functions abortif and abortifnot to be ..., to increase their similarity with stopifnot, allowing testing of multiple conditions with a single call.

rdecision 1.1.3

• Method threshold in DecisionTree now has no default value for parameter outcome.
• Method chance_nodes in DecisionTree now has the option to return nodes, indices or labels, consistent with similar functions for decision nodes and leaf nodes.
• The incidence matrix of Digraph now contains integers.
• The adjacency matrices of Graph and Digraph now contain integers.
• The sample size of the empirical distribution associated with an expression model variable must be specified as an integer.
• Added utility function abortif, which is identical to abortifnot but with a negated condition. Intended to make argument checks more readable by avoiding double negatives.
• Function is_probabilistic for ExprModVar now returns correct result if the expression involves integers (previously and erroneously it returned NA).
• Function is_probabilistic for base class ModVar now returns FALSE rather then NA.
• Various internal improvements suggested by linter to increase efficiency and maintainability.
• Changed the name of function as_value to as_numeric to more accurately reflect its behaviour.

rdecision 1.1.2

• Confirmed that utilities > 1 are supported in semi Markov models and added an example to the test suite to check it. See similar notes on DecisionTree.
• Removed the warning issued if a utility value of > 1 is sampled via function MarkovState$utility.
• Confirmed that utilities > 1 are supported in decision trees and added a fictitious model to the test suite to check it. To achieve this, the utility should be defined as a model variable, e.g.  u <- ConstModVar$new(description = "", units = "", const = 2) and passed as the utility argument to LeafNode. Scalar arguments remain subject to range checking in [-Inf,1] for normal usage and to retain the previous behaviour.
• Added vectorised function as_value to return the value of an object if it is a ModVar (via its get() method) or if it is a numeric object. Intended as an internal function to avoid type testing on polymorphic variables.
• Added vectorised function is_ModVar to test whether an object is a model variable. Intended as an internal function to the package.
• Added function abortifnot (a replacement for stopifnot using rlang but with limited capability). It is a non-exported function intended for use in checking function arguments without increasing the cyclomatic complexity of the function itself.
• Clarified the documentation for argument W (list of walks) for DecisionTree$evaluate_walks. Added the alternative argument Wi in which the indices of edges in each walk are provided, to improve efficiency in avoiding repeated conversion between edges and indices during PSA. Added function edge_properties to collect information for computing path products and sums without repeated tree walking.
• Added functions vertex_along, edge_along, vertex_at and edge_at to class Graph to clarify the relationship between nodes and edges and their indices, and to help optimise iterations in graph algorithms.

rdecision 1.1.1

• Edited codecov badge reference in readme.Rmd with revised preferred URL.
• Changed citation style to one that does not write DOIs (which sometimes cause errors on CRAN checks).
• Changed difftime class checks to use inherits(), not class(), as per CRAN checks.
• Removed empty labels in blocks for DecisionTree$evaluate(), as per new CRAN warnings.
• Improved code efficiency in SemiMarkovModel$cycle() by generating intermediate results as matrices.
• Added Paola to the package author list.
• Added Paola’s Decision Tree tutorial vignette.
• Added extra tests to the test harness for ExprModVar to check that nested autocorrelation is supported (i.e. when at least one model variable appears twice or more as an operand of an expression, when it is evaluated recursively).
• Clarified the meanings of the options to set for ModVar and ExprModVar in the documentation for those classes.
• Each test in test-ExprModVar that involves sampling has an expected failure rate of around 0.1% and is excluded from CRAN.
• Each ExprModVar now has an empirical distribution, which is sampled on creation, to optimize functions mu_hat, sigma_hat and q_hat, at Paola’s suggestion.
• Added class EmpiricalDistribution and its test harness.
• Changed CohortMarkovModel to SemiMarkovModel in README.
• Corrected OccCost and EntryCost columns in SemiMarkovModel$cycle to make them per person costs.
• Default occupancy cost per state set to zero in SemiMarkovModel.

rdecision 1.1.0

• Added data/BriggsEx47, as example 4.7 from Briggs et al to /data.
• Added elementary semi-Markov model vignette (Chancellor).
• Added narrative to SemiMarkovModel as caution for converting between transition rates and per-cycle probabilities. Cited work of Jones et al
  2017. and Welton (2005) which motivated the approach taken.
• Added set_probabilities method to SemiMarkovModel to set transition probabilities from a matrix.
• Added multivariate DirichletDistribution class, mainly to support PSA in semi-Markov models.
• Refactored model variable classes into much smaller convenience classes with an underlying distribution. For example BetaModVar has a BetaDistribution uncertainty.
• Refactored ModVar with a “has-a” relationship to an underlying uncertainty distribution. Incorporated ability to link several model variables to a common underlying distribution (for use with multinomial Dirichlet etc.).
• Added distribution class DiracDistribution.
• Added subclasses of Distribution for each of the currently supported distributions (Beta, Normal, Log Normal, Gamma).
• Added base class Distribution to represent multivariate distributions.
• Added single/combined therapy HIV vignette.
• Added class SemitMarkovModel and its test script.
• Added class Transition (inherits from Node) and its test script.
• Added class MarkovState (inherits from Edge) and its test script.
• Self loops in digraphs have a value of zero in the incidence matrix.

