Add documentation about fitting planetary RVs

[sblunt]

We should document better and add a tutorial about fitting planetary RVs. In particular, should emphasize that pl RV data is assumed to be relative to the barycenter in the current implementation.

[sblunt]

^^ wrong! RV is relative to the star. More reason to make this clear in the documentation.

[chihchunhsu]

Does the sampler.results.plot_orbits() support plotting the planet/companion RVs? I have issues with plotting it with version 2.1.3 (I have no issues with plotting the orbit if I don't include companion RVs)

>>> orbit_plot = betaPic_sampler.results.plot_orbits(start_mjd=betaPic_sampler.system.data_table['epoch'][0], rv_time_series=True)

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/var/folders/n5/99sz4kvx3dd1wmcsjdsj9xh00000gn/T/ipykernel_26636/4025753964.py in <module>
----> 1 orbit_plot = betaPic_sampler.results.plot_orbits(start_mjd=betaPic_sampler.system.data_table['epoch'][0], rv_time_series=True)

~/anaconda3/lib/python3.7/site-packages/orbitize/results.py in plot_orbits(self, object_to_plot, start_mjd, num_orbits_to_plot, num_epochs_to_plot, square_plot, show_colorbar, cmap, sep_pa_color, sep_pa_end_year, cbar_param, mod180, rv_time_series, plot_astrometry, plot_astrometry_insts, plot_errorbars, fig)
    336             plot_astrometry=plot_astrometry,
    337             plot_astrometry_insts=plot_astrometry_insts,
--> 338             plot_errorbars=plot_errorbars, fig=fig
    339         )
    340 

~/anaconda3/lib/python3.7/site-packages/orbitize/plot.py in plot_orbits(results, object_to_plot, start_mjd, num_orbits_to_plot, num_epochs_to_plot, square_plot, show_colorbar, cmap, sep_pa_color, sep_pa_end_year, cbar_param, mod180, rv_time_series, plot_astrometry, plot_astrometry_insts, plot_errorbars, fig)
    562 
    563             plt.sca(ax1)
--> 564             plt.errorbar(Time(astr_epochs,format='mjd').decimalyear,sep_data,yerr=serr,ms=5, linestyle='',marker='o',c='purple',zorder=2, capsize=2)
    565             plt.sca(ax2)
    566             plt.errorbar(Time(astr_epochs,format='mjd').decimalyear,pa_data,yerr=perr,ms=5, linestyle='',marker='o',c='purple',zorder=2, capsize=2)

~/anaconda3/lib/python3.7/site-packages/matplotlib/pyplot.py in errorbar(x, y, yerr, xerr, fmt, ecolor, elinewidth, capsize, barsabove, lolims, uplims, xlolims, xuplims, errorevery, capthick, data, **kwargs)
   2522         lolims=lolims, uplims=uplims, xlolims=xlolims,
   2523         xuplims=xuplims, errorevery=errorevery, capthick=capthick,
-> 2524         **({"data": data} if data is not None else {}), **kwargs)
   2525 
   2526 

~/anaconda3/lib/python3.7/site-packages/matplotlib/__init__.py in inner(ax, data, *args, **kwargs)
   1412     def inner(ax, *args, data=None, **kwargs):
   1413         if data is None:
-> 1414             return func(ax, *map(sanitize_sequence, args), **kwargs)
   1415 
   1416         bound = new_sig.bind(ax, *args, **kwargs)

~/anaconda3/lib/python3.7/site-packages/matplotlib/axes/_axes.py in errorbar(self, x, y, yerr, xerr, fmt, ecolor, elinewidth, capsize, barsabove, lolims, uplims, xlolims, xuplims, errorevery, capthick, **kwargs)
   3333         x, y = np.atleast_1d(x, y)  # Make sure all the args are iterable.
   3334         if len(x) != len(y):
-> 3335             raise ValueError("'x' and 'y' must have the same size")
   3336 
   3337         if isinstance(errorevery, Integral):

ValueError: 'x' and 'y' must have the same size

<Figure size 1400x600 with 0 Axes>

[semaphoreP]

@chihchunhsu can you check if the most recent updates to orbitize fix this? we just merged in a bugfix for this onto the main branch

[chihchunhsu]

I pulled the most recent version 2.2.2 but the issue still persists, unfortunately.

[semaphoreP]

Is this the most recent version on pip, or did you directly pull the most recent changes on the main branch? We have yet to formally release this version.

[chihchunhsu]

Ah right. Actually I used the pip version, and it is fixed with the version on github! Thanks for the catch!