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Ability to change date modes in time-series types (#30)
* [WIP] Old dates support in Time * [WIP] no errors in time module * [WIP] Refactoring for new time format * [WIP] New time format compiles * New time tests pass * Fantomas formatted * Time tests passing * Benchmarks run again * Annual mode and subsequently reworked dendro functions * Sunrise tests * Fix orchestrator with new timemodes * Basic time-series docs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| (** | ||
| --- | ||
| title: Time-Series and Time-Frames | ||
| category: Components | ||
| categoryindex: 4 | ||
| index: 1 | ||
| --- | ||
| []({{root}}/{{fsdocs-source-basename}}.fsx)  | ||
| []({{root}}/{{fsdocs-source-basename}}.ipynb) | ||
| *) | ||
|
|
||
| (*** condition: prepare ***) | ||
| #nowarn "211" | ||
| #r "../src/Bristlecone/bin/Debug/netstandard2.0/Bristlecone.dll" | ||
| (*** condition: fsx ***) | ||
| #if FSX | ||
| #r "nuget: Bristlecone,{{fsdocs-package-version}}" | ||
| #endif // FSX | ||
| (*** condition: ipynb ***) | ||
| #if IPYNB | ||
| #r "nuget: Bristlecone,{{fsdocs-package-version}}" | ||
| #endif // IPYNB | ||
|
|
||
| (** | ||
| Time-series and time-frames | ||
| ======================== | ||
| Bristlecone includes core representations of time-series,, time-frames, and | ||
| time indexes. | ||
| A key concept is the date mode. Bristlecone supports using different modes of measuring | ||
| time, from simple `DateTime` representation (calendar time) to various dating methods | ||
| commonly used in long-term ecology and archaeology. | ||
| The time-related types are included in the `Bristlecone.Time` module: | ||
| *) | ||
|
|
||
| open System | ||
| open Bristlecone | ||
| open Bristlecone.Time | ||
|
|
||
| (*** | ||
| ## Time Series | ||
| A time-series is a representation of data ordered in time by the date | ||
| of observation. | ||
| ### From calendar-date observations | ||
| Time-series may be created from date-time observations using built-in .NET | ||
| types and the `TimeSeries.fromNeoObservations` function: | ||
| *) | ||
|
|
||
| let someObservations = [ | ||
| 2.1, DateTime(2020, 03, 21) | ||
| 5.4, DateTime(2020, 03, 22) | ||
| -54.2, DateTime(2020, 03, 23) | ||
| ] | ||
|
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| let ts = TimeSeries.fromNeoObservations someObservations | ||
| (*** include-value: ts ***) | ||
|
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| (** | ||
| ### From radiocarbon dates | ||
| As an example of an alternative date format, uncalibrated radiocarbon dates | ||
| may be used as follows: | ||
| *) | ||
|
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| let someDatedValues = [ | ||
| 1654, DatingMethods.Radiocarbon 345<``BP (radiocarbon)``> | ||
| 982, DatingMethods.Radiocarbon -2<``BP (radiocarbon)``> | ||
| 5433, DatingMethods.Radiocarbon 1023<``BP (radiocarbon)``> | ||
| ] | ||
|
|
||
| let tsRadiocarbon = TimeSeries.fromObservations DateMode.radiocarbonDateMode someDatedValues | ||
| (*** include-value: tsRadiocarbon ***) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,45 +1,58 @@ | ||
| namespace Bristlecone.Data | ||
|
|
||
| open Bristlecone | ||
| open Bristlecone.Time | ||
| open Bristlecone.Dendro | ||
|
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| module PlantIndividual = | ||
|
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| open FSharp.Data | ||
|
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| type RingWidthData = CsvProvider<"data-types/ring-width.csv"> | ||
| type EnvironmentVariableData = CsvProvider<"data-types/env-variable.csv"> | ||
|
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| let loadRingWidths (fileName: string) = | ||
| let data = RingWidthData.Load fileName | ||
|
