media-design 1.0.0__tar.gz

media_design-1.0.0/PKG-INFO

@@ -0,0 +1,26 @@
+Metadata-Version: 2.4
+Name: media-design
+Version: 1.0.0
+Summary: Provides tools for making geochemically informed microbial media.
+Author-email: Siena Smania <siena.smania@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/s-smania/Microbial-Media-Tools
+Project-URL: Issues, https://github.com/s-smania/Microbial-Media-Tools/issues
+Keywords: geochemistry,microbiology,media
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: numpy<2.0,>=1.23
+Requires-Dist: pandas<2.3,>=2.0
+Requires-Dist: scipy<2.0,>=1.9
+Requires-Dist: matplotlib<4.0,>=3.7
+Requires-Dist: ipython<9,>=8
+Provides-Extra: geochem
+Requires-Dist: aqequil>=1.2; extra == "geochem"
+Requires-Dist: pychnosz>=1.2; extra == "geochem"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+
+# Microbial-Media-Tools
+Computational tools for designing geochemically informed microbial media. Converts environmental chemistry into lab recipes, calculates ion compositions of existing recipes, and enables downstream analysis of speciation and redox energy supplies to support targeted cultivation and metabolic studies.

media_design-1.0.0/README.md

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+# Microbial-Media-Tools
+Computational tools for designing geochemically informed microbial media. Converts environmental chemistry into lab recipes, calculates ion compositions of existing recipes, and enables downstream analysis of speciation and redox energy supplies to support targeted cultivation and metabolic studies.

media_design-1.0.0/media_design/__init__.py

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+#Media-recipe tools
+from .data_formatter import format_input, _norm_str, _is_unit, _drop_excluded_ion_columns, _ensure_hco3_molality, _find_sample_row, _extract_molality_cols_standard, _extract_molality_cols_input, _clean_input_ion_name, _slice_to_one_sample, _find_log_activity_col
+from .reagents_loader import load_reagents, check_ion_coverage
+from .recipe_maker import solve_media_lp, split_geochem_targets, solve_two_recipe_media, create_recipe
+from .exporter import export_final_ion_concentrations
+from .recipe_organizer import _parse_rule, _fmt_mass, _fmt_mL, _build_master_maps, _classify_type, _can_place, _find_stock_factor, _split_trace_by_mass_window, merge_trace_into_base, print_organized_recipe
+from .stats import calculate_similarity, percent_diff_per_ion
+from .adjust_ions import adjust_ion_concentrations
+from .speciation_formatter import build_speciation_recipe_file
+from .ions_of_recipe import convert_reagents_to_ions
+from .reselect_reagents import select_reagents
+
+#Gas-headspace tools
+from .gas_dissolution import subcrt_out, vapor_pressure_H2O_bar, logK_gas_to_aq, dissolved_gases_from_headspace, headspace_from_dissolved_target
+
+#Media-speciator tools 
+from .top_energy_supplies import print_top_energy_supplies, plot_top_energy_supplies

