diff --git a/README.md b/README.md
index c436c0b..2f75d0c 100644
--- a/README.md
+++ b/README.md
@@ -25,18 +25,9 @@
Prerequisites
-
- Installation
+ Basic Installation
Usage
@@ -44,23 +35,7 @@
As a Toolbox
Jupyter Notebook Examples
Using Command Line Interface (CLI)
-
- Example inputs
-
- Example outputs
-
- Configuration
-
+
Documentation
Contributing
License
@@ -104,55 +79,9 @@ Preliminary results of our first case study (for presentation use only), are sho
If you would like to generate output documents in a PDF format, you will need to install LaTeX. Without LaTeX, upon an attempt to compile the generated LaTeX source code to PDF, ```pylatex``` library implemented in this software will throw ```pylatex.errors.CompilerError```. LaTeX source file with output results will still be created but it will not be able to get compiled to PostScript or PDF.
-### LaTeX installation guidelines
-
-#### Debian-based Linux Distributions
-For basic LaTeX version (recommended)
-```bash
-sudo apt install texlive
-```
-`texlive` requires additional manual installation of the following two packages: `type1ec.sty` and `siunitx.sty`. These two packages can be installed by issuing the following commands in the Terminal:
-```bash
-sudo apt install cm-super && sudo apt install texlive-science
-```
-For full LaTeX version with all packages (requires around 2GB to download and 5GB free space on a local hard drive)
-```bash
-sudo apt install texlive-full
-```
-
-
-#### Mac OS
-BasicTeX (100MB) - minimum install without editor
-```brew
-brew install --cask basictex
-```
-MacTeX with built-in editor (3.2GB) - uses TeXLive
-```brew
-brew install --cask mactex
-```
-
-#### Windows
-For easy install, download and run [install-tl-windows.exe](https://mirror.ctan.org/systems/texlive/tlnet/install-tl-windows.exe)
-For more installation options, visit [https://tug.org/texlive/windows.html](https://tug.org/texlive/windows.html). Or, make your life easier by getting yourself a Linux. :smirk:
-
-(back to top)
-
-## Installation
-
-### From PyPi
-
-Use the package manager [pip](https://pip.pypa.io/en/stable/) to install ```reemission```.
-
-```bash
-pip install reemission
-```
-
-Type
-```bash
-pip install reemission -e .
-```
-if you'd like to use the package in a development mode.
+LaTeX installation guidelines can be found alonside the software installation guidelines in the documentation [Documentation](https://tomjanus.github.io/reemission/install.html)
+## Basic Installation
### From GitHub
1. Clone the repository using either:
@@ -171,13 +100,7 @@ if you'd like to use the package in a development mode.
```
- or as a build
```bash
- pip install build .
- ```
-
- or
-
- ```sh
- python3 -m build --sdist --wheel .
+ pip install .
```
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@@ -217,468 +140,15 @@ and
reemission-geocaret --help
```
-For more examples, please refer to the [Documentation](https://example.com)
-
-### Example inputs
-#### Input JSON file for a single reservoir
-
-```json
-{
- "Reservoir 1": {
- "coordinates": [23.698, 97.506],
- "monthly_temps": [13.9, 16.0, 19.3, 22.8, 24.2, 24.5,
- 24.2, 24.3, 23.9, 22.1, 18.5, 14.8],
- "year_vector": [1, 5, 10, 20, 30, 40, 50, 65, 80, 100],
- "gasses": ["co2", "ch4", "n2o"],
- "catchment": {
- "runoff": 1115.0,
- "area": 12582.613,
- "riv_length": 0.0,
- "population": 1587524.0,
- "area_fractions": [0.000, 0.000, 0.003, 0.002,
- 0.001, 0.146, 0.391, 0.457, 0.000],
- "slope": 23.0,
