updates to doc, fixed some bugs in error examples

PennyWieser · Feb 9, 2024 · 5000cc1 · 5000cc1
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diff --git a/docs/Examples/Error_propagation/Cpx_Liq_Thermobarometry_Error_prop.ipynb b/docs/Examples/Error_propagation/Cpx_Liq_Thermobarometry_Error_prop.ipynb
diff --git a/docs/Examples/Error_propagation/Cpx_only_Error.png b/docs/Examples/Error_propagation/Cpx_only_Error.png
diff --git a/docs/Examples/Error_propagation/Cpx_only_contour_plot.ipynb b/docs/Examples/Error_propagation/Cpx_only_contour_plot.ipynb
diff --git a/docs/Examples/Error_propagation/Manuscript_2CpxNoises.png b/docs/Examples/Error_propagation/Manuscript_2CpxNoises.png
diff --git a/docs/Examples/Error_propagation/confidence_intervals_vs_errorbars.png b/docs/Examples/Error_propagation/confidence_intervals_vs_errorbars.png
diff --git a/docs/worked_examples_liqs_ols.rst b/docs/worked_examples_liqs_ols.rst
@@ -77,23 +77,43 @@ This :doc:`example <Examples/Feldspar_Thermobarometry/Feldspar_Liquid_Thermobaro
 This :doc:`example <Examples/Feldspar_Thermobarometry/Feldspar_Liquid_Thermobarometry>` shows how to perform plagioclase-liquid hygrometry calculations.
 
 
-This :doc:`example <Examples/Feldspar_Thermobarometry/Two_Feldspar_All_Possible_Pairs> shows how to perform two feldspar thermobarometry. 
+This :doc:`example <Examples/Feldspar_Thermobarometry/Two_Feldspar_All_Possible_Pairs>'' shows how to perform two feldspar thermobarometry. 
 
 
-This :doc:`example <Examples/Feldspar_Thermobarometry/Fspar_Liq_Matching> shows how to perform Kspar-liq and plag-liq melt matching. 
+This :doc:`example <Examples/Feldspar_Thermobarometry/Fspar_Liq_Matching>' shows how to perform Kspar-liq and plag-liq melt matching. 
 
 
-This :doc:`example <Examples/Feldspar_Thermobarometry/Fspar_Ternary_Plot> shows how to plot a feldspar ternary diagram.
+This :doc:`example <Examples/Feldspar_Thermobarometry/Fspar_Ternary_Plot>' shows how to plot a feldspar ternary diagram.
 
-This :doc:`example <Examples/General_Plotting/Plagioclase_Classification_Kilauea> shows how to plot a plagioclase ternary diagram segmented by sample. 
+This :doc:`example <Examples/General_Plotting/Plagioclase_Classification_Kilauea>' shows how to plot a plagioclase ternary diagram segmented by sample. 
 
 
 
 Garnet
 -----------------------------------
-This :doc:`example <Examples/Garnet_Geotherms/Garnet_Functions> shows how to perform garnet thermobarometry and plot a garnet compositional section with a geotherm etc. 
+This :doc:`example <Examples/Garnet_Geotherms/Garnet_Functions>' shows how to perform garnet thermobarometry and plot a garnet compositional section with a geotherm etc. 
 
-This :doc:`example <Examples/Garnet_Geotherms/Geotherm_functions> shows how to calculate a garnet geotherm
+This :doc:`example <Examples/Garnet_Geotherms/Geotherm_functions>' shows how to calculate a garnet geotherm
+
+
+
+
+
+Error Propagation
+-----------------------------------
+We do not include examples for all phases, but each example below shows some different data vis strategies, so you should be able to adapt them for your problem of interest (e.g. look at them all, even if you are only interested in Cpx!)
+
+This :doc:`example <Examples/Error_propagation/Liquid_Thermometry_Error_prop>'  shows how to propagate analytical error when performing liquid thermometry.  It also shows how to plot error ellipses.
+
+This :doc:`example <Examples/Error_propagation/Cpx_only_contour_plot>'  shows how to propagate analytical error when performing Cpx-Liq thermobarometry.
+
+
+Melt inclusions
+-----------------------------------
+
+This :doc:`example <Examples/Melt_Inclusion_FeMg_Equilibrium/Ol_Melt_Inclusion_Mg_Fe_Eq_SingleSamples>' shows how to assess Fe-Mg disequilibrium between melt inclusion glasses and the host olivine for a single sample, this :doc:`example <Examples/Melt_Inclusion_FeMg_Equilibrium/Ol_Melt_Inclusion_Mg_Fe_Eq_MultipleSamples> shows the same but for multiple different samples
+
+This :doc:`example <Examples/Integration_with_VESIcal/Combining_VESIcal_Thermobar_SatPs>' shows how to integrate Thermobar with VESical to get a saturation pressure for each melt inclusion. 
 