media_design-1.0.0/media_design/adjust_ions.py

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+import pandas as pd
+
+def adjust_ion_concentrations(
+    input_csv="final_ion_concentrations.csv",
+    output_csv=None
+):
+    """
+    Interactively modify ion concentrations from a CSV file.
+    
+    Parameters
+    ----------
+    input_csv : str, optional
+        Path to the input CSV file containing ion data. Default is
+        "final_ion_concentrations.csv". The file must contain two columns:
+        'ion' (str) and 'concentration' (float).
+    
+    output_csv : str or None, optional
+        Path to write the updated CSV file. If None, the input file is
+        overwritten. Default is None.
+    
+    Returns
+    -------
+    pandas.DataFrame or None
+        Updated DataFrame containing modified ion concentrations if changes
+        were made. Returns None if the user opts not to modify any values.
+    
+    Behavior
+    --------
+    - Prompts the user to confirm whether they want to adjust concentrations.
+    - If 'n', exits without reading or writing any files.
+    - If 'y', loads the input CSV and allows iterative modification of ion
+        concentrations via terminal prompts.
+    - Validates that selected ions exist in the dataset.
+    - Re-prompts on invalid ion names or non-numeric inputs.
+    - Allows repeated adjustments until the user exits.
+    - Writes updated data to `output_csv` (or overwrites `input_csv` if None).
+    
+    Notes
+    -----
+    - Ion matching is case-sensitive and must exactly match entries in the
+          'ion' column.
+    - Only one concentration value per ion is assumed.
+
+    """
+
+    response = input("Do you want to change the concentrations of any ions? (y/n): ").strip().lower()
+
+    if response != "y":
+        print("No changes made.")
+        return None  # signals: skip modification
+
+    # Only load file if user wants changes
+    df = pd.read_csv(input_csv)
+
+    if "ion" not in df.columns or "concentration" not in df.columns:
+        raise ValueError("CSV must contain columns: 'ion' and 'concentration'")
+
+    while True:
+
+        ion = input("What ion do you want to adjust?: ").strip()
+
+        if ion not in df["ion"].values:
+            print(f"Ion '{ion}' not found.")
+            print("Available ions:")
+            print(", ".join(df["ion"].values))
+            continue
+
+        current_value = df.loc[df["ion"] == ion, "concentration"].values[0]
+        print(f"Your current concentration of {ion} is {current_value}")
+
+        try:
+            new_value = float(input("What would you like to change it to?: ").strip())
+        except ValueError:
+            print("Invalid number. Try again.")
+            continue
+
+        df.loc[df["ion"] == ion, "concentration"] = new_value
+        print(f"{ion} updated from {current_value} → {new_value}")
+
+        again = input("Would you like to adjust another ion? (y/n): ").strip().lower()
+        if again != "y":
+            break
+
+    # Determine output file
+    if output_csv is None:
+        output_csv = input_csv  # overwrite default
+
+    df.to_csv(output_csv, index=False)
+
+    print(f"\nUpdated concentrations exported to: {output_csv}")
+
+    return df

media_design-1.0.0/media_design/data/example-input.csv

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+Sample,Name,Year,Pressure,H+,Temperature,O2,HCO3-,Cl-,F-,Br-,SO4-2,Na+,K+,SiO2,Be+2,B(OH)3,Al+3,VO+2,CrO4-2,Mn+2,Co+2,Ni+2,Cu+2,Zn+2,Ga+3,H2AsO4-,Rb+,Sr+2,Y+3,Zr+4,NbO3-,MoO4-2,Cd+2,Sn+2,SbO2-,Cs+,Ba+2,La+3,Hf+4,WO4-2,Tl+,Pb+2,Th+4,U+4,HS-,H2,CH4,CO,Fe+2,Fe+3,HPO4-2,Li+,Mg+2,Ca+2,NH4+,NO2-,NO3-
+id,name,year,bar,pH,degC,ppm,ppm,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality
+River Sample,North Bay,2023,1,8.34,17.19,9.561652,,0.0003633478138,0.000005282623434,0.000002105249549,0.0002265969689,0.0005902100913,0.00004393460075,0.000004343955848,,,0.000001000667111,,,0.0000002366303833,,,0.00000003147326346,0,,,,0.0000004679296964,,,,0.00000001042209484,,,,,0.0000001893249836,,,,,,,,,,,1.00E-18,1.00E-18,0.000001074402364,,0.0000002377204611,0.0003163874421,0.0005264906882,0.00001478866068,0.000001464420389,
+Hot Spring Sample,Perpetual Spouter,2011,1,7.267,88.3,0.368,1.2665822,0.019152117,0.000415298,2.66E-05,0.000400749,0.020577638,0.001340996,0.005267099,8.77E-08,0.00111923,3.45E-06,2.94E-09,1.15E-09,5.82E-07,1.70E-10,1.53E-09,1.26E-09,4.43E-08,4.30E-08,4.00E-05,5.85E-06,3.99E-07,4.50E-10,5.48E-10,6.46E-10,6.98E-07,1.78E-10,5.05E-10,1.16E-06,4.84E-06,9.98E-08,3.60E-10,1.12E-10,9.03E-07,2.64E-09,9.65E-11,4.31E-11,4.20E-11,9.69E-07,,,,8.95E-07,1.00E-18,4.55E-07,0.000950872,2.96E-06,0.000284445,,,
+Hydrothermal Vent Sample,Trans-Atlantic Geotraverse,2026,367,4.4012,82,0.172296,158.5,0.57719,,,0.0203602,0.496411,0.0120154,0.00606141,,,2.72E-06,,,0.00019185,,,3.56E-07,2.24E-05,,,,,,,,,,,,,5.51E-06,,,,,2.97E-08,,,0.00181042,,3.97E-05,,0.00139699,1.09E-09,,,0.0384582,0.014469,,,

