Adding reference.qmd

NERC-CEH · Feb 11, 2024 · d834f43 · d834f43
1 parent 4f59c04
commit d834f43
Show file tree

Hide file tree

Showing 8 changed files with 61 additions and 5 deletions.
diff --git a/Project.toml b/Project.toml
@@ -9,6 +9,7 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NamedArrays = "86f7a689-2022-50b4-a561-43c23ac3c673"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
+Skipper = "fc65d762-6112-4b1c-b428-ad0792653d81"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -5,6 +5,7 @@ EcoVeg = "a2c99ba7-3265-411d-b6fc-9affb657b665"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NamedArrays = "86f7a689-2022-50b4-a561-43c23ac3c673"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
+Skipper = "fc65d762-6112-4b1c-b428-ad0792653d81"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
diff --git a/docs/make.jl b/docs/make.jl
@@ -15,6 +15,7 @@ makedocs(;
     ),
     pages=[
         "Home" => "index.md",
+        "Reference" => "reference.md"
     ],
 )
 

diff --git a/docs/setup_docs.jl b/docs/setup_docs.jl
@@ -12,9 +12,9 @@ setup_docs = quote
     using PrettyTables
     using Statistics
     using Suppressor
+    using Skipper
 
     # Setup:
-    theme(:wong)
     Random.seed!(2023)
     www_path = "$(pwd())/docs/src/www"
 end;
diff --git a/docs/src/_intro.qmd b/docs/src/_intro.qmd
@@ -8,8 +8,13 @@ using EcoVeg
 
 `EcoVeg.jl` is a package containing functions for the analysis of vegetation plot sample data....
 
-## Example Pluto Notebook 
+in vegetation science using the Julia programming language [@bezanson2017]
+
+Solves two language problem [@roesch2023]
 
+Aims to collate functionality found in JUICE, vegan, MAVIS into a single location with a user-friendly API and transparent methodologies.
+
+## Example Pluto Notebook 
 
 ### Local Tour
 
@@ -28,18 +33,18 @@ All notebooks are contained in `docs/pluto`.
 
 ## Installation 
 
-You can install the latest stable release from the general registry:
+To install the latest stable release of `EcoVeg`:
 
 ```{.julia}
 using Pkg
 Pkg.add("EcoVeg")
 ```
 
-The development version can be installed as follows:
+To install the development version of `Ecoveg`:
 
 ```{.julia}
 using Pkg
-Pkg.add(url="https://github.com/ZekeMarshall/EcoVeg.jl")
+Pkg.add(url="https://github.com/ZekeMarshall/EcoVeg.jl", rev = "develop")
 ```
 
 ## Usage Example 

diff --git a/docs/src/index.qmd b/docs/src/index.qmd
@@ -0,0 +1,9 @@
+```@meta
+CurrentModule = EcoVeg
+```
+
+<!-- ![](assets/wide_logo.png) -->
+
+Documentation for [EcoVeg.jl](https://github.com/ZekeMarhshall/EcoVeg.jl).
+
+{{< include _intro.qmd >}}
diff --git a/docs/src/methods/SyntopicTables.qmd b/docs/src/methods/SyntopicTables.qmd
@@ -22,6 +22,7 @@ using CSV
 using BenchmarkTools
 using SparseArrays
 using Statistics
+using Skipper
 ```
 
 ## Create example data
@@ -72,6 +73,9 @@ nzfunc(f, A; dims=:) = _nzfunc(f, A, dims)
 
 @elapsed nzfunc(minimum, mat, dims=1)
 
+@btime map(x -> minimum(skip(iszero, x)), eachcol(mat))
+@btime mapslices(x -> minimum(skip(iszero, x)), mat, dims=1)
+
 ```
 
 ## Composing a syntopic table

diff --git a/docs/src/reference.qmd b/docs/src/reference.qmd
@@ -0,0 +1,35 @@
+```@meta
+CurrentModule = EcoVeg
+```
+
+# Reference
+
+
+## Content
+
+```@contents
+Pages = ["_reference.md"]
+```
+
+## Index
+
+```@index
+```
+
+## Public Interface
+
+```@autodocs
+Modules = [
+    EcoVeg,
+]
+Private = false
+```
+
+## Internal functions
+
+```@autodocs
+Modules = [
+    EcoVeg,
+]
+Public = false
+```