- "precip": 1498.0,
- "etransp": 1123.0,
- "soil_wetness": 144.0,
- "mean_olsen": 5.85,
- "biogenic_factors": {
- "biome": "tropical moist broadleaf",
- "climate": "temperate",
- "soil_type": "mineral",
- "treatment_factor": "primary (mechanical)",
- "landuse_intensity": "low intensity"
- }
- },
- "reservoir": {
- "volume": 7238166.0,
- "area": 1.604,
- "max_depth": 22.0,
- "mean_depth": 4.5,
- "area_fractions": [
- 0.0, 0.0, 0.0, 0.0, 0.0, 0.45, 0.15, 0.4, 0.0,
- 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
- 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
- "soil_carbon": 6.281,
- "mean_radiance": 4.66,
- "mean_radiance_may_sept": 4.328,
- "mean_radiance_nov_mar": 4.852,
- "mean_monthly_windspeed": 1.08,
- "water_intake_depth": null
- }
- },
-}
-```
-
-(back to top)
-
-### Example outputs
-#### `model.outputs` dictionary
-```json
-{"Reservoir 2": {
- "ch4_degassing": 769.76,
- "ch4_diffusion": 230.98,
- "ch4_ebullition": 210.60,
- "ch4_net": 1211.35,
- "ch4_preimp": 0.0,
- "ch4_profile": [3525.45, 3119.39, 2681.04, 1992.56, 1495.95, 1137.74, 879.35, 620.29, 461.58, 341.18],
- "ch4_total_lifetime": 5353.45,
- "ch4_total_per_year": 53534.55,
- "co2_diffusion": 994.36,
- "co2_diffusion_nonanthro": 682.41,
- "co2_minus_nonanthro": 311.95,
- "co2_net": 311.95,
- "co2_preimp": 0.00,
- "co2_profile": [2436.81, 1151.53, 776.55, 478.25,332.89, 240.93, 175.38, 104.24, 52.14, 0.00],
- "co2_total_lifetime": 1378.64,
- "co2_total_per_year": 13786.49,
- "n2o_mean": 3.610,
- "n2o_methodA": 3.61,
- "n2o_methodB": 2.24,
- "n2o_profile": [3.61, 3.61, 3.61, 3.61, 3.61, 3.61, 3.61, 3.61, 3.61, 3.61],
- "n2o_total_lifetime": 15.95,
- "n2o_total_per_year": 159.54}
-}
-```
-
-#### Outputs in JSON format
-This is a formatted output format containing the input and the output data including variable names and units.
-```json
-{
- "Reservoir 3": {
- "inputs": {
- "coordinates": {
- "name": "Reservoir coordinates (lat/lon)",
- "unit": "deg",
- "value": [23.698,97.506]},
- "monthly_temps": {
- "name": "Monthly Temperatures",
- "unit": "deg C",
- "value": [13.9,16.0,19.3,22.8,24.2,24.5,24.2,24.3,23.9,22.1,18.5,14.8]},
- "year_profile": {
- "name": "Year vector for emission profiles",
- "unit": "yr",
- "value": [1,5,10,20,30,40,50,65,80,100]},
- "gasses": {
- "name": "Calculated gas emissions",
- "unit": "-",
- "value": ["co2","ch4","n2o"]},
- "biogenic_factors": {
- "name": "Biogenic factors",
- "biome": {
- "name": "Biome",
- "unit": "",
- "value": "tropical moist broadleaf"},
- "climate": {
- "name": "Climate",
- "unit": "",
- "value": "temperate"},
- "soil_type": {
- "name": "Soil Type",
- "unit": "",
- "value": "mineral"},
- "treatment_factor": {
- "name": "Treatment Factor",
- "unit": "",
- "value": "primary (mechanical)"},
- "landuse_intensity": {
- "name": "Landuse Intensity",
- "unit": "",
- "value": "low intensity"}},
- "catchment_inputs": {
- "name": "Inputs for catchment-level process calculations",
- "runoff": {
- "name": "Annual runoff",
- "unit": "mm/year",
- "value": 1115.0},
- "area": {
- "name": "Catchment area",
- "unit": "km2",
- "value": 12582.613},
- "riv_length": {
- "name": "Length of inundated river",
- "unit": "km",
- "value": 0.0},
- "population": {
- "name": "Population",
- "unit": "capita",
- "value": 1587524.0},
- "area_fractions": {
- "name": "Area fractions",
- "unit": "-",
- "value": "0.0, 0.0, 0.003, 0.002, 0.001, 0.146, 0.391, 0.457, 0.0"},
- "slope": {
