Merge pull request #281 from ArnoStrouwen/LT

[skip ci] LanguageTool

docs/src/faq.md

@@ -36,7 +36,7 @@ jump_prob = JumpProblem(prob, Direct(), jset)
 sol = solve(jump_prob, SSAStepper())
 ```
 
-If you have many jumps in tuples or vectors it is easiest to use the keyword
+If you have many jumps in tuples or vectors, it is easiest to use the keyword
 argument-based constructor:
 ```julia
 cj1 = ConstantRateJump(rate1, affect1!)
@@ -65,7 +65,7 @@ jprob = JumpProblem(dprob, Direct(), maj,
 uses the `Xoroshiro128Star` generator from
 [RandomNumbers.jl](https://github.com/JuliaRandom/RandomNumbers.jl).
 
-On version 1.7 and up JumpProcesses uses Julia's builtin random number generator by
+On version 1.7 and up, JumpProcesses uses Julia's builtin random number generator by
 default. On versions below 1.7 it uses `Xoroshiro128Star`.
 
 ## What are these aggregators and aggregations in JumpProcesses?
@@ -76,14 +76,14 @@ jump type happens at that time. These methods are examples of stochastic
 simulation algorithms (SSAs), also known as Gillespie methods, Doob's method, or
 Kinetic Monte Carlo methods. These are all names for jump (or point) processes
 simulation methods used across the biology, chemistry, engineering, mathematics,
-and physics literature. In the JumpProcesses terminology we call such methods
+and physics literature. In the JumpProcesses terminology, we call such methods
 "aggregators", and the cache structures that hold their basic data
 "aggregations". See [Jump Aggregators for Exact Simulation](@ref) for a list of
 the available SSA aggregators.
 
 ## How should jumps be ordered in dependency graphs?
 Internally, JumpProcesses SSAs (aggregators) order all `MassActionJump`s first,
-then all `ConstantRateJumps` and/or `VariableRateJumps`. i.e. in the example
+then all `ConstantRateJumps` and/or `VariableRateJumps`. i.e., in the example
 
 ```julia
 using JumpProcesses
@@ -115,12 +115,12 @@ more on dependency graphs needed for the various SSAs.
 Callbacks can be used with `ConstantRateJump`s, `MassActionJump`s, and
 `VariableRateJump`s. When solving a pure jump system with `SSAStepper`, only
 discrete callbacks can be used (otherwise a different time stepper is needed).
-When using an ODE or SDE time stepper any callback should work.
+When using an ODE or SDE time stepper, any callback should work.
 
 *Note, when modifying `u` or `p` within a callback, you must call
 [`reset_aggregated_jumps!`](@ref) after making updates.* This ensures that the
 underlying jump simulation algorithms know to reinitialize their internal data
-structures. Leaving out this call will lead to incorrect behavior!
+structures. Omitting this call will lead to incorrect behavior!
 
 A simple example that uses a `MassActionJump` and changes the parameters at a
 specified time in the simulation using a `DiscreteCallback` is
@@ -151,10 +151,10 @@ of `u[1]`, giving
 
 ## How can I access earlier solution values in callbacks?
 When using an ODE or SDE time-stepper that conforms to the [integrator
-interface](https://docs.sciml.ai/DiffEqDocs/stable/basics/integrator/) one
+interface](https://docs.sciml.ai/DiffEqDocs/stable/basics/integrator/), one
 can simply use `integrator.uprev`. For efficiency reasons, the pure jump
 [`SSAStepper`](@ref) integrator does not have such a field. If one needs
-solution components at earlier times one can save them within the callback
+solution components at earlier times, one can save them within the callback
 condition by making a functor:
 ```julia
 # stores the previous value of u[2] and represents the callback functions

docs/src/index.md

@@ -1,8 +1,8 @@
 # JumpProcesses.jl: Stochastic Simulation Algorithms for Jump Processes, Jump-ODEs, and Jump-Diffusions
 JumpProcesses.jl, formerly DiffEqJump.jl, provides methods for simulating jump
-(or point) processes. Across different fields of science such methods are also
+(or point) processes. Across different fields of science, such methods are also
 known as stochastic simulation algorithms (SSAs), Doob's method, Gillespie
-methods, or Kinetic Monte Carlo methods . It also enables the incorporation of
+methods, or Kinetic Monte Carlo methods. It also enables the incorporation of
 jump processes into hybrid jump-ODE and jump-SDE models, including jump
 diffusions.
 
