$R$ is a proportionality constant between the units we use to measure temperature (kelvins) and the units we use to measure energy (joules) and number of particles (moles). If you measure temperature in energy units and use the number of particles instead of the number of moles, the constant $R$ (and $k_\mathrm{B}$) disappears from your formulas.
$k_\mathrm{B}$ and $R$ exist for historical reasons, due to choices made in the definition of the Kelvin temperature scale and the Celsius temperature scale before it, as well as the fact that the link between temperature and energy was not understood at the time when the scales were conceived. The concept of temperature seems to predate that of energy, with attempts systematically at standardizing its measurement dating to 170 CE. The modern concept of energy didn't exist until Newton's mechanics (although Aristotle had a qualitative idea of potentiality). The earliest energy concept was the vis viva, which is proportional to kinetic energy and was proposed by Leibniz around 1676. The Fahrenheit scale, the first popular quantification of temperature, was invented around 1724, and was based on the boiling point of pure water and the freezing point of a salt water mixture. A scale similar to the modern Celsius scale based on the freezing and boiling points of pure water, was proposed in 1743. The fact that mechanical energy could be converted into a change in temperature was not understood mathematically until the experiments of Joule in around 1843.
The value of $R$ was deduced from studies of mechanical properties of gases and was known at least by 1856. Its development required the concept that gases were made of small particles and the relation between the number of particles and molecular mass. The first value of Avogadro's number was estimated by Lochschmidt in 1865. This is allowed the Boltzmann constant ($k_\mathrm{B}$) to be defined, linking temperature directly to the microscopic kinetic energy of particles in an ideal gas.
The modern understanding of the relation between temperature, energy, and entropy wasn't arrived at until the work of Boltzmann and Gibbs in the late 1800s:
$$\frac{1}{k_\mathrm{B} T} = \left( \frac{\partial \ln \Omega}{\delta U} \right)_{V,N}$$
Here $U$ is the internal energy, $\Omega$ is the number of microstates corresponding to the system's macrostate, and the derivative is taken with the volume of the system ($V$) and number of particles ($N$) fixed.
Some good statistical mechanics textbooks (for example, Landau and Lifshitz), present formulas with temperature in energy units (or equivalently, with energy in temperature units), so neither $R$ nor $k_\mathrm{B}$ appear in their formulas.