- "name": "Mean catchment slope",
- "unit": "%",
- "value": 23.0},
- "precip": {
- "name": "Mean annual precipitation",
- "unit": "mm/year",
- "value": 1498.0},
- "etransp": {
- "name": "Mean annual evapotranspiration",
- "unit": "mm/year",
- "value": 1123.0},
- "soil_wetness": {
- "name": "Soil wetness",
- "unit": "mm over profile",
- "value": 144.0},
- "mean_olsen": {
- "name": "Soil Olsen P content",
- "unit": "kgP/ha",
- "value": 5.85}},
- "reservoir_inputs": {
- "name": "Inputs for reservoir-level process calculations",
- "volume": {
- "name": "Reservoir volume",
- "unit": "m3",
- "value": 7238166.0},
- "area": {
- "name": "Reservoir area",
- "unit": "km2",
- "value": 1.604},
- "max_depth": {
- "name": "Maximum reservoir depth",
- "unit": "m",
- "value": 22.0},
- "mean_depth": {
- "name": "Mean reservoir depth",
- "unit": "m",
- "value": 4.5},
- "area_fractions": {
- "name": "Inundated area fractions",
- "unit": "-",
- "value": "0.0, 0.0, 0.0, 0.0, 0.0, 0.45, 0.15, 0.4, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0"},
- "soil_carbon": {
- "name": "Soil carbon in inundated area",
- "unit": "kgC/m2",
- "value": 6.281},
- "mean_radiance": {
- "name": "Mean monthly horizontal radiance",
- "unit": "kWh/m2/d",
- "value": 4.66},
- "mean_radiance_may_sept": {
- "name": "Mean monthly horizontal radiance: May - Sept",
- "unit": "kWh/m2/d",
- "value": 4.328},
- "mean_radiance_nov_mar": {
- "name": "Mean monthly horizontal radiance: Nov - Mar",
- "unit": "kWh/m2/d",
- "value": 4.852},
- "mean_monthly_windspeed": {
- "name": "Mean monthly wind speed",
- "unit": "m/s",
- "value": 1.08},
- "water_intake_depth": {
- "name": "Water intake depth below surface",
- "unit": "m",
- "value": null}
- }
- },
- "outputs": {
- "co2_diffusion": {
- "name": "CO2 diffusion flux",
- "gas_name": "CO2",
- "unit": "gCO2eq m-2 yr-1",
- "long_description": "Total CO2 emissions from a reservoir integrated over lifetime",
- "value": 572.82},
- "co2_diffusion_nonanthro": {
- "name": "Nonanthropogenic CO2 diffusion flux",
- "gas_name": "CO2",
- "unit": "gCO2eq m-2 yr-1",
- "long_description": "CO2 diffusion flux taken at (after) 100 years",
- "value": 393.12},
- "co2_preimp": {
- "name": "Preimpoundment CO2 emissions",
- "gas_name": "CO2",
- "unit": "gCO2eq m-2 yr-1",
- "long_description": "CO2 emission in the area covered by the reservoir prior to impoundment",
- "value": 0.0},
- "co2_minus_nonanthro": {
- "name": "CO2 emission minus non-anthropogenic",
- "gas_name": "CO2",
- "unit": "gCO2eq m-2 yr-1",
- "long_description": "CO2 emissions minus non-anthropogenic over a number of years",
- "value": 179.71},
- "co2_net": {
- "name": "Net CO2 emission",
- "gas_name": "CO2",
- "unit": "gCO2eq m-2 yr-1",
- "long_description": "Overall integrated emissions for lifetime",
- "value": 179.71},
- "co2_total_per_year": {
- "name": "Total CO2 emission per year",
- "gas_name": "CO2",
- "unit": "tCO2eq yr-1",
- "long_description": "Total CO2 emission per year integrated over lifetime",
- "value": 288.25},
- "co2_total_lifetime": {
- "name": "Total CO2 emission per lifetime",
- "gas_name": "CO2",
- "unit": "tCO2eq",
- "long_description": "Total CO2 emission integrated over lifetime",
- "value": 28.83},
- "co2_profile": {
- "name": "CO2 emission profile",
- "gas_name": "CO2",
- "unit": "gCO2eq m-2 yr-1",
- "long_description": "CO2 emission per year for a defined list of years",
- "value": [1403.78,663.36,447.35,275.51,191.77,138.8,101.04,60.05,30.04,0.0]},
