Solartime

.github/workflows/CI.yml

@@ -57,6 +57,6 @@ jobs:
       - run: |
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
-            using bigleaf
-            DocMeta.setdocmeta!(bigleaf, :DocTestSetup, :(using bigleaf); recursive=true)
-            doctest(bigleaf)'
+            using Bigleaf
+            DocMeta.setdocmeta!(Bigleaf, :DocTestSetup, :(using Bigleaf); recursive=true)
+            doctest(Bigleaf)'

Project.toml

@@ -4,7 +4,13 @@ authors = ["Thomas Wutzler <twutz@bgc-jena.mpg.de> and contributors"]
 version = "0.1.0"
 
 [deps]
+AstroLib = "c7932e45-9af1-51e7-9da9-f004cd3a462b"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [compat]
 julia = "1"

README.md

@@ -1,13 +1,13 @@
-# bigleaf
+# Bigleaf
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://bgctw.github.io/bigleaf.jl/stable)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://bgctw.github.io/bigleaf.jl/dev)
-[![Build Status](https://github.com/bgctw/bigleaf.jl/workflows/CI/badge.svg)](https://github.com/bgctw/bigleaf.jl/actions)
-[![Coverage](https://codecov.io/gh/bgctw/bigleaf.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/bgctw/bigleaf.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://bgctw.github.io/Bigleaf.jl/stable)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://bgctw.github.io/Bigleaf.jl/dev)
+[![Build Status](https://github.com/bgctw/Bigleaf.jl/workflows/CI/badge.svg)](https://github.com/bgctw/Bigleaf.jl/actions)
+[![Coverage](https://codecov.io/gh/bgctw/Bigleaf.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/bgctw/Bigleaf.jl)
 
 
-**bigleaf.jl** is a partial Julia port of Jürgen Knauer's 
-[**bigleaf** R package](https://bitbucket.org/juergenknauer/bigleaf) 
+**Bigleaf.jl** is a partial Julia port of Jürgen Knauer's 
+[**bigleaf** R package](https://bitbucket.org/juergenknauer/Bigleaf) 
 for the calculation of physical (e.g. aerodynamic conductance, surface temperature) 
 and physiological (e.g. canopy conductance, water-use efficiency) ecosystem properties 
 from eddy covariance data and accompanying meteorological measurements. 
@@ -26,23 +26,23 @@ The `bigleaf.jl` R package can be installed with the usual command once:
 
 ```julia
 using Pkg
-Pkg.add(bigleaf)
+Pkg.add(Bigleaf)
 ```
 
 And then importet to the every Julia session by:
 ```julia
-using bigleaf
+using Bigleaf
 ```
 
 ## Usage
-See the [Documentation](https://bgctw.github.io/bigleaf.jl/dev/) 
-that includes a [walkthrough](https://bgctw.github.io/bigleaf.jl/dev/walkthrough/).
+See the [Documentation](https://bgctw.github.io/Bigleaf.jl/dev/) 
+that includes a [walkthrough](https://bgctw.github.io/Bigleaf.jl/dev/walkthrough/).
 
-[Please report bugs or issues here](https://github.com/bgctw/bigleaf.jl/issues)
+[Please report bugs or issues here](https://github.com/bgctw/Bigleaf.jl/issues)
 
 ## Package content 
-We are porting functionality of the [R package](https://bitbucket.org/juergenknauer/bigleaf) as needed. Please
-file an [issue](https://github.com/bgctw/bigleaf.jl/issues) if you need a specific feature.
+We are porting functionality of the [R package](https://bitbucket.org/juergenknauer/Bigleaf) as needed. Please
+file an [issue](https://github.com/bgctw/Bigleaf.jl/issues) if you need a specific feature.
 
