You can create Link objects programatically for cases where you might want to add links to a Hyper field in your own code. To do this, you'll need to create the Link object, and assign it to the field on the element that stores your Hyper field.
For example, let's say we have a Hyper field called ctaLink attached to an entry.
$value = new \verbb\hyper\links\Url();
$value->linkText = 'some text';
$value->linkValue = 'http://…';
$value->fields = [
'myCustomField' => 'some value',
];
$entry->setFieldValue('ctaLink', [$value]);
Here, we set the type of link we want to use, the linkText and linkValue as applicable, and any custom fields (fields) that are set for the link type. We then use $entry->setFieldValue() or $entry->setFieldValues() to add that link to the field's value. Note that we always deal with an array of links!
Similarly, for an Entry link type:
$value = new \verbb\hyper\links\Entry();
$value->linkValue = 1234;
$entry->setFieldValue('ctaLink', [$value]);
Where the linkValue represents the ID of the entry you are linking to.