Soil class (#25)

* soil_classes dev version

* adding soil-class dataset - temporary solution

* updating the branch and soil_class.sh to accept additional argument --include-na

* descriptions for modis and soil class updated - added info on the classification and accompanying .csv file

* adding documentation

* bumping version to 0.1.2

README.md

@@ -55,7 +55,8 @@ Script options:
 |**3**|Soil Grids (v1)				   |Not Applicable (N/A)  |4326	|10.1371/journal.pone.0169748	|[link](soil_grids)   |
 |**4**|Landsat NALCMS				   |2010 and 2015	  |4326 |10.3390/rs9111098		|[link](landsat)      |
 |**5**|Global Depth to Bedrock			   |Not Applicable (N/A)  |     |10.1002/2016MS000686		|[link](depth_to_bedrock) |
-
+|**6**|USDA Soil Class				   |Not Applicable (N/A)  |4326 |10.4211/hs.1361509511e44adfba814f6950c6e742|[link](soil_class)|
+|**7**|Global Soil Dataset for Earth System Modelling (GSDE)|Not Applicable (N/A)|4326 |10.1002/2013MS000293	|[link](GSDE)	      |
 
 # General Example 
 As an example, follow the code block below. Please remember that you MUST have access to Graham cluster with Digital Alliance of Canada and have access to `MERIT-Hydro` dataset. Also, remember to generate a [Personal Access Token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token) with GitHub in advance. Enter the following codes in your Graham shell as a test case:

VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

modis/README.md

@@ -76,3 +76,30 @@ This dataset has 1 main variable that is described in the following table:
 |-------|---------------------------------------|---------------------------------------|---------------|
 |1	|`MCD12Q1.006`				|Global land cover classes		|		|
 
+# Other relevant information
+## Land Cover Types
+Below the land cover types for each values of the `.tif` files is detailed based on [1].
+
+|Class Value (used in `gistool`)	|Name					|Land Cover Description						|
+|---------------------------------------|---------------------------------------|---------------------------------------------------------------|
+|1					|Evergreen Needleleaf Forests		|Dominated by evergreen conifer trees (canopy>2m). Tree cover>60%.|
+|2					|Evergreen Broadleaf Forests		|Dominated by evergreen broadleaf and palmate trees (canopy >2m). Tree cover >60%.|
+|3					|Deciduous Needleleaf Forests		|Dominated by deciduous needleleaf (larch) trees (canopy >2m). Tree cover >60%.|
+|4					|Deciduous Broadleaf Forests		|Dominated by deciduous broadleaf trees (canopy >2m). Tree cover >60%.|
+|5					|Mixed Forests				|Dominated by neither deciduous nor evergreen (40-60% of each) tree type (canopy >2m). Tree cover >60%.|
+|6					|Closed Shrublands			|Dominated by woody perennials (1-2m height) >60% cover.	|
+|7					|Open Shrublands			|Dominated by woody perennials (1-2m height) 10-60% cover.	|
+|8					|Woody Savannas 			|Tree cover 30-60% (canopy >2m).				|
+|9					|Savannas				|Tree cover 10-30% (canopy >2m).				|
+|10					|Grasslands				|Dominated by herbaceous annuals (<2m).				|
+|11					|Permanent Wetlands			|Permanently inundated lands with 30-60% water cover and >10% vegetated cover.|
+|12					|Croplands				|At least 60% of area is cultivated cropland.			|
+|13					|Urban and Built-up Lands		|At least 30% impervious surface area including building materials, asphalt, and vehicles.|
+|14					|Cropland/Natural Vegetation Mosaics	|Mosaics of small-scale cultivation 40-60% with natural tree, shrub, or herbaceous vegetation.|
+|15					|Permanent Snow and Ice			|At least 60% of area is covered by snow and ice for at least 10 months of the year.|
+|16					|Barren					|At least 60% of area is non-vegetated barren (sand, rock, soil) areas with less than 10% veg- etation.|
+|17					|Water Bodies				|At least 60% of area is covered by permanent wa- ter bodies.	|
+|255					|Unclassified				|Has not received a map label because of missing inputs.	|
+
+Also, the details of the above table has been included in the following files: [modis_classes.csv](./modis_classes.csv).
+

modis/modis_classes.csv

@@ -0,0 +1,18 @@
+1,Evergreen Needleleaf Forests
+2,Evergreen Broadleaf Forests
+3,Deciduous Needleleaf Forests
+4,Deciduous Broadleaf Forests 
+5,Mixed Forests
+6,Closed Shrublands
+7,Open Shrublands
+8,Woody Savannas
+9,Savannas
+10,Grasslands
+11,Permanent Wetlands
+12,Croplands
+13,Urban and Built-up Lands
+14,Cropland/Natural Vegetation Mosaics
+15,Permanent Snow and Ice
+16,Barren
+17,Water Bodies
+18,Unclassified

soil_class/README.md

@@ -0,0 +1,50 @@
+# `soil_class` Geospatial Dataset
+In this file, the necessary technical details of the dataset is explained.
+
+## Location of the `soil_class` Dataset Files
+The `soil_class` geospatial dataset files are located under the following directory accessible from Digital Research Alliance of Canada (DRA, formerly Compute Canada) Graham cluster:
+
+```console
+/project/6008034/wknoben/CWARHM_data/domain_NorthAmerica/parameters/soilclass/2_soil_classes_domain/
+```
+
+And the structure of the files is as following:
+
+```console
+/project/6008034/wknoben/CWARHM_data/domain_NorthAmerica/parameters/soilclass/2_soil_classes_domain/
+└── soil_classes.tif 
+```
+
+## Spatial and Temporal Extents
+The spatial extent of this dataset covers longitudes from approximately `-180` to `+180` degress and latitudes from approximately `-90` to `+90` degress. This dataset is static and does not vary with time. 
+
+## Dataset Variables
+This variables of this dataset are detailed in the table below:
+
+|#	|Variable Name (used in `gistool`)	|Description				|Comments	|
+|-------|---------------------------------------|---------------------------------------|---------------|
+|1      |soil-class			        |USDA soil class 			|[link](https://www.hydroshare.org/resource/1361509511e44adfba814f6950c6e742/)|
+
+
+# Other relevant information
+## Land Cover Types
+Below the land cover types for each values of the `.tif` files is detailed based on [1].
+
+|Class Value (used in `gistool`)	|Soil Type			|
+|---------------------------------------|-------------------------------|
+|0					|no class assigned		|
+|1					|Clay				|
+|2					|Clay loam			|
+|3					|Loam				|
+|4					|Loamy sand			|
+|5					|Sand				|
+|6					|Sandy clay			|
+|7					|Sandy clay loam		|
+|8					|Sandy loam			|
+|9					|Silt				|
+|10					|Silty Clay			|
+|11					|Silty clay loam		|
+|12					|Silt loam			|
+
+Also, the details of the above table has been included in the following files: [soil_classes.csv](./soil_classes.csv).
+