@@ -12,7 +12,7 @@ and one of the core solver libraries included in
 
 The documentation includes
 - [a tutorial on simulating basic Poisson processes](@ref poisson_proc_tutorial)
-- [a tutorial and details on using JumpProcesses to simulate jump processes via SSAs (i.e. Gillespie methods)](@ref ssa_tutorial),
+- [a tutorial and details on using JumpProcesses to simulate jump processes via SSAs (i.e., Gillespie methods)](@ref ssa_tutorial),
 - [a tutorial on simulating jump-diffusion processes](@ref jump_diffusion_tutorial),
 - [a reference on the types of jumps and available simulation methods](@ref jump_problem_type),
 - [a reference on jump time stepping methods](@ref jump_solve)
@@ -24,14 +24,14 @@ There are two ways to install `JumpProcesses.jl`. First, users may install the m
 `DifferentialEquations.jl` package, which installs and wraps `OrdinaryDiffEq.jl`
 for solving ODEs, `StochasticDiffEq.jl` for solving SDEs, and `JumpProcesses.jl`,
 along with a number of other useful packages for solving models involving ODEs,
-SDEs and/or jump process. This single install will provide the user with all of
+SDEs and/or jump process. This single install will provide the user with all
 the facilities for developing and solving Jump problems.
 
 To install the `DifferentialEquations.jl` package, refer to the following link
 for complete [installation
 details](https://docs.sciml.ai/DiffEqDocs/stable).
 
