I think what you are asking can be carried out using Web of Science. I used address == "Canada" for the past 5 years, and immediately had published records for 241, 711 articles! You can ask for a citation report, which provides the information that Scimago has at the top. I think the issue you'll face is the sheer volume of data you're asking for. Even limiting the category to "ecology" (my field) yields over 3000 articles.
Of course, this answer won't be much use if your university doesn't have access to WoS.
The other thought I had was using Harzing's Publish or Perish (http://www.harzing.com/index.htm) which uses Google Scholar data. I tried a direct google scholar search, but can't immediately see how to limit it to articles published by people in the country as opposed to being about the country.
I hadn't heard of Microsoft Academic Search (see comment by Gopi) - so I had a look. The short answer is yes, it will show you publications by geographic region, but you have to go in by institution. You can get a google scholar like list of papers - and export those in various formats, but I only found the export option at the level of individual author.
For example, Université du Burundi has 16 publications by 5 authors, with an H-index of 4.
Pretty cool map though.