media_design-1.0.0/media_design/data/example-speciation-input.csv

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+Sample,Name,Year,Pressure,H+,Temperature,logfO2,O2,HCO3-,Cl-,F-,Br-,SO4-2,Na+,K+,SiO2,Be+2,B(OH)3,Al+3,VO+2,CrO4-2,Mn+2,Co+2,Ni+2,Cu+2,Zn+2,Ga+3,H2AsO4-,Rb+,Sr+2,Y+3,Zr+4,NbO3-,MoO4-2,Cd+2,Sn+2,SbO2-,Cs+,Ba+2,La+3,Hf+4,WO4-2,Tl+,Pb+2,Th+4,U+4,HS-,H2,CH4,CO,Fe+2,Fe+3,PO4-3,Li+,Mg+2,Ca+2,NH4+,NO2-,HPO4-2,N2
+id,name,year,bar,pH,degC,logfO2,ppm,ppm,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,ppm
+NB Recipe,North Bay,2023,1,8.3,17,,9.59987,,0.001749218625,5.28E-06,2.11E-06,0.0002266284422,0.0005902309355,4.39E-05,4.34E-06,0,0,1.00E-06,0,0,2.37E-07,0,0,3.15E-08,0,0,0,0,4.68E-07,0,0,0,1.04E-08,0,0,,0,1.89E-07,0,0,0,,0,,,0,,,,1.00E-18,1.07E-06,0,0,0.0003163874421,0.0005264906882,1.48E-05,1.46E-06,0,
+NB Source,North Bay,2023,1,8.34,17.19,,9.561652,,0.0003633478138,0.000005282623434,0.000002105249549,0.0002265969689,0.0005902100913,0.00004393460075,0.000004343955848,,,0.000001000667111,,,0.0000002366303833,,,0.00000003147326346,0,,,,0.0000004679296964,,,,0.00000001042209484,,,,,0.0000001893249836,,,,,,,,,,,1.00E-18,1.00E-18,0.000001074402364,,0.0000002377204611,0.0003163874421,0.0005264906882,0.00001478866068,0.000001464420389,,
+PS Recipe,Perpetual Spouter,2011,1,7.3,85,,2.228744,2.08E-05,0.01776449768,0.000415298,2.66E-05,6.12E-06,0.02057994694,0.001340996,0.002135667696,0,0.00111923,3.45E-06,2.94E-09,0,5.82E-07,1.70E-10,1.53E-09,1.26E-09,4.43E-08,0,0,5.85E-06,3.99E-07,0,0,0,6.98E-07,1.78E-10,0,,0,9.98E-08,0,0,9.03E-07,,0,,,9.69E-07,,,,8.95E-07,1.00E-18,0,0,2.96E-06,0.000284445,0,0,4.55E-07,
+PS Source,Perpetual Spouter,2011,1,7.267,88.3,,0.368,1.2665822,0.019152117,0.000415298,2.66E-05,4.01E-04,0.020577638,0.001340996,0.005267099,8.77E-08,0.00111923,3.45E-06,2.94E-09,1.15E-09,5.82E-07,1.70E-10,1.53E-09,1.26E-09,4.43E-08,4.30E-08,4.00E-05,5.85E-06,3.99E-07,4.50E-10,5.48E-10,6.46E-10,6.98E-07,1.78E-10,5.05E-10,1.16E-06,4.84E-06,9.98E-08,3.60E-10,1.12E-10,9.03E-07,2.64E-09,9.65E-11,4.31E-11,4.20E-11,9.69E-07,,,1.00E-18,8.95E-07,1.00E-18,4.55E-07,0.000950872,2.96E-06,0.000284445,,,,
+TAG Recipe 75C 1b,Trans-Atlantic Geotraverse,2015,1,3.3,75,,3.322547,206.997286,0.659,0,0.00105,0,0.584,0.018,0.001603045854,0,0,1.00E-05,0,1.10E-07,0.00071,0,0,1.30E-06,8.30E-05,0,0,0,0,0,0,0,0,0,0,,0,2.00E-05,0,0,0,,1.10E-07,,,6.70E-03,,,,5.17E-03,0,0,0,0,0.026,0.00065,0,0,
+TAG Source 350C 200b,Trans-Atlantic Geotraverse,2015,200,3.31,350,-28.97,,207,6.59E-01,,1.05E-03,1.00E-18,5.84E-01,1.80E-02,2.20E-02,,,1.00E-05,,,7.10E-04,,,1.30E-06,8.30E-05,,,,,,,,,,,,,2.00E-05,,,,,1.10E-07,,,6.70E-03,3.70E-04,1.47E-04,,5.17E-03,1.00E-18,1.00E-18,,1.00E-18,2.60E-02,6.50E-04,,,
+TAG Source 75C 1b,Trans-Atlantic Geotraverse,2015,1,3.31,75,-28.97,,207,6.59E-01,,1.05E-03,1.00E-18,5.84E-01,1.80E-02,2.20E-02,,,1.00E-05,,,7.10E-04,,,1.30E-06,8.30E-05,,,,,,,,,,,,,2.00E-05,,,,,1.10E-07,,,6.70E-03,3.70E-04,1.47E-04,,5.17E-03,1.00E-18,1.00E-18,,1.00E-18,2.60E-02,6.50E-04,,,