-If the user wishes to separately install the `JumpProcesses.jl` library, which is a
+If the user wishes to install the `JumpProcesses.jl` library separately, which is a
 lighter dependency than `DifferentialEquations.jl`, then the following code will
 install `JumpProcesses.jl` using the Julia package manager:
 ```julia

docs/src/jump_solve.md

@@ -18,13 +18,13 @@ use with exact simulation methods can be defined as `ConstantRateJump`s,
 τ-leaping methods should be defined as `RegularJump`s.
 
 There are special algorithms available for efficiently simulating an exact, pure
-`JumpProblem` (i.e. a `JumpProblem` over a `DiscreteProblem`).  `SSAStepper()`
+`JumpProblem` (i.e., a `JumpProblem` over a `DiscreteProblem`).  `SSAStepper()`
 is an efficient streamlined integrator for time stepping such problems from
 individual jump to jump. This integrator is named after Stochastic Simulation
 Algorithms (SSAs), commonly used naming in chemistry and biology applications
 for the class of exact jump process simulation algorithms. In turn, we denote by
 "aggregators" the algorithms that `SSAStepper` calls to calculate the next jump
-time and to execute a jump (i.e. change the system state appropriately). All
+time and to execute a jump (i.e., change the system state appropriately). All
 JumpProcesses aggregators can be used with `ConstantRateJump`s and
 `MassActionJump`s, with a subset of aggregators also working with bounded
  `VariableRateJump`s (see [the first tutorial](@ref poisson_proc_tutorial) for
@@ -35,7 +35,7 @@ performant `FunctionMap` time-stepper can be used.
 
 If there is a `RegularJump`, then inexact τ-leaping methods must be used. The
 current recommended method is `TauLeaping` if one needs adaptivity, events, etc.
-If ones only needs the most barebones fixed time-step leaping method, then
+If one only needs the most barebones fixed time-step leaping method, then
 `SimpleTauLeaping` can have performance benefits.
 
 ## Special Methods for Pure Jump Problems

docs/src/jump_types.md

@@ -39,19 +39,19 @@ jump events occur. These jumps can be specified as a [`ConstantRateJump`](@ref),
 [`MassActionJump`](@ref), or a [`VariableRateJump`](@ref).
 
 Each individual type of jump that can occur is represented through (implicitly
-or explicitly) specifying two pieces of information; a `rate` function (i.e.
+or explicitly) specifying two pieces of information; a `rate` function (i.e.,
 intensity or propensity) for the jump and an `affect!` function for the jump.
 The former gives the probability per time a particular jump can occur given the
 current state of the system, and hence determines the time at which jumps can
-happen. The later specifies the instantaneous change in the state of the system
+happen. The latter specifies the instantaneous change in the state of the system
 when the jump occurs.
 
 A specific jump type is a [`VariableRateJump`](@ref) if its rate function is
 dependent on values which may change between the occurrence of any two jump
 events of the process. Examples include jumps where the rate is an explicit
 function of time, or depends on a state variable that is modified via continuous
 dynamics such as an ODE or SDE. Such "general" `VariableRateJump`s can be
-expensive to simulate because it is necessary to take into account the (possibly
+expensive to simulate because it is necessary to consider the (possibly
 continuous) changes in the rate function when calculating the next jump time.
 
 *Bounded* [`VariableRateJump`](@ref)s represent a special subset of
@@ -84,12 +84,12 @@ discrete steps through time, over which they simultaneously execute many jumps.
 These methods can be much faster as they do not need to simulate the realization
 of every individual jump event. τ-leaping methods trade accuracy for speed, and
 are best used when a set of jumps do not make significant changes to the
-processes' state and/or rates over the course of one time-step (i.e. during a
+processes' state and/or rates over the course of one time-step (i.e., during a
 leap interval). A single [`RegularJump`](@ref) is used to encode jumps for
 τ-leaping algorithms. While τ-leaping methods can be proven to converge in the
 limit that the time-step approaches zero, their accuracy can be highly dependent
 on the chosen time-step. As a rule of thumb, if changes to the state variable
-`u` during a time-step (i.e. leap interval) are "minimal" compared to size of
+`u` during a time-step (i.e., leap interval) are "minimal" compared to the size of
 the system, an τ-leaping method can often provide reasonable solution
 approximations.
 
@@ -145,7 +145,7 @@ MassActionJump(reactant_stoich, net_stoich; scale_rates = true, param_idxs=nothi
   ``3A \overset{k}{\rightarrow} B`` the rate function would be
   `k*A*(A-1)*(A-2)/3!`. To *avoid* having the reaction rates rescaled (by `1/2`
   and `1/6` for these two examples), one can pass the `MassActionJump`
-  constructor the optional named parameter `scale_rates = false`, i.e. use
+  constructor the optional named parameter `scale_rates = false`, i.e., use
   ```julia
   MassActionJump(reactant_stoich, net_stoich; scale_rates = false, param_idxs)
   ```
@@ -158,7 +158,7 @@ MassActionJump(reactant_stoich, net_stoich; scale_rates = true, param_idxs=nothi
   net_stoich = [[1 => 1]]
   jump = MassActionJump(reactant_stoich, net_stoich; param_idxs=[1])
