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Merge pull request #4 from jagoosw/1.1.0
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Changed parameter organisation
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@jagoosw
jagoosw committed Jul 6, 2022
2 parents 7f16404 + e91cd03 commit d55ece8
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Showing 10 changed files with 208 additions and 154 deletions.
4 changes: 2 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "SugarKelp"
uuid = "7cd05660-c499-409f-9aa8-d8700f4bb051"
authors = ["Jago <jagoosw@protonmail.com>"]
version = "1.0.0"
version = "1.1.0"

[deps]
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
Expand All @@ -23,4 +23,4 @@ DiffEqCallbacks = "2.17.0"
Interpolations = "0.13.4"
OrdinaryDiffEq = "5.63.5"
RecursiveArrayTools = "2.17.2"
Roots = "1.3.3"
Roots = "1.3.3"
12 changes: 5 additions & 7 deletions README.md
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Expand Up @@ -80,11 +80,10 @@ irr_itp=Interpolations.LinearInterpolation(time,irr)
u_itp=Interpolations.LinearInterpolation(time,u);
```

Now the model can be run, the parameter file must be passed and in this run the respiration model proposed in Broch, 2013 is being used

Now the model can be run, the parameter must be passed as a NamedTuple and in this run the respiration model proposed in Broch, 2013 is being used

```julia
solution, results = SugarKelp.solve(t_i, nd, u_itp, temp_itp, irr_itp, no3_itp, lat, a_0, n_0, c_0, "src/parameters/2013.jl",2);
solution, results = SugarKelp.solve(t_i, nd, u_itp, temp_itp, irr_itp, no3_itp, lat, a_0, n_0, c_0, SugarKelp.broch2013params, 2);
```

Solutions contains the raw output of the ODE solver while results is refactored into a dataframe (this can optionally be turned off for an array to be returned)
Expand All @@ -99,9 +98,8 @@ It is useful to convert the results into total carbon and nitrogen masses (rathe


```julia
include("src/parameters/2013.jl")
total_carbon = results.area .* K_A .* (results.carbon .+ C_struct)
total_nitrogen = results.area .* K_A .* (results.nitrogen .+ N_struct);
total_carbon = results.area .* SugarKelp.broch2013params.K_A .* (results.carbon .+ SugarKelp.broch2013params.C_struct)
total_nitrogen = results.area .* SugarKelp.broch2013params.K_A .* (results.nitrogen .+ SugarKelp.broch2013params.N_struct);
```


Expand Down Expand Up @@ -153,7 +151,7 @@ This function automatically parallelised to however many threads you start Julia


```julia
@time results = SugarKelp.solvegrid(t_i, nd, a_0, n_0, c_0, arr_lon, arr_lat, arr_dep, arr_t, arr_no3, arr_temp, arr_u, (arr_irr, arr_t, NaN), (nothing, nothing, nothing), arr_beta, "src/parameters/2013.jl", 2);
@time results = SugarKelp.solvegrid(t_i, nd, a_0, n_0, c_0, arr_lon, arr_lat, arr_dep, arr_t, arr_no3, arr_temp, arr_u, (arr_irr, arr_t, NaN), (nothing, nothing, nothing), arr_beta, SugarKelp.broch2013params, 2);
```
...

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8 changes: 4 additions & 4 deletions docs/src/index.md
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Expand Up @@ -74,11 +74,11 @@ irr_itp=Interpolations.LinearInterpolation(time,irr)
u_itp=Interpolations.LinearInterpolation(time,u);
```

Now the model can be run, the parameter file must be passed and in this run the resparation model proposed in Broch, 2013 is being used
Now the model can be run, the parameter must be passed as a NamedTuple and in this run the respiration model proposed in Broch, 2013 is being used


```julia
solution, results = SugarKelp.solve(t_i, nd, u_itp, temp_itp, irr_itp, no3_itp, lat, a_0, n_0, c_0, "../src/parameters/2013.jl",2);
solution, results = SugarKelp.solve(t_i, nd, u_itp, temp_itp, irr_itp, no3_itp, lat, a_0, n_0, c_0, SugarKelp.broch2013params,2);
```

Solutions contains the raw output of the ODE solver while results is refactored into a dataframe (this can optionally be turned off for an array to be returned)
Expand Down Expand Up @@ -147,11 +147,11 @@ This function automatically paralalises to however many threads you start julia


```julia
@time results = SugarKelp.solvegrid(t_i, nd, a_0, n_0, c_0, arr_lon, arr_lat, arr_dep, arr_t, arr_no3, arr_temp, arr_u, (arr_irr, arr_t, NaN), (nothing, nothing, nothing), arr_beta, "../src/parameters/2013.jl", 2);
@time results = SugarKelp.solvegrid(t_i, nd, a_0, n_0, c_0, arr_lon, arr_lat, arr_dep, arr_t, arr_no3, arr_temp, arr_u, (arr_irr, arr_t, NaN), (nothing, nothing, nothing), arr_beta, SugarKelp.broch2013params, 2);
```
...