media_design-1.0.0/media_design/data/master-reagents.csv

@@ -0,0 +1,149 @@
+reagent_name,ion,stoichiometry,molar_mass,print,rule
+(NH4)2SO4,NH4+,2,132.1,,
+(NH4)2SO4,SO4-2,1,132.1,,
+AlCl3•6H2O,Al+3,1,241.43,WARNING: Do not autoclave. Releases hazardous vapors when heated.,No
+AlCl3•6H2O,Cl-,3,241.43,WARNING: Do not autoclave. Releases hazardous vapors when heated.,No
+Al(NO3)3•9H2O,Al+3,1,375.13,WARNING: Do not autoclave. Rapid hydrolysis in water.,
+Al(NO3)3•9H2O,NO3-,3,375.13,WARNING: Do not autoclave. Rapid hydrolysis in water.,
+Al2(SO4)3,Al+3,2,342.2,,
+Al2(SO4)3,SO4-2,3,342.2,,
+AlK(SO4)2•12H2O,Al+3,1,474.4,,
+AlK(SO4)2•12H2O,K+,1,474.4,,
+AlK(SO4)2•12H2O,SO4-2,2,474.4,,
+BaCl2,Ba+2,1,208.2,,
+BaCl2,Cl-,2,208.2,,
+BeSO4,Be+2,1,105.1,,
+BeSO4,SO4-2,1,105.1,,
+CaBr2,Ca+2,1,199.9,WARNING: May precipitate with carbonates or phosphates during autoclaving.,"HCO3-, PO4-3"
+CaBr2,Br-,2,199.9,WARNING: May precipitate with carbonates or phosphates during autoclaving.,"HCO3-, PO4-3"
+CaCl2•2H2O,Ca+2,1,111,WARNING: May precipitate with carbonates or phosphates during autoclaving.,"HCO3-, PO4-3"
+CaCl2•2H2O,Cl-,2,111,WARNING: May precipitate with carbonates or phosphates during autoclaving.,"HCO3-, PO4-3"
+CaCl2,Ca+2,1,110.98,,
+CaCl2,Cl-,2,110.98,,
+CaC2O4,Ca+2,1,128.097,,
+CaC2O4,oxalate-2,1,128.097,,
+CdSO4•8/3H2O,Cd+2,3,769.5,,
+CdSO4•8/3H2O,SO4-2,3,769.5,,
+CoCl2•6H2O,Co+2,1,237.9,,
+CoCl2•6H2O,Cl-,2,237.9,,
+CsCl,Cs+,1,168.4,,
+CsCl,Cl-,1,168.4,,
+CuCl2•2H2O,Cu+2,1,170.5,,
+CuCl2•2H2O,Cl-,2,170.5,,
+CuSO4•5H2O,Cu+2,1,249.7,"WARNING: May precipitate with phosphate, carbonate, or sulfide during autoclaving.","HCO3-, PO4-3, HS-"
+CuSO4•5H2O,SO4-2,1,249.7,"WARNING: May precipitate with phosphate, carbonate, or sulfide during autoclaving.","HCO3-, PO4-3, HS-"
+Fe(NO3)3•9H2O,Fe+3,1,404,,
+Fe(NO3)3•9H2O,NO3-,3,404,,
+Fe2(SO4)3,Fe+3,2,399.9,"WARNING: May precipitate with phosphate, carbonate, or at elevated pH during autoclaving.","HCO3-, PO4-3"
+Fe2(SO4)3,SO4-2,3,399.9,"WARNING: May precipitate with phosphate, carbonate, or at elevated pH during autoclaving.","HCO3-, PO4-3"
+FeCl3•6H2O,Fe+3,1,270.3,WARNING: Autoclavable but prone to hydrolysis and precipitation; commonly filter-sterilized.,No