 At the current state we ported
 - Meteorological variables

docs/make.jl

@@ -1,21 +1,21 @@
-using bigleaf
+using Bigleaf
 using Documenter, Latexify
 
 # allow plot to work without display
 # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988/2
 ENV["GKSwstype"] = "100"
 
-DocMeta.setdocmeta!(bigleaf, :DocTestSetup, :(using bigleaf, Latexify); recursive=true, warn=false)
-doctest(bigleaf, manual = false)
+DocMeta.setdocmeta!(Bigleaf, :DocTestSetup, :(using Bigleaf, Latexify); recursive=true, warn=false)
+doctest(Bigleaf, manual = false)
 
 makedocs(;
-    modules=[bigleaf],
+    modules=[Bigleaf],
     authors="Thomas Wutzler <twutz@bgc-jena.mpg.de>. Jürgen Knauer <Juergen.Knauer@csiro.au> and contributors",
-    repo="https://github.com/bgctw/bigleaf.jl/blob/{commit}{path}#{line}",
-    sitename="bigleaf.jl",
+    repo="https://github.com/bgctw/Bigleaf.jl/blob/{commit}{path}#{line}",
+    sitename="Bigleaf.jl",
     format=Documenter.HTML(;
         prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://bgctw.github.io/bigleaf.jl",
+        canonical="https://bgctw.github.io/Bigleaf.jl",
         assets=String[],
     ),
     pages=[
@@ -31,6 +31,6 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/bgctw/bigleaf.jl",
+    repo="github.com/bgctw/Bigleaf.jl",
     devbranch="main",
 )

docs/src/autodocs.md

@@ -1,11 +1,11 @@
 ```@meta
-CurrentModule = bigleaf
+CurrentModule = Bigleaf
 ```
 # Index
 ```@index
 ```
 
 # Autodocs
 ```@autodocs
-Modules = [bigleaf]
+Modules = [Bigleaf]
 ```

docs/src/bigleaf_constants.md

@@ -1,4 +1,4 @@
-## Constants used in bigleaf
+## Constants used in Bigleaf
 
 ```@docs
 bigleaf_constants

docs/src/index.md

@@ -1,9 +1,9 @@
 ```@meta
-CurrentModule = bigleaf
+CurrentModule = Bigleaf
 ```
 
-# bigleaf
-Documentation for [bigleaf](https://github.com/bgctw/bigleaf.jl).
+# Bigleaf
+Documentation for [Bigleaf](https://github.com/bgctw/Bigleaf.jl).
 
 ```@contents
 Pages = ["index.md",]

docs/src/walkthrough.md

@@ -1,26 +1,26 @@
-This vignette is a short introduction to the functionalities of the `bigleaf.jl` package. 
+This vignette is a short introduction to the functionalities of the `Bigleaf.jl` package. 
 It is directed to first-time package users who are familiar with the basic concepts of Julia. 
 After presenting the use of several key functions of the package, 
 some useful hints and guidelines are given at the end of the vignette.
 
 
 # Package scope and important conceptual considerations
 
-`bigleaf.jl` calculates physical and physiological ecosystem properties from eddy covariance data. Examples for such properties are aerodynamic and surface conductance, surface conditions(e.g. temperature, VPD), wind profile, roughness parameters, vegetation-atmosphere decoupling, potential evapotranspiration, (intrinsic) water-use efficiency, stomatal sensitivity to VPD, or intercellular CO2 concentration.  All calculations in the `bigleaf.jl` package assume that the ecosystem behaves like a  "big-leaf", i.e. a single, homogenous plane which acts as the only source and sink of the measured fluxes. This assumption comes with the advantages that calculations are simplified considerably and that (in most cases) little ancillary information on the EC sites is required. It is important to keep in mind that these simplifications go hand in hand with critical limitations. All derived variables are bulk ecosystem characteristics and have to be interpreted as such. It is for example not possible to infer within-canopy variations of a certain property.
+`Bigleaf.jl` calculates physical and physiological ecosystem properties from eddy covariance data. Examples for such properties are aerodynamic and surface conductance, surface conditions(e.g. temperature, VPD), wind profile, roughness parameters, vegetation-atmosphere decoupling, potential evapotranspiration, (intrinsic) water-use efficiency, stomatal sensitivity to VPD, or intercellular CO2 concentration.  All calculations in the `Bigleaf.jl` package assume that the ecosystem behaves like a  "big-leaf", i.e. a single, homogenous plane which acts as the only source and sink of the measured fluxes. This assumption comes with the advantages that calculations are simplified considerably and that (in most cases) little ancillary information on the EC sites is required. It is important to keep in mind that these simplifications go hand in hand with critical limitations. All derived variables are bulk ecosystem characteristics and have to be interpreted as such. It is for example not possible to infer within-canopy variations of a certain property.
 
