Use latest fsdocs

.config/dotnet-tools.json

@@ -14,17 +14,17 @@
         "paket"
       ]
     },
-    "fsharp.formatting.commandtool": {
-      "version": "11.4.3",
-      "commands": [
-        "fsdocs"
-      ]
-    },
     "fantomas": {
       "version": "6.3.1",
       "commands": [
         "fantomas"
       ]
+    },
+    "fsdocs-tool": {
+      "version": "20.0.0",
+      "commands": [
+        "fsdocs"
+      ]
     }
   }
 }

build.fsx

@@ -97,7 +97,7 @@ Target.create "RunTests" (fun _ ->
     let rHome = Environment.environVarOrFail "R_HOME"
     Trace.logf "R_HOME is set as %s" rHome
     let result = Fake.DotNet.DotNet.exec (fun args -> 
-        { args with Verbosity = Some Fake.DotNet.DotNet.Verbosity.Normal}) "test" ("bristlecone.sln")
+        { args with Verbosity = Some Fake.DotNet.DotNet.Verbosity.Normal}) "run" ("--project tests/Bristlecone.Tests")
     if result.ExitCode <> 0 then failwith "Tests failed"
 )
 
@@ -157,9 +157,9 @@ Target.create "DocsMeta" (fun _ ->
       sprintf "<PackageIconUrl>%s/master/docs/content/logo.png</PackageIconUrl>" repositoryContentUrl
       sprintf "<PackageTags>%s</PackageTags>" tags
       sprintf "<Version>%s</Version>" release.NugetVersion
-      sprintf "<FsDocsLogoSource>%s/master/docs/img/logo.png</FsDocsLogoSource>" repositoryContentUrl
-      sprintf "<FsDocsLicenseLink>%s/blob/master/LICENSE.md</FsDocsLicenseLink>" repositoryUrl
-      sprintf "<FsDocsReleaseNotesLink>%s/blob/master/RELEASE_NOTES.md</FsDocsReleaseNotesLink>" repositoryUrl
+      sprintf "<FsDocsLogoSource>/img/logo.png</FsDocsLogoSource>"
+      sprintf "<FsDocsLicenseLink>%s/blob/master/LICENSE</FsDocsLicenseLink>" repositoryUrl
+      sprintf "<FsDocsReleaseNotesLink>%s/blob/master/RELEASE_NOTES.MD</FsDocsReleaseNotesLink>" repositoryUrl
       "<FsDocsWarnOnMissingDocs>true</FsDocsWarnOnMissingDocs>"
       "<FsDocsTheme>default</FsDocsTheme>"
       "</PropertyGroup>"
@@ -169,7 +169,7 @@ Target.create "DocsMeta" (fun _ ->
 
 Target.create "GenerateDocs" (fun _ ->
    Fake.IO.Shell.cleanDir ".fsdocs"
-   DotNet.exec id "fsdocs" "build --clean" |> ignore
+   DotNet.exec id "fsdocs" "build --clean --eval --strict" |> ignore
 )
 
 // --------------------------------------------------------------------------------------

docs/_head.html

@@ -0,0 +1 @@
+<script src="https://cdn.plot.ly/plotly-2.21.0.min.js"></script>

docs/confidence-intervals.fsx

@@ -12,11 +12,11 @@ index: 5
 #r "../src/Bristlecone/bin/Release/netstandard2.0/Bristlecone.dll"
 (*** condition: fsx ***)
 #if FSX
-#r "nuget: Bristlecone,{{package-version}}"
+#r "nuget: Bristlecone,{{fsdocs-package-version}}"
 #endif // FSX
 (*** condition: ipynb ***)
 #if IPYNB
-#r "nuget: Bristlecone,{{package-version}}"
+#r "nuget: Bristlecone,{{fsdocs-package-version}}"
 #endif // IPYNB
 
 (**
@@ -37,20 +37,20 @@ open Bristlecone
 open Bristlecone.Optimisation
 open Bristlecone.Data
 
-// fitFn = 
-fun engine dataset hypothesis result ->
+// // fitFn = 
+// fun engine dataset hypothesis result ->
 
-    // The function used to fit the model, which unless an
-    // advanced scenario is usually Bristlecone.fit
-    let fitFn = Bristlecone.fit
+//     // The function used to fit the model, which unless an
+//     // advanced scenario is usually Bristlecone.fit
+//     let fitFn = Bristlecone.fit
 
-    // The number of jumps to perform in parameter space
-    let n = 10000
+//     // The number of jumps to perform in parameter space
+//     let n = 10000
 
-    let ci = ConfidenceInterval.ProfileLikelihood.profile fitFn engine dataset hypothesis n result
+//     let ci = ConfidenceInterval.ProfileLikelihood.profile fitFn engine dataset hypothesis n result
 
-    // Optionally, save the result
-    let saveDir = "/some/save/dir"
-    let subjectName = "some subject"
-    let modelId = "some model hypothesis"
-    Confidence.save saveDir subjectName modelId result.ResultId ci
+//     // Optionally, save the result
+//     let saveDir = "/some/save/dir"
+//     let subjectName = "some subject"
+//     let modelId = "some model hypothesis"
+//     Confidence.save saveDir subjectName modelId result.ResultId ci

docs/data.fsx

@@ -3,7 +3,7 @@
 title: Loading and Saving Data
 category: Techniques
 categoryindex: 2
-index: 1
+index: 6
 ---
 *)
 