+FeCl3•6H2O,Cl-,3,270.3,WARNING: Autoclavable but prone to hydrolysis and precipitation; commonly filter-sterilized.,No
+FeCl3,Fe+3,1,162.2,WARNING: Do not autoclave. Will hydrolyze and preciptate.,No
+FeCl3,Cl-,3,162.2,WARNING: Do not autoclave. Will hydrolyze and preciptate.,No
+FeCl2,Fe+2,1,126.75,WARNING: Do not autoclave. Iron will oxidize.,No
+FeCl2,Cl-,2,126.75,WARNING: Do not autoclave. Iron will oxidize.,No
+FeSO4•7H2O,Fe+2,1,278,WARNING: Do not autoclave. Iron will oxidize.,No
+FeSO4•7H2O,SO4-2,1,278,WARNING: Do not autoclave. Iron will oxidize.,No
+FeNaEDTA,Fe+3,1,371.1,,
+FeNaEDTA,Na+,1,371.1,,
+FeNaEDTA,EDTA-4,1,371.1,,
+Ga(NO3)3,Ga+3,1,255.7,,
+Ga(NO3)3,NO3-,3,255.7,,
+H2WO4,WO4-2,1,249.9,WARNING: May precipitate if autoclaved with oxalic acid,No
+H3BO3,B(OH)3,1,61.8,,
+HfCl4,Hf+4,1,320.3,WARNING: Do not autoclave. Rapid hydrolysis in water.,No
+HfCl4,Cl-,4,320.3,WARNING: Do not autoclave. Rapid hydrolysis in water.,No
+KHCO3,K+,1,100.1,WARNING: Autoclaving not recommended.,No
+KHCO3,HCO3-,1,100.1,WARNING: Autoclaving not recommended.,No
+K2HPO4,K+,2,174.2,,
+K2HPO4,HPO4-2,1,174.2,,
+K2SO4,K+,2,174.3,,
+K2SO4,SO4-2,1,174.3,,
+KBr,K+,1,119,,
+KBr,Br-,1,119,,
+KCl,K+,1,74.6,,
+KCl,Cl-,1,74.6,,
+KH2AsO4,K+,1,180,,
+KH2AsO4,H2AsO4-,1,180,,
+KH2PO4,K+,1,136.1,,
+KH2PO4,PO4-3,1,136.1,,
+KNO2,K+,1,85.1,,
+KNO2,NO2-,1,85.1,,
+LaCl3,La+3,1,245.3,,
+LaCl3,Cl-,3,245.3,,
+LiCl,Li+,1,42.4,,
+LiCl,Cl-,1,42.4,,
+MgSO4•7H2O,Mg+2,1,246.5,"WARNING: May precipitate with phosphate, carbonate, or fluoride during autoclaving.","HCO3-, PO4-3, F-"
+MgSO4•7H2O,SO4-2,1,246.5,"WARNING: May precipitate with phosphate, carbonate, or fluoride during autoclaving.","HCO3-, PO4-3, F-"
+MgCl2•6H2O,Mg+2,1,203.3,,
+MgCl2•6H2O,Cl-,2,203.3,,
+MgCl2,Mg+2,1,95.211,,
+MgCl2,Cl-,1,95.211,,
+MnCl2•4H2O,Mn+2,1,197.9,WARNING: Autoclavable. Avoid sulfide and high-pH conditions.,HS-
+MnCl2•4H2O,Cl-,2,197.9,WARNING: Autoclavable. Avoid sulfide and high-pH conditions.,HS-
+Na2HPO4,Na+,2,142,"WARNING: Autoclavable. At very high concentrations or with certain reagents, may crystallize; rare peroxide formation has been reported with some sugars ",No
+Na2HPO4,HPO4-2,1,142,"WARNING: Autoclavable. At very high concentrations or with certain reagents, may crystallize; rare peroxide formation has been reported with some sugars ",No
