Example: Programmatically create and update field collection with Entity API
The Entity API provides classes and methods / functions that make CRUD for entities much, much easier and less prone to errors and bugs.
The first example show the creation of a field collection entity that will be attached to a node that has a field collection field already defined for it through the Manage Fields tab of the node type creation / modification UI. The example shows creating the field collection entity (using the entity_create function of the Entity API, attaching it to a node, and using the Entity API then to set values of fields within the field collection.
<?php
// Code that would be here but is omitted loads a node called $my_node
// Nodes of the type that is $my_node have a field of the field collection
// type called field_text_files, which in turn is defined as having two
// fields called field_source_txt_filename and field_source_txt_content
// Begin by using the entity_create function to create a new entity of
// type field_collection_item. The second parameter to the function
// provides "an array of values to set, keyed by property name".
// In our example, the field in my_node that holds the field collection is
