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LogNormModVar
and LogNormDistribution
to reference the article in BioInformatics
.test_that
expectations, and referenced code from the vignette’s markdown. This avoided duplication of code between the vignette and test code.set_utility
to LeafNode
.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
.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
.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.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.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.test_that
expectations, and referenced code from the vignette’s markdown. This reduced duplication of code between vignette and test harness.vertex_label
and edge_label
to Graph
to support checked iteration of lists of nodes and edges when retrieving labels.edge_index
, edge_at
and has_edge
in Graph
.vertex_index
, vertex_at
and has_vertex
in Graph
.arrow_source
and arrow_target
to Digraph
to support checked iteration of lists of arrows to retrieve their source or target nodes.test-model-Sumatriptan.R
), to avoid replicating code in test scripts.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.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.vutils.R
in folder vignettes as a home for helper functions used in vignette building.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.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).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.test_that
context, thus avoiding repetition of code between the vignette and the test case.rankdir
, width
and height
in Digraph::as_DOT
to permit the drawing direction and size of canvas to be adjusted in the dot syntax.abortif
and abortifnot
to be ...
, to increase their similarity with stopifnot
, allowing testing of multiple conditions with a single call.threshold
in DecisionTree
now has no default value for parameter outcome
.chance_nodes
in DecisionTree
now has the option to return nodes, indices or labels, consistent with similar functions for decision nodes and leaf nodes.Digraph
now contains integers.Graph
and Digraph
now contain integers.abortif
, which is identical to abortifnot
but with a negated condition. Intended to make argument checks more readable by avoiding double negatives.is_probabilistic
for ExprModVar
now returns correct result if the expression involves integers (previously and erroneously it returned NA).is_probabilistic
for base class ModVar
now returns FALSE
rather then NA
.as_value
to as_numeric
to more accurately reflect its behaviour.DecisionTree
.MarkovState$utility
.u <- ConstModVar$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.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.is_ModVar
to test whether an object is a model variable. Intended as an internal function to the package.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.W
(list of walks) for DecisionTree$evaluate_walks
. Added the alternative argument Wi
in which the indices of edges in each walk are provided, to improve efficiency in avoiding repeated conversion between edges and indices during PSA. Added function edge_properties
to collect information for computing path products and sums without repeated tree walking.vertex_along
, edge_along
, vertex_at
and edge_at
to class Graph
to clarify the relationship between nodes and edges and their indices, and to help optimise iterations in graph algorithms.SemiMarkovModel$cycle()
by generating intermediate results as matrices.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).set
for ModVar
and ExprModVar
in the documentation for those classes.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.EmpiricalDistribution
and its test harness.CohortMarkovModel
to SemiMarkovModel
in README.OccCost
and EntryCost
columns in SemiMarkovModel$cycle
to make them per person costs.SemiMarkovModel
.SemiMarkovModel
as caution for converting between transition rates and per-cycle probabilities. Cited work of Jones et al
set_probabilities
method to SemiMarkovModel
to set transition probabilities from a matrix.DirichletDistribution
class, mainly to support PSA in semi-Markov models.BetaModVar
has a BetaDistribution
uncertainty.ModVar
with a “has-a” relationship to an underlying uncertainty distribution. Incorporated ability to link several model variables to a common underlying distribution (for use with multinomial Dirichlet etc.).DiracDistribution
.Distribution
for each of the currently supported distributions (Beta, Normal, Log Normal, Gamma).Distribution
to represent multivariate distributions.SemitMarkovModel
and its test script.Transition
(inherits from Node
) and its test script.MarkovState
(inherits from Edge
) and its test script.value
to method set
in class ModVar
. This allows variables to be set to an explicit value; used in threshold finding.threshold
function to DecisionTree
to calculate the value of a model variable at which the cost difference becomes zero or ICER crosses a threshold.run
to by
argument of DecisionTree$evaluate()
. Avoids application having to reshape
output before reporting PSA results.DecisionTree$tornado
which caused bars to be clipped under some circumstances.testthat/setup.R
.as_DOT
to Graph
and Digraph
for export to graphviz DOT file format to aid visualization of graphs.tolerance
in expect_equal
with abs
in expect_true for approximate equality tests.WORDLIST
file and sundry administrative changes for clean package build.README
file, with an example and acknowledgements.draw()
method to DecisionTree
.tornado()
method to DecisionTree
for univariate sensitivity analysis.DecisionTree
(1000 evaluations of a typical HTA tree takes < 5s on a typical PC).ModelVariable
as ModVar
for compactness, and renamed its derived classes similarly.ModelVariable
.ModelVariable
.CITATION
file to inst folder in CRAN preparation.tests/testthat
folder with tests for ModelVariable
.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.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.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 ExpressionModelVariable
s are themselves ModelVariables
, they can can appear in an expression that is used to define another model variable.Node
and its sub classes to accept ModelVariables
as arguments to costs, utilities and probabilities, thus embedding probabilistic sensitivity analysis into decision tree models.ModelVariable
approach to PSA.Node
classes.node.apply
and path.apply
functions, and subsumed them into Node
.node.apply
and path.apply
, and subsumed them into Node
.Node
objects with a Document Object Model (DOM) interface, as far as practicable.references.bib
to directly embed them in the YAML headers. To do: explore whether references can be saved in preferred bib format.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).des
Node
, LeafNode
, ChanceNode
, DecisionNode
) and pathway detection and traversal functions.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.