   ```
-  Alternatively one can create an empty vector of pairs to represent the reaction:
+  Alternatively, one can create an empty vector of pairs to represent the reaction:
   ```julia
   p = [1.]
   reactant_stoich = [Vector{Pair{Int,Int}}()]
@@ -222,7 +222,7 @@ Note that
 - It is currently only possible to simulate `VariableRateJump`s with
   `SSAStepper` when using systems with only bounded `VariableRateJump`s and the
   `Coevolve` aggregator.
-- When choosing a different aggregator than `Coevolve`, `SSAStepper` can not
+- When choosing a different aggregator than `Coevolve`, `SSAStepper` cannot
   currently be used, and the `JumpProblem` must be coupled to a continuous
   problem type such as an `ODEProblem` to handle time-stepping. The continuous
   time-stepper treats *all* `VariableRateJump`s as `ContinuousCallback`s, using
@@ -242,7 +242,7 @@ RegularJump(rate, c, numjumps; mark_dist = nothing)
   jump process
 - `c(du, u, p, t, counts, mark)` calculates the update given `counts` number of
   jumps for each jump process in the interval.
-- `numjumps` is the number of jump processes, i.e. the number of `rate`
+- `numjumps` is the number of jump processes, i.e., the number of `rate`
   equations and the number of `counts`.
 - `mark_dist` is the distribution for a mark.
 
@@ -300,24 +300,24 @@ aggregator requires various types of dependency graphs, see the next section):
   aggregator uses a different internal storage format for collections of
   `ConstantRateJumps`.
 - *`DirectCR`*: The Composition-Rejection Direct method of Slepoy et al [2]. For
-  large networks and linear chain-type networks it will often give better
+  large networks and linear chain-type networks, it will often give better
   performance than `Direct`.
 - *`SortingDirect`*: The Sorting Direct Method of McCollum et al [3]. It will
   usually offer performance as good as `Direct`, and for some systems can offer
   substantially better performance.
 - *`RSSA`*: The Rejection SSA (RSSA) method of Thanh et al [4,5]. With `RSSACR`,
-  for very large reaction networks it often offers the best performance of all
+  for very large reaction networks, it often offers the best performance of all
   methods.
 - *`RSSACR`*: The Rejection SSA (RSSA) with Composition-Rejection method of
-  Thanh et al [6]. With `RSSA`, for very large reaction networks it often offers
+  Thanh et al [6]. With `RSSA`, for very large reaction networks, it often offers
   the best performance of all methods.
 - `RDirect`: A variant of Gillespie's Direct method [1] that uses rejection to
   sample the next reaction.
 - `FRM`: The Gillespie first reaction method SSA [1]. `Direct` should generally
   offer better performance and be preferred to `FRM`.
 - `FRMFW`: The Gillespie first reaction method SSA [1] with `FunctionWrappers`.
 - *`NRM`*: The Gibson-Bruck Next Reaction Method [7]. For some reaction network
-   structures this may offer better performance than `Direct` (for example,
+   structures, this may offer better performance than `Direct` (for example,
    large, linear chains of reactions).
 - *`Coevolve`*: An adaptation of the COEVOLVE algorithm of Farajtabar et al [8].
   Currently the only aggregator that also supports *bounded*
@@ -372,7 +372,7 @@ evolution, Journal of Machine Learning Research 18(1), 1305–1353 (2017). doi:
 Italicized constant rate jump aggregators above require the user to pass a
 dependency graph to `JumpProblem`. `Coevolve`, `DirectCR`, `NRM`, and
  `SortingDirect` require a jump-jump dependency graph, passed through the named
-parameter `dep_graph`. i.e.
+parameter `dep_graph`. i.e.,
 ```julia
 JumpProblem(prob, DirectCR(), jump1, jump2; dep_graph = your_dependency_graph)
 ```
@@ -388,7 +388,7 @@ when the `i`th jump occurs. Internally, all `MassActionJump`s are ordered before
 `ConstantRateJump`s and bounded `VariableRateJump`s. General `VariableRateJump`s
 are not handled by aggregators, and so not included in the jump ordering for
 dependency graphs. Note that the relative order between `ConstantRateJump`s and
-relative order between bounded `VariableRateJump`s is preserved. In this way one
+relative order between bounded `VariableRateJump`s is preserved. In this way, one
 can precalculate the jump order to manually construct dependency graphs.
 
 `RSSA` and `RSSACR` require two different types of dependency graphs, passed
@@ -401,7 +401,7 @@ through the following `JumpProblem` kwargs:
    value, `u[i]`, altered when the jump occurs.
 
 For systems generated from a [Catalyst](https://docs.sciml.ai/Catalyst/stable/)
-`reaction_network` these will be auto-generated. Otherwise you must explicitly
+`reaction_network` these will be auto-generated. Otherwise, you must explicitly
 construct and pass in these mappings.
 
 ## Recommendations for exact methods
@@ -430,7 +430,7 @@ For systems with only `ConstantRateJump`s and `MassActionJump`s,
   often substantially outperform the other methods.
 
 For pure jump systems, time-step using `SSAStepper()` with a `DiscreteProblem`
-unless one has general (i.e. non-bounded) `VariableRateJump`s.
+unless one has general (i.e., non-bounded) `VariableRateJump`s.
 
 In general, for systems with sparse dependency graphs if `Direct` is slow, one
 of `SortingDirect`, `RSSA` or `RSSACR` will usually offer substantially better