The output from this is an array with area/nitrogen reserve/carbon reserve/nitrate uptake in the first dimention, then lon,lat,dep,time in the others. We can extract the total carbon and nitrogen again:
The output from this is an array with area/nitrogen reserve/carbon reserve/nitrate uptake in the first dimension, then lon,lat,dep,time in the others. We can extract the total carbon and nitrogen again:


```julia
Expand Down
13 changes: 6 additions & 7 deletions examples/example.ipynb
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Expand Up @@ -121,7 +121,7 @@
"cell_type": "code",
"execution_count": 6,
"source": [
"solution, results = SugarKelp.solve(t_i, nd, u_itp, temp_itp, irr_itp, no3_itp, lat, a_0, n_0, c_0, \"../src/parameters/2013.jl\",2);"
"solution, results = SugarKelp.solve(t_i, nd, u_itp, temp_itp, irr_itp, no3_itp, lat, a_0, n_0, c_0, SugarKelp.broch2013params,2);"
],
"outputs": [],
"metadata": {}
Expand Down Expand Up @@ -234,9 +234,8 @@
"cell_type": "code",
"execution_count": 8,
"source": [
"include(\"../src/parameters/2013.jl\")\n",
"total_carbon = results.area .* K_A .* (results.carbon .+ C_struct)\n",
"total_nitrogen = results.area .* K_A .* (results.nitrogen .+ N_struct);"
"total_carbon = results.area .* SugarKelp.broch2013params.K_A .* (results.carbon .+ SugarKelp.broch2013params.C_struct)\n",
"total_nitrogen = results.area .* SugarKelp.broch2013params.K_A .* (results.nitrogen .+ SugarKelp.broch2013params.N_struct);"
],
"outputs": [],
"metadata": {}
Expand Down Expand Up @@ -324,7 +323,7 @@
"cell_type": "code",
"execution_count": 12,
"source": [
"@time results = SugarKelp.solvegrid(t_i, nd, a_0, n_0, c_0, arr_lon, arr_lat, arr_dep, arr_t, arr_no3, arr_temp, arr_u, (arr_irr, arr_t, NaN), (nothing, nothing, nothing), arr_beta, \"../src/parameters/2013.jl\", 2);"
"@time results = SugarKelp.solvegrid(t_i, nd, a_0, n_0, c_0, arr_lon, arr_lat, arr_dep, arr_t, arr_no3, arr_temp, arr_u, (arr_irr, arr_t, NaN), (nothing, nothing, nothing), arr_beta, SugarKelp.broch2013params, 2);"
],
"outputs": [
{
Expand Down Expand Up @@ -388,8 +387,8 @@
"cell_type": "code",
"execution_count": 13,
"source": [
"total_carbon = results[1,:,:,:,:] .* K_A .* (results[3,:,:,:,:] .+ C_struct)\n",
"total_nitrogen = results[1,:,:,:,:] .* K_A .* (results[2,:,:,:,:] .+ N_struct);"
"total_carbon = results[1,:,:,:,:] .* SugarKelp.broch2013params.K_A .* (results[3,:,:,:,:] .+ SugarKelp.broch2013params.C_struct)\n",
"total_nitrogen = results[1,:,:,:,:] .* SugarKelp.broch2013params.K_A .* (results[2,:,:,:,:] .+ SugarKelp.broch2013params.N_struct);"
],
"outputs": [],
"metadata": {}
Expand Down
2 changes: 1 addition & 1 deletion examples/paper.jl
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Expand Up @@ -25,7 +25,7 @@ irr_arr = Interpolations.LinearInterpolation(irr_t, irr, extrapolation_bc=Flat()

a_0 = 30;n_0 = 0.01;c_0 = 0.6

solution, results = SugarKelp.solve(t_i, nd, u_arr, temp_arr, irr_arr, no3_arr, lat, a_0, n_0, c_0, "../src/parameters/2013.jl", 1)
solution, results = SugarKelp.solve(t_i, nd, u_arr, temp_arr, irr_arr, no3_arr, lat, a_0, n_0, c_0, SugarKelp.broch2013params, 1)

# Horrible plotting and loading/inline horriblness from their paper from here down
pyplot()
Expand Down
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Registration pull request created: JuliaRegistries/General/63774

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v1.1.0 -m "<description of version>" d55ece871a3c8bc9d452560c3efa8155451a1a33
git push origin v1.1.0

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