improve docs & add documenter key (szcf-weiya/Clouds#31)

szcf-weiya · Jan 12, 2024 · 81358d1 · 81358d1
1 parent c0f1a64
commit 81358d1
Show file tree

Hide file tree

Showing 3 changed files with 28 additions and 13 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -30,14 +30,10 @@ jobs:
         r["CRAN"] = "https://cloud.r-project.org/"
         options(repos=r)
         options(download.file.method = "wget")
-        install.packages("remotes")
         install.packages("RCurl", INSTALL_opts = "--no-test-load") # required by fda
         install.packages("fda")
         install.packages("lsei")
-        install.packages("Iso")
-        install.packages("cobs")
         install.packages("splines")
-        install.packages("monmlp")
       shell: Rscript {0}
       env:
         MAKEFLAGS: LDFLAGS=-Wl,-rpath,/opt/hostedtoolcache/julia/${{ matrix.julia-version }}/x64/bin/../lib/julia/\ -L/opt/hostedtoolcache/julia/${{ matrix.julia-version }}/x64/bin/../lib/julia/
@@ -87,14 +83,10 @@ jobs:
           r["CRAN"] = "https://cloud.r-project.org/"
           options(repos=r)
           options(download.file.method = "wget")
-          install.packages("remotes")
           install.packages("RCurl", INSTALL_opts = "--no-test-load") # required by fda
           install.packages("fda")
           install.packages("lsei")
-          install.packages("Iso")
-          install.packages("cobs")
           install.packages("splines")
-          install.packages("monmlp")
         shell: Rscript {0}
         env:
           MAKEFLAGS: LDFLAGS=-Wl,-rpath,/opt/hostedtoolcache/julia/${{ matrix.julia-version }}/x64/bin/../lib/julia/\ -L/opt/hostedtoolcache/julia/${{ matrix.julia-version }}/x64/bin/../lib/julia/
@@ -105,5 +97,5 @@ jobs:
         env:
           LD_LIBRARY_PATH: /opt/R/${{ matrix.r-version }}/lib/R/lib
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
-          # DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
 
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,11 +1,13 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
 
 [compat]
 Documenter = "0.27"
+LaTeXStrings = "1.3"
 Literate = "2.14"
 Plots = "1.35"
 RCall = "0.13"
diff --git a/src/mono_decomp.jl b/src/mono_decomp.jl
@@ -545,11 +545,19 @@ function cv_mono_decomp_ss(x::AbstractVector{T}, y::AbstractVector{T}; figname =
 end
 
 """
-    benchmarking_cs(n, σ, f)
-    benchmarking_ss(n, σ, f)
-    benchmarking(f)
+    benchmarking_cs(n, σ, f; figname_cv = nothing, figname_fit = nothing)
+
+Run benchmarking experiments for decomposition with cubic splines on `n` observations sampled from curve `f` with noise `σ`.
+
+## Optional Arguments
 
-Run benchmarking experiments on `n` observations sampled from curve `f` with noise `σ`.
+- `figname_cv`: if not `nothing`, the cross-validation error will be plotted and saved to the given path.
+- `figname_fit`: if not `nothing`, the fitted curves will be plotted and saved to the given path.
+- `Js`: the candidates of number of basis functions.
+- `fixJ`: whether to use the CV-tuned `J` from the crossponding cubic spline fitting.
+- `nfold`: the number of folds in cross-validation procedure
+- `one_se_rule`: whether to use the one-standard-error rule to select the parameter after cross-validation procedure
+- `μs`: the candidates of tuning parameters for the discrepancy parameter
 """
 function benchmarking_cs(n::Int = 100, σ::Float64 = 0.5, f::Union{Function, String} = x->x^3; fixJ = true,
                                                                                figname_cv = nothing,
@@ -577,6 +585,11 @@ function benchmarking_cs(n::Int = 100, σ::Float64 = 0.5, f::Union{Function, Str
     return err
 end
 
+"""
+    benchmarking_ss(n, σ, f)
+
+Run benchmarking experiments for decomposition with smoothing splines on `n` observations sampled from curve `f` with noise `σ`.
+"""
 function benchmarking_ss(n::Int = 100, σ::Float64 = 0.5, 
                             f::Union{Function, String} = x->x^3; 
                                 nfold = 5, one_se_rule = true,
@@ -603,6 +616,14 @@ function benchmarking_ss(n::Int = 100, σ::Float64 = 0.5,
     return err
 end
 
+"""
+    benchmarking(f::String)
+
+Run benchmarking experiments for monotone decomposition on curve `f`. The candidates of `f` include:
+
+- simple functions: `x^2`, `x^3`, `exp(x)`, `sigmoid`
+- random functions generated from Gaussian Process: "SE_1" "SE_0.1" "Mat12_1" "Mat12_0.1" "Mat32_1" "Mat32_0.1" "RQ_0.1_0.5" "Periodic_0.1_4"
+"""
 function benchmarking(f::String = "x^3"; n = 100, σs = 0.2:0.2:1,
                             J = 10, 
                             μs = 10.0 .^ (-6:0.5:0), ## bspl