Assume I have a function $f = f(y, \phi(y,x))$ and I want to calculate $\frac{\partial f}{\partial y}$, I use the chain rule to get
\begin{equation} \frac{\partial f}{\partial y} = \frac{\partial f}{\partial y} + \frac{\partial f}{\partial \phi}\frac{\partial \phi}{\partial y} \end{equation}
but obviously the $\frac{\partial f}{\partial y}$ represent different things on each side of equality. How do I explain this? I'm guessing it is a notational issue.
Edit: Just to give some context why this troubles me. Here $x_i$ refers to the ith component of the vector $\mathbf{x}$ in euclidean space. In an acoustic textbook the Lighthill stress tensor $T_{ij}$ is involved in the following identity:
\begin{equation} \frac{\partial}{\partial x_i} \frac{T_{ij}(\mathbf{y},t-|\mathbf{x}-\mathbf{y}|/c)}{|\mathbf{x}-\mathbf{y}|} = \frac{\frac{\partial T_{ij}}{\partial y_i}}{|\mathbf{x}-\mathbf{y}|} - \frac{\partial}{\partial y_i} \frac{T_{ij}(\mathbf{y},t-|\mathbf{x}-\mathbf{y}|/c)}{|\mathbf{x}-\mathbf{