HTML codes for Turkish characters will work (example from wikipedia):
---
title: "My doc"
output: pdf_document
---
HTML char detail anglicized
------- -- ------------------------------ ---
Ğ Ğ Uppercase "G" with breve accent gh1
İ İ Uppercase dotted "I"² i (as in "tree")
Ş Ş Uppercase "S" with cedilla sh
ğ ğ Lowercase "g" with breve accent gh1
ı ı Lowercase dotless "i"³ ou (as in "in")
ş ş Lowercase "s" with cedilla sh
------- -- ------------------------------- --
Which renders the PDF like this:

For article templates, see the rticles
package, or make your own
For book templates, have a look at pandoc ebook, gitbook and bookdown
This xelatex option I initially suggested will not work for Turkish characters:
The xelatex
engine is recommended for this kind of thing. Then you can access your system fonts with the mainfont
argument:
---
title: "My doc"
output:
pdf_document:
latex_engine: xelatex
mainfont: "name of your system font that has all those characters"
---
PDF output will be in the font you specify.
Just type as normal with no special codes.