rdecision 1.0.4

• Added option value to method set in class ModVar. This allows variables to be set to an explicit value; used in threshold finding.
• Added threshold function to DecisionTree to calculate the value of a model variable at which the cost difference becomes zero or ICER crosses a threshold.
• Added option run to by argument of DecisionTree$evaluate(). Avoids application having to reshape output before reporting PSA results.
• Fixed bug in method DecisionTree$tornado which caused bars to be clipped under some circumstances.
• Minor revisions to the Tegaderm vignette.

rdecision 1.0.3

• Package tests that involve sampling randomly from a distribution and comparing the results with parameters of an expected distribution have been excluded when running CRAN tests. Otherwise the central limit theorem or empirical distributions are used to find 99.9% confidence limits on sample mean and SD.
• Added common test helpers and bespoke expectations to testthat/setup.R.
• Changed vignette titles to reflect what kind of problem they illustrate, rather than the problems themselves, to make it clearer on the CRAN page.
• Added method as_DOT to Graph and Digraph for export to graphviz DOT file format to aid visualization of graphs.

rdecision 1.0.2

• Added tests to give 100% coverage and replaced tolerance in expect_equal with abs in expect_true for approximate equality tests.
• Further description for documentation.
• Converted vignettes to HTML.
• Added WORDLIST file and sundry administrative changes for clean package build.
• Added README file, with an example and acknowledgements.

rdecision 1.0.1

• Added draw() method to DecisionTree.
• Added tornado() method to DecisionTree for univariate sensitivity analysis.
• Optimized probabilistic sensitivity analysis loop in DecisionTree (1000 evaluations of a typical HTA tree takes < 5s on a typical PC).

rdecision 1.0.0

• First full release of the package.
• Added graph theory classes. Decision trees and Markov models are forms of graph.
• Renamed ModelVariable as ModVar for compactness, and renamed its derived classes similarly.
• Added test harnesses for more classes.
• Collected vignette citations to file references.bib and changed to BMJ csl style.
• Added extra graph theory and decision tree vignettes.

rdecision 0.1.7

• Removed the label argument from ModelVariable.
• Improved auto-detection of variable label in ModelVariable.
• Added NEWS.md and CITATION file to inst folder in CRAN preparation.
• Added tests/testthat folder with tests for ModelVariable.
• Added scripts to call devtools::check/build on Windows/Mac.
• Fixed notes issued by R CMD check.

rdecision 0.1.6

• Introduced the ModelVariable class as the new base class from which to construct the variables in an economic model. The class includes methods to support parametrization of uncertainty in the model variable.
• Introduced sub-classes of ModelVariable to model particular forms of uncertainty. These are ConstModelVariable, NormalModelVariable, GammaModelVariable, BetaModelVariable, LogNormalModelVariable. They do as expected from their names. Some support alternative forms of parametrization.
• Introduced ExpressionModelVariable. A sub-class of ModelVariable, objects of this class are defined with an expression involving other model variables. The concept permits variables to be combined in any mathematical expression that R itself will support. Because ExpressionModelVariables are themselves ModelVariables, they can can appear in an expression that is used to define another model variable.
• Introduced tabulation functions to list the properties of a model variable and its operands.
• Revised Node and its sub classes to accept ModelVariables as arguments to costs, utilities and probabilities, thus embedding probabilistic sensitivity analysis into decision tree models.
• Added the Tegaderm vignette. This is a published example of a decision tree model with PSA and is partial validation of the ModelVariable approach to PSA.
• Updated the Sumatriptan vignette, after subsuming some of its pathway traversal code into Node classes.
• Removed node.apply and path.apply functions, and subsumed them into Node.
• Removed functions intended for use with node.apply and path.apply, and subsumed them into Node.
• Provided Node objects with a Document Object Model (DOM) interface, as far as practicable.

rdecision 0.1.3

• Moved citations in vignettes from external file references.bib to directly embed them in the YAML headers. To do: explore whether references can be saved in preferred bib format.
• Replaced call to nullfile(), for suppressed output, in function des with detection of OS to support older R versions (nullfile was introduced to base R at 3.6.0).

rdecision 0.1.2

• For the Markov solver:
  • Function is now called des
  • It returns a list of summary matrices (the same ones written to csv files) instead of a single number.
  • Output can be suppressed by setting stub=NA.
  • Some minor bugs fixed.

rdecision 0.1.1

• First local release of rdecision as a package.
• Added classes for solving decision trees (Node, LeafNode, ChanceNode, DecisionNode) and pathway detection and traversal functions.
• Incorporated our discrete event solver, originally written in Matlab for the WatchBP model, then translated as a stand-alone R script, into the package.
• Added vignettes for Sumatriptan model from Briggs (Box 2.3) and from Sonnenberg and Beck’s original 3-state example.