- "ch4_diffusion": {
- "name": "CH4 emission via diffusion",
- "gas_name": "CH4",
- "unit": "g CO2eq m-2 yr-1",
- "long_description": "CH4 emission via diffusion integrated over a number of years.",
- "value": 222.13},
- "ch4_ebullition": {
- "name": "CH4 emission via ebullition",
- "gas_name": "CH4",
- "unit": "g CO2eq m-2 yr-1",
- "long_description": "CH4 emission via ebullition",
- "value": 321.23},
- "ch4_degassing": {
- "name": "CH4 emission via degassing",
- "gas_name": "CH4",
- "unit": "g CO2eq m-2 yr-1",
- "long_description": "CH4 emission via degassing integrated for a number of years",
- "value": 3857.24},
- "ch4_preimp": {
- "name": "Pre-impounment CH4 emission",
- "gas_name": "CH4",
- "unit": "g CO2eq m-2 yr-1",
- "long_description": "Pre-impounment CH4 emission",
- "value": 0.0},
- "ch4_net": {
- "name": "Net CH4 emission",
- "gas_name": "CH4",
- "unit": "g CO2eq m-2 yr-1",
- "long_description": "Net per area CH4 emission",
- "value": 4400.6},
- "ch4_total_per_year": {
- "name": "Total CH4 emission per year",
- "gas_name": "CH4",
- "unit": "tCO2eq yr-1",
- "long_description": "Total CH4 emission per year integrated over lifetime",
- "value": 7058.56},
- "ch4_total_lifetime": {
- "name": "Total CH4 emission per lifetime",
- "gas_name": "CH4",
- "unit": "ktCO2eq",
- "long_description": "Total CH4 emission integrated over lifetime",
- "value": 705.86},
- "ch4_profile": {
- "name": "CH4 emission profile",
- "gas_name": "CH4",
- "unit": "g CO2eq m-2 yr-1",
- "long_description": "CH4 emission per year for a defined list of years",
- "value": [13754.64,12109.16,10332.79,7542.77,5530.28,4078.62,3031.52,1981.61,1338.42,850.48]},
- "n2o_methodA": {
- "name": "N2O emission, method A",
- "gas_name": "N2O",
- "unit": "g CO2eq m-2 yr-1",
- "long_description": "N2O emission, method A",
- "value": 0.04},
- "n2o_methodB": {
- "name": "N2O emission, method B",
- "gas_name": "N2O",
- "unit": "g CO2eq m-2 yr-1",
- "long_description": "N2O emission, method B",
- "value": 0.05},
- "n2o_mean": {
- "name": "N2O emission, mean value",
- "gas_name": "N2O",
- "unit": "g CO2eq m-2 yr-1",
- "long_description": "N2O emission factor, average of two methods",
- "value": 0.04},
- "n2o_total_per_year": {
- "name": "Total N2O emission per year",
- "gas_name": "N2O",
- "unit": "tCO2eq yr-1",
- "long_description": "Total N2O emission per year integrated over lifetime",
- "value": 0.07},
- "n2o_total_lifetime": {
- "name": "Total N2O emission per lifetime",
- "gas_name": "N2O",
- "unit": "ktCO2eq",
- "long_description": "Total N2O emission integrated over lifetime",
- "value": 0.01},
- "n2o_profile": {
- "name": "N2O emission profile",
- "gas_name": "N2O",
- "unit": "g CO2eq m-2 yr-1",
- "long_description": "N2O emission per year for a defined list of years",
- "value": [0.04,0.04,0.04,0.04,0.04,0.04,0.04,0.04,0.04,0.04]}
- }
- },
-}
-```
-
-(back to top)
-
-#### Outputs in a PDF report format
-1. Input data in a tabular format in the output report in PDF format
-
-
-
-2. Output data in a tabular format in the output report in PDF format
-
-
-
-2. Output plots in the output report in PDF format
-
-
-
-(back to top)
+For more examples, please refer to the [Documentation](https://tomjanus.github.io/reemission/)
-## Configuration
-Coefficients of the regressions constituting the model as well as parameters of different categories of soil and land use are stored in a number of **yaml** files in ```parameters/emissions/```.