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| data.Rows | ||
| |> Seq.groupBy (fun row -> row.``Plant Code``) | ||
| |> Seq.map (fun (code, rows) -> | ||
| let growth = | ||
| open Bristlecone | ||
| open Bristlecone.Time | ||
| open Bristlecone.Dendro | ||
| open Bristlecone.Dendro.Units | ||
|
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| /// Load plant-specific time-series from CSV files. | ||
| module Csv = | ||
|
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| open FSharp.Data | ||
|
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| type RingWidthData = CsvProvider<"data-types/ring-width.csv"> | ||
| type EnvironmentVariableData = CsvProvider<"data-types/env-variable.csv"> | ||
|
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| /// <summary>Load ring widths from a CSV file that contains 'Year', 'Plant Code', | ||
| /// and 'Increment (mm)' columns.</summary> | ||
| /// <param name="csvFileName">The file to load</param> | ||
| /// <returns>A plant individual containing the growth series.</returns> | ||
| let loadRingWidths (csvFileName: string) = | ||
| let data = RingWidthData.Load csvFileName | ||
|
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||
| data.Rows | ||
| |> Seq.groupBy (fun row -> row.``Plant Code``) | ||
| |> Seq.map (fun (code, rows) -> | ||
| let growth = | ||
| rows | ||
| |> Seq.sortBy (fun i -> i.Year) | ||
| |> Seq.map (fun i -> | ||
| (float i.``Increment (mm)`` * 1.<millimetre / year>, i.Year * 1<year> |> DatingMethods.Annual)) | ||
| |> TimeSeries.fromObservations DateMode.annualDateMode | ||
| |> GrowthSeries.Absolute | ||
| |> PlantIndividual.PlantGrowth.RingWidth | ||
|
|
||
| { Identifier = code |> ShortCode.create |> Option.get | ||
| Growth = growth | ||
| InternalControls = [] |> Map.ofList | ||
| Environment = [] |> Map.ofList } | ||
| : PlantIndividual.PlantIndividual<DatingMethods.Annual, int<year>, int<year>>) | ||
| |> Seq.toList | ||
|
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| /// <summary>Load plant-specific environmental time-series from | ||
| /// a CSV file, where all time-series are specified in a single CSV.</summary> | ||
| /// <param name="fileName">The CSV file to load from.</param> | ||
| /// <returns>A map of time-series by their plant individual.</returns> | ||
| let loadPlantSpecificEnvironments (fileName: string) = | ||
| let data = EnvironmentVariableData.Load fileName | ||
|
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||
| data.Rows | ||
| |> Seq.groupBy (fun row -> row.``Plant Code``) | ||
| |> Seq.map (fun (code, rows) -> | ||
| code, | ||
| rows | ||
| |> Seq.sortBy (fun i -> i.Date) | ||
| |> Seq.map (fun i -> (float i.``Increment (mm)`` * 1.<mm>, i.Date)) | ||
| |> TimeSeries.fromObservations | ||
| |> GrowthSeries.Absolute | ||
| |> PlantIndividual.RingWidth | ||
|
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| { Identifier = code |> ShortCode.create |> Option.get | ||
| Growth = growth | ||
| InternalControls = [] |> Map.ofList | ||
| Environment = [] |> Map.ofList } | ||
| : PlantIndividual.PlantIndividual) | ||
| |> Seq.toList | ||
|
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| let loadLocalEnvironmentVariable (fileName: string) = | ||
| let data = EnvironmentVariableData.Load fileName | ||
|
|
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| data.Rows | ||
| |> Seq.groupBy (fun row -> row.``Plant Code``) | ||
| |> Seq.map (fun (code, rows) -> | ||
| code, | ||
| rows | ||
| |> Seq.map (fun i -> float i.Predictor, i.Date) | ||
| |> TimeSeries.fromObservations) | ||
| |> Seq.toList | ||
| |> Seq.map (fun i -> float i.Predictor, i.Year * 1<year> |> DatingMethods.Annual) | ||
| |> TimeSeries.fromObservations DateMode.annualDateMode) | ||
| |> Seq.toList |
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