+NaHCO3,Na+,1,84,WARNING: Autoclaving possible but not recommended. May form preciptates with other common reagents.,No
+NaHCO3,HCO3-,1,84,WARNING: Autoclaving possible but not recommended. May form preciptates with other common reagents.,No
+Na2MoO4•2H2O,Na+,2,242,,
+Na2MoO4•2H2O,MoO4-2,1,242,,
+Na2S•9H2O,HS-,1,240.2,WARNING: Recommended to autoclave anaerobically,No
+Na2SiO3,SiO2,1,122.1,WARNING: May precipitate if autoclaved,No
+Na2SiO3,Na+,2,122.1,WARNING: May precipitate if autoclaved,No
+Na2SO4,Na+,2,142,,
+Na2SO4,SO4-2,1,142,,
+Na2WO4,Na+,2,293.8,,
+Na2WO4,WO4-2,1,293.8,,
+NaBr,Na+,1,102.9,,
+NaBr,Br-,1,102.9,,
+NaCl,Na+,1,58.4,,
+NaCl,Cl-,1,58.4,,
+NaHCO3,Na+,1,84,,
+NaHCO3,HCO3-,1,84,,
+NaH2AsO4,Na+,1,181.9,WARNING: Do not autoclave. Releases hazardous vapors when heated.,No
+NaH2AsO4,H2AsO4-,1,181.9,WARNING: Do not autoclave. Releases hazardous vapors when heated.,No
+NaHS,Na+,1,56.1,WARNING: Do not autoclave. Releases hazardous vapors when heated.,No
+NaHS,HS-,1,56.1,WARNING: Do not autoclave. Releases hazardous vapors when heated.,No
+NaF,Na+,1,42,,
+NaF,F-,1,42,,
+NaNbO3,Na+,1,163.9,,
+NaNbO3,NbO3-,1,163.9,,
+NaNO2,Na+,1,69,WARNING: Autoclavable alone. Chemically reactive; may oxidize or react with reduced species or organics. Often filter-sterilized and added separately.,No
+NaNO2,NO2-,1,69,WARNING: Autoclavable alone. Chemically reactive; may oxidize or react with reduced species or organics. Often filter-sterilized and added separately.,No
+NaNO3,Na+,1,85,,
+NaNO3,NO3-,1,85,,
+NaVO3,Na+,1,121.9,,
+NaVO3,VO+2,1,121.9,,
+NH4Br,NH4+,1,97.9,WARNING: Autoclaving not recommended. Ammonium decomposes into ammonia.,No
+NH4Br,Br-,1,97.9,WARNING: Autoclaving not recommended. Ammonium decomposes into ammonia.,No
+NH4Cl,NH4+,1,53.5,,
+NH4Cl,Cl-,1,53.5,,
+NH4H2PO4,NH4+,1,115,,
+NH4H2PO4,PO4-3,1,115,,
+NH4NO3,NH4+,1,80,WARNING: Do not autoclave. Heating produces nitrous oxide.,No
+NH4NO3,NO3-,1,80,WARNING: Do not autoclave. Heating produces nitrous oxide.,No
+NiCl2•6H2O,Ni+2,1,237.7,,
+NiCl2•6H2O,Cl-,2,237.7,,
+PbCrO4,Pb+2,1,323.2,WARNING: Do not autoclave. Heating produces toxic chromium fumes,No
+PbCrO4,CrO4-2,1,323.2,WARNING: Do not autoclave. Heating produces toxic chromium fumes,No