@@ -12,11 +12,11 @@ index: 1
 #r "../src/Bristlecone/bin/Release/netstandard2.0/Bristlecone.dll"
 (*** condition: fsx ***)
 #if FSX
-#r "nuget: Bristlecone,{{package-version}}"
+#r "nuget: Bristlecone,{{fsdocs-package-version}}"
 #endif // FSX
 (*** condition: ipynb ***)
 #if IPYNB
-#r "nuget: Bristlecone,{{package-version}}"
+#r "nuget: Bristlecone,{{fsdocs-package-version}}"
 #endif // IPYNB
 
 (**

docs/dendro.fsx

@@ -11,11 +11,11 @@ index: 1
 #r "../src/Bristlecone/bin/Release/netstandard2.0/Bristlecone.dll"
 (*** condition: fsx ***)
 #if FSX
-#r "nuget: Bristlecone,{{package-version}}"
+#r "nuget: Bristlecone,{{fsdocs-package-version}}"
 #endif // FSX
 (*** condition: ipynb ***)
 #if IPYNB
-#r "nuget: Bristlecone,{{package-version}}"
+#r "nuget: Bristlecone,{{fsdocs-package-version}}"
 #endif // IPYNB
 
 (**

docs/diagnostics.fsx

@@ -12,11 +12,11 @@ index: 5
 #r "../src/Bristlecone/bin/Release/netstandard2.0/Bristlecone.dll"
 (*** condition: fsx ***)
 #if FSX
-#r "nuget: Bristlecone,{{package-version}}"
+#r "nuget: Bristlecone,{{fsdocs-package-version}}"
 #endif // FSX
 (*** condition: ipynb ***)
 #if IPYNB
-#r "nuget: Bristlecone,{{package-version}}"
+#r "nuget: Bristlecone,{{fsdocs-package-version}}"
 #endif // IPYNB
 
 (**
@@ -69,9 +69,9 @@ of the `IComponentLogger<float>)` type:
 [ NB TODO: This function must be refactored to work with the new Bristlecone Language ]
 *)
 
-open Bristlecone
-open Bristlecone.Language
-open Bristlecone.Diagnostics.ModelComponents
+// open Bristlecone
+// open Bristlecone.Language
+// open Bristlecone.Diagnostics.ModelComponents
 
 // let hypothesis (cLog:IComponentLogger<ModelExpression>) =
 

docs/estimation-engine.fsx

@@ -12,11 +12,11 @@ index: 3
 #r "../src/Bristlecone/bin/Release/netstandard2.0/Bristlecone.dll"
 (*** condition: fsx ***)
 #if FSX
-#r "nuget: Bristlecone,{{package-version}}"
+#r "nuget: Bristlecone,{{fsdocs-package-version}}"
 #endif // FSX
 (*** condition: ipynb ***)
 #if IPYNB
-#r "nuget: Bristlecone,{{package-version}}"
+#r "nuget: Bristlecone,{{fsdocs-package-version}}"
 #endif // IPYNB
 
 (**
@@ -31,4 +31,49 @@ will suffice for all model hypotheses.
 
 Forthcoming
 
-*)
+*)
+
+
+(**## Time Modes
+
+Bristlecone can run models in either discrete time, or continuous time. When running models in continuous time, an integration function is required:
+*)
+
+(**
+Currently only fixed timesteps are supported, but variable timestep support (e.g. for sediment core data) is planned. 
+
+Two integration functions are included:
+
+| Solver | Function | Description |
+| - | - | - |
+| Runge-Kutta 4 (MathNet Numerics) | ``Integration.MathNet.integrate`` | A fourth-order Runge Kutta method to provide approximate solutions to ODE systems. |
+| Runge-Kutta 547M (Open Solving Library for ODEs - Microsoft Research) | ``Integration.MsftOslo.integrate`` | A method based on classic Runge-Kutta, but with automatic error and step size control. [See the documentation](https://www.microsoft.com/en-us/research/wp-content/uploads/2014/07/osloUserGuide.pdf).|
+
+## Optimisation
+
+Bristlecone supports optimisation functions that have the following type signature:
+
+```fsharp
+type Optimise<'data> = int -> int -> Domain -> ('data[] -> 'data) -> ('data * 'data []) list
+```
+
+There are two optimsation techniques currently built-in:
+
+| Method | Function | Description |
+| - | - | - |
+| Amoeba (Nelder-Mead) | ``Optimisation.Amoeba.solve`` | A gradient-descent method. |
+| MCMC Random Walk | ``Optimisation.MonteCarlo.randomWalk`` | A method based on classic Runge-Kutta, but with automatic error and step size control. [See the documentation](https://www.microsoft.com/en-us/research/wp-content/uploads/2014/07/osloUserGuide.pdf).|
+
+
+## Estimation Engines
+
+To use Bristlecone functions requires a configured ``EstimationEngine``. The easiest way is with the helper functions within the ``Bristlecone`` module:
+
+| Function | Type | Description |
+| - | - | - |
+| ``mkContinuous`` | EstimationEngine | Default continuous engine |
+| ``mkDiscrete`` | EstimationEngine | Default discrete model engine |
+| ``withContinuousTime`` | t : Integrate<'a,'b> -> engine: EstimationEngine<'a,'b> -> EstimationEngine<'a,'b> | Transforms engine to continuous time mode, using the given integrator function. |
+| ``withConditioning`` | c: Conditioning -> engine: EstimationEngine<'a,'b> -> EstimationEngine<'a,'b> | Choose how the start point is chosen when solving the model system. |
+
+**)