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Say there's a star in our local neighborhood with a Jupiter-sized planet orbiting around it. This planet's orbit happens to lie approximately in our line-of-sight – we can only see a quarter of it transit in front of its star.

All scientists do is look at the amount of starlight blocked during a transit and deduce the size of the planet.

So since this planet only partially transits, are scientists able to tell it's a partial transit and the planet is actually Jupiter-sized? OR are they going to naively assume it's just a smaller planet passing in front of its star?

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The shape of the transit is different if there is a partial transit, not just the depth.

As a planet passes fully in front of the star, the brightness is almost constant while it is transiting (bar the limb darkening effect). Hence you get a "bucket-shaped" eclipse with a wide, flat bottom.

If the transit is partial then you get a more "U-shaped" and finally a "V-shaped" eclipse because there is a singular minimum point when the maximum area of star is obscured.

In this way you have both the shape and depth of the transit to work with and this can give you both the inclination (or rather the "impact parameter") of the exoplanet orbit and the exoplanet size.

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