 
 
@@ -107,14 +127,31 @@ This :doc:`example <Examples/General_Plotting/Pyroxene_Classification_Kilauea>`
 This :doc:`example <Examples/Amphibole/Amphibole_Classification_Diagrams>` shows how to plot amphibole classification diagrams.
 
 
-This :doc:`example <Examples/Feldspar_Thermobarometry/Fspar_Ternary_Plot> shows how to plot a feldspar ternary diagram.
+This :doc:`example <Examples/Feldspar_Thermobarometry/Fspar_Ternary_Plot>' shows how to plot a feldspar ternary diagram.
 
-This :doc:`example <Examples/General_Plotting/Plagioclase_Classification_Kilauea> shows how to plot a plagioclase ternary diagram segmented by sample. 
+This :doc:`example <Examples/General_Plotting/Plagioclase_Classification_Kilauea>' shows how to plot a plagioclase ternary diagram segmented by sample. 
 
 
-Error Propagation
------------------------------------
+Other Useful examples
+------------------------------
+
+Calculating equilibrium mineral contents from a liquid line of descent
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This :doc:`example <Examples/Mineral_Eq_Contents_from_LLD/Calculating_Eq_Min_Contents>` shows how to calculate equilibrium mineral contents from a Petrolog3 liquid line of descent (it could be an output from any other model, or experiments)
+
+Assesing the calibration range of models
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This :doc:`example <Examples/Other_features/Calibration_Plot_Example>` shows how to get and plot the data used to calibrate various models in Thermobar
+
 
+Calculating viscosity
+^^^^^^^^^^^^^^^^^^^^^^
 
+This :doc:`example <Examples/Other_features/Calculating_Viscosity>` shows how to calculate viscosity using the model of Giordano et al. (2008).
 
 
+Converting pressures to depths
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+This :doc:`example <Examples/Other_features/Pressure_to_depth>` shows how to convert pressures you have calculated into depths using a variety of crustal density models. 
diff --git a/src/Thermobar/clinopyroxene_thermobarometry.py b/src/Thermobar/clinopyroxene_thermobarometry.py
@@ -3448,8 +3448,7 @@ def calculate_cpx_only_press_all_eqs(cpx_comps, plot=False, return_cpx=True, H2O
             plt.xlabel('P_kbar')
             plt.xlim([-3, 16])
 
-    cols_to_move = ['P_Wang21_eq1', 'T_Wang21_eq2', 'T_Jorgenson22', 'P_Jorgenson22', 'T_Petrelli20', 'T_Petrelli21_H2O',
-    'P_Petrelli21_H2O', 'T_Put_Teq32d_Peq32a', 'T_Put_Teq32d_Peq32b', 'P_Petrelli20',
+    cols_to_move = ['P_Wang21_eq1', 'T_Wang21_eq2', 'T_Jorgenson22', 'P_Jorgenson22', 'T_Petrelli20', 'T_Put_Teq32d_Peq32a', 'T_Put_Teq32d_Peq32b', 'P_Petrelli20',
     'P_Put_Teq32d_Peq32a', 'P_Put_Teq32d_Peq32b', 'Jd_from 0=Na, 1=Al']
     cpx_comps_c_move = cpx_comps_c[cols_to_move + [
         col for col in cpx_comps_c.columns if col not in cols_to_move]]