I use lyx , elsevier class. I choose the citations to be natbib/numerical, style : plainnat. The citations in the produced pdf are not numbered. I am not sure how to number the citations. The lyx exported latex code is shown blow.
%% LyX 2.1.4 created this file. For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass[10pt,authoryear]{elsarticle}
\usepackage{fontspec}
\usepackage{geometry}
\geometry{verbose,tmargin=1in,bmargin=1in,lmargin=1in,rmargin=1in}
\usepackage{color}
\usepackage{array}
\usepackage{graphicx}
\usepackage{setspace}
\usepackage{esint}
\doublespacing
\makeatletter
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.
%% Because html converters don't know tabularnewline
\providecommand{\tabularnewline}{\\}
\usepackage{geometry}
\usepackage{caption}
\captionsetup{labelfont=large}
\renewcommand{\arraystretch}{1.5}
\makeatother
\begin{document}
{\large{}\bibliographystyle{kluwer}
\bibliography{citation}
}{\large \par}
\end{document}
.lyxfile to your question? (Remove all the content except for a citation or two first, so best make a copy.) – Torbjørn T. Oct 12 '15 at 20:50