+RbCl,Rb+,1,120.9,WARNING: Autoclaving not recommended. Will degrade.,No
+RbCl,Cl-,1,120.9,WARNING: Autoclaving not recommended. Will degrade.,No
+SnCl2,Sn+2,1,189.6,"WARNING: When autoclaved with sulfates or phosphates, preciptation may occur","SO4-2, PO4-3"
+SnCl2,Cl-,2,189.6,"WARNING: When autoclaved with sulfates or phosphates, preciptation may occur","SO4-2, PO4-3"
+SrCl2•6H2O,Sr+2,1,266.4,"WARNING: When autoclaved with sulfates or phosphates, preciptation may occur","SO4-2, PO4-3"
+SrCl2•6H2O,Cl-,2,266.4,"WARNING: When autoclaved with sulfates or phosphates, preciptation may occur","SO4-2, PO4-3"
+SrCl2,Sr+2,1,158.53,,
+SrCl2,Cl-,2,158.53,,
+VOSO4•3.5H2O,VO+2,1,226.1,WARNING: Do not autoclave. Will oxidize and precipitate.,No
+VOSO4•3.5H2O,SO4-2,1,226.1,WARNING: Do not autoclave. Will oxidize and precipitate.,No
+YCl3,Y+3,1,195.3,"WARNING: Above pH 6, insoluble yttrium hydroxides will form",No
+YCl3,Cl-,3,195.3,"WARNING: Above pH 6, insoluble yttrium hydroxides will form",No
+ZnCl2,Zn+2,1,136.286,WARNING: May precipitate if autoclaved,No
+ZnCl2,Cl-,2,136.286,WARNING: May precipitate if autoclaved,No
+Zn(NO3)2•6H2O,Zn+2,1,297.48,,
+Zn(NO3)2•6H2O,NO3-,2,297.48,,
+ZnSO4•7H2O,Zn+2,1,287.5,"WARNING: When autoclaved with phosphates, preciptation may occur",PO4-3
+ZnSO4•7H2O,SO4-2,1,287.5,"WARNING: When autoclaved with phosphates, preciptation may occur",PO4-3
+ZrOCl2,Zr+4,1,233,WARNING: Autoclaving possible but might hydrolyze to form hydrated zirconia species at high temperatures,No
+ZrOCl2,O-2,1,233,WARNING: Autoclaving possible but might hydrolyze to form hydrated zirconia species at high temperatures,No
+ZrOCl2,Cl-,2,233,WARNING: Autoclaving possible but might hydrolyze to form hydrated zirconia species at high temperatures,No

media_design-1.0.0/media_design/data/speciation-formatting.csv

@@ -0,0 +1,2 @@
+Sample,Name,Pressure,Year,H+,Temperature,O2,HCO3-,Cl-,F-,Br-,SO4-2,Na+,K+,SiO2,Be+2,B(OH)3,Al+3,VO+2,CrO4-2,Mn+2,Co+2,Ni+2,Cu+2,Zn+2,Ga+3,H2AsO4-,Rb+,Sr+2,Y+3,Zr+4,NbO3-,MoO4-2,Cd+2,Sn+2,SbO2-,Cs+,Ba+2,La+3,Hf+4,WO4-2,Tl+,Pb+2,Th+4,U+4,HS-,H2,CH4,CO,Fe+2,Fe+3,PO4-3,Li+,Mg+2,Ca+2,NH4+,NO2-,NO3-
+id,name,bar,year,pH,degC,ppm,ppm,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality,Molality