v2 release

.gitignore

@@ -1,16 +1,13 @@
-data/datasets/modified
 notes/
 data/maxent_src/out/java_first_run
 data/phytoclass/
 sophy.db
-test.db
-data/datasets/unmodified/righetti2020/Phytoplankton_harmonized_database_revised.csv
+data/datasets/unmodified/phytobase/Phytoplankton_harmonized_database_revised.csv
 data/datasets/unmodified/davies2016/The_Australian_Phytoplankton_Database_(1844_-_2016)_-_abundance_and_biovolume_(SUPERSEDED_BY_ONGOING_COLLECTION).csv
 sophy/utils/__pycache__/
-sophy/utils/sophy2.xlsx
-sophy/utils/test.db
+sophy/transformations/__pycache__/
+sophy/utils/sophytest.xlsx
+sophy/utils/sophytest.db
 .idea/
 .DS_Store
-
-# while working ignore the entire maxent_src directory
-# comment out when pushing to github
+*.log

README.md

@@ -8,7 +8,7 @@ In situ observations combined with phytoplankton taxonomies, ocean fronts, and o
 - Built with SQLite and Python
 - Helper functions to make accessing data easy
 - Visualizations to see data over time, regions, and biological parameters
-- Data: [sophy.xlsx](data/out/sophy.xlsx)
+- Data: [sophy.xlsx](sophy.xlsx)
 
 <p align="center">
   <img 
@@ -24,7 +24,7 @@ Create new environment
 To explore the data in table form through a web browser using [Datasette](https://datasette.io/)
 1) ```conda create -n sophyvenv datasette pandas jupyter tqdm```
 2) ```conda activate sophyvenv```
-3) Run the cell for Option 1 in [sophy.ipynb](sophy/sophy.ipynb) to build sophy.db
+3) Run the cell for Option 1 in [sophy.ipynb](examples/sophy_example.ipynb) to build sophy.db
 4) ```datasette sophy.db -o```
 
 
@@ -37,7 +37,7 @@ To explore the data in table form through a web browser using [Datasette](https:
 To visualize the data using a Jupyter Notebook
 1) ```conda create -n sophyvenv geopandas cartopy jupyter seaborn tqdm```
 2) ```conda activate sophyvenv```
-3) Follow the steps in [sophy.ipynb](sophy/sophy.ipynb) for sample queries and plotting
+3) Follow the steps in [sophy.ipynb](examples/sophy_example.ipynb) for sample queries and plotting
 
 <p align="center">
   <img 
@@ -47,9 +47,12 @@ To visualize the data using a Jupyter Notebook
 
 # Data Sources
 - Palmer Station Antartica LTER (lter)
-  - Citation: Palmer Station Antarctica LTER and N. Waite. 2022. Merged discrete water-column data from annual PAL LTER field seasons at Palmer Station, Antarctica, from 1991 to 2021. ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/7358be99bd7ec1c73293893defb289d3 (Accessed 2023-02-13).
+  - Palmer Station Antarctica LTER and N. Waite. 2022. Merged discrete water-column data from annual PAL LTER field seasons at Palmer Station, Antarctica, from 1991 to 2021. ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/7358be99bd7ec1c73293893defb289d3 (Accessed 2023-02-13).
 - Phytobase (phytobase)
-  - Citation: Righetti, D., Vogt, M., Zimmermann, N. E., Guiry, M. D., and Gruber, N.: PhytoBase: A global synthesis of open-ocean phytoplankton occurrences, Earth Syst. Sci. Data, 12, 907–933, https://doi.org/10.5194/essd-12-907-2020, 2020.
-- Joy-Warren 2019 (joyw)
-  - Joy‐Warren, Hannah L., et al. "Light is the primary driver of early season phytoplankton production along the Western Antarctic Peninsula." Journal of Geophysical Research: Oceans 124.11 (2019): 7375-7399.
+  - Righetti, D., Vogt, M., Zimmermann, N. E., Guiry, M. D., and Gruber, N.: PhytoBase: A global synthesis of open-ocean phytoplankton occurrences, Earth Syst. Sci. Data, 12, 907–933, https://doi.org/10.5194/essd-12-907-2020, 2020.
+- AMT Cruises (AMT)
+  - Rees, A., Robinson, C., Smyth, T., Aiken, J., Nightingale, P., & Zubkov, M. (2015). 20 years of the Atlantic Meridional Transect-AMT. Limnology and Oceanography Bulletin, 24(4), 101-107.
+  - https://doi.org/10.1002/lob.10069
+  - https://www.amt-uk.org/
+
 Note: This database modifies the original datasets and is NOT a replacement for the original datasets.