(back to top)
-### Configuration of inputs
-
-Information about the names and the units of the model inputs is stored and can be configured in ```config/emissions/inputs.yaml```
-e.g. for monthly temperatures which are represented in variable ```monthly_temps```:
-
-```yaml
-monthly_temps:
- include: True
- name: "Monthly Temperatures"
- long_description: ""
- unit: "deg C"
- unit_latex: "$^o$C"
-```
-
-- ```include```: (boolean): If the variable is to be included in the output files for reporting.
-- ```name```: (string): Name of the variable
-- ```long_description```: (string): Description of the variable
-- ```unit```: (string): Unit in text format
-- ```unit_latex```: (string): Unit in LaTeX format
-
-Finally, a global flag ```print_long_descriptions``` controls whether long descriptions are included alongside the included input variables in the output files.
-
-(back to top)
-
-### Configuration of outputs
-
-Similarly to inputs, definitions and units of model outputs and whether they are to be output in the output files, are stored in ```config/emissions/outputs.yaml```, e.g. for pre-impoundment CO2 emissions defined in variable ```co2_preimp```:
-```yaml
-co2_preimp:
- include: True
- name: "Preimpoundment CO2 emissions"
- gas_name: "CO2"
- name_latex: "Preimpoundment CO$_2$ emissions"
- unit: "gCO2eq m-2 yr-1"
- unit_latex: "gCO$_2$ m$^{-2}$ yr$^{-1}$"
- long_description: "CO2 emission in the area covered by the reservoir prior to impoundment"
- hint: "Negative values denote C sink (atmosphere to land flux)"
-```
-- ```include```: (boolean): If the variable is to be included in the output files for reporting.
-- ```name```: (string): Name of the variable
-- ```gas_name```: (string): Name of the gas the variable is related to
-- ```name_latex```: (string): variable name in LaTeX format
-- ```unit```: (string): Unit in text format
-- ```unit_latex```: (string): Unit in LaTeX format
-- ```long_description```: (string): Description of the variable
-- ```hint```: (string): Further information about the variable
-
-(back to top)
-
-### Configuration of global parameters
-Information about global parameters such as e.g. Global Warming Potentials ```gwp100``` is stored in ```config/emissions/parameters.yaml```
-
-```yaml
-gwp100:
- include: True
- name: "Global Warming Potential for a 100-year timescale"
- name_latex: "Global Warming Potential for a 100-year timescale"
- unit: "-"
- unit_latex: "-"
- long_description: ""
-```
-
-### Model coefficients
-Values of model coefficients, i.e. regressions used to estimate different gas emissions are stored in ```config/emissions/config.ini``` file. E.g. coefficients for CO2 emission calculations are listed below.
-```ini
-[CARBON_DIOXIDE]
-# Parameters reated to CO2 emissions
-k1_diff = 1.8569682
-age = -0.329955
-temp = 0.0332459
-resArea = 0.0799146
-soilC = 0.015512
-ResTP = 0.2263344
-calc = -0.32996
-# Conversion from mg~CO2-C~m-2~d-1 to g~CO2eq~m-2~yr-1
-# Based on stoichiometric relationship CO2/C = 44/12 and GWP100 of 1.0
-conv_coeff = 1.33833
-# Global Warming Potential of CO2 over 100 years
-co2_gwp100 = 1.0
-```
-In addition, various coefficient tables and parameters required to calculate various emission components are stored in multiple YAML files in ```parameters/emissions/```.
-
## :books: Documentation
+The software documentation can be accessed [here](https://tomjanus.github.io/reemission/)
+
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