-Please also keep in mind that the `bigleaf.jl` package does NOT provide formulations for bottom-up modelling. The principle applied here is to use an inversion approach in which ecosystem properties are inferred top-down from the measured fluxes. Such an inversion can, in principle, be also be conducted with more complex models (e.g. sun/shade or canopy/soil models), but keep in mind that these approaches also require that the additional, site-specific parameters are adequately well known. 
+Please also keep in mind that the `Bigleaf.jl` package does NOT provide formulations for bottom-up modelling. The principle applied here is to use an inversion approach in which ecosystem properties are inferred top-down from the measured fluxes. Such an inversion can, in principle, be also be conducted with more complex models (e.g. sun/shade or canopy/soil models), but keep in mind that these approaches also require that the additional, site-specific parameters are adequately well known. 
 
-The use of more detailed models is not within the scope of the `bigleaf.jl` package, but it is preferable to use such approaches when important assumptions of the "big-leaf" approach are not met. This is the case in particular when the ecosystem is sparsely covered with vegetation (low LAI, e.g. sparse crops, some savanna systems). 
+The use of more detailed models is not within the scope of the `Bigleaf.jl` package, but it is preferable to use such approaches when important assumptions of the "big-leaf" approach are not met. This is the case in particular when the ecosystem is sparsely covered with vegetation (low LAI, e.g. sparse crops, some savanna systems). 
 
 
 # Preparing the data
 
 In this tutorial, we will work with a dataset from the eddy covariance site Tharandt (DE-Tha), a spruce forest in Eastern Germany. The DataFrame `DE_Tha_Jun_2014` is downloaded from the `bigleaf` 
-[R package](https://bitbucket.org/juergenknauer/bigleaf/) repository and contains half-hourly data of meteorological and flux measurements made in June 2014. For loading the RData into Julia, see the 
-[source](https://github.com/bgctw/bigleaf.jl/blob/main/docs/src/walkthrough.md?plain=1#L26) of this file. We give the data.frame a shorter name here.
+[R package](https://bitbucket.org/juergenknauer/Bigleaf/) repository and contains half-hourly data of meteorological and flux measurements made in June 2014. For loading the RData into Julia, see the 
+[source](https://github.com/bgctw/Bigleaf.jl/blob/main/docs/src/walkthrough.md?plain=1#L26) of this file. We give the data.frame a shorter name here.
 
 ```@example doc
-using bigleaf
+using Bigleaf
 using DataFrames
 ```
 ```@setup doc
@@ -65,7 +65,7 @@ nothing # hide
 
 # General guidelines on package usage
 
-There are a few general guidelines that are important to consider when using the `bigleaf.jl` package. 
+There are a few general guidelines that are important to consider when using the `Bigleaf.jl` package. 
 
 
 ## Units
@@ -76,7 +76,7 @@ It is imperative that variables are provided in the right units, as the plausibi
 
 ## Meteorological variables
 
-The `bigleaf.jl` package provides calculation routines for a number of meteorological variables, which are basic to the calculation of many other variables. A few examples on their usage are given below:
+The `Bigleaf.jl` package provides calculation routines for a number of meteorological variables, which are basic to the calculation of many other variables. A few examples on their usage are given below:
 
 ```@example doc
 # Saturation vapor pressure (kPa) and slope of the saturation vapor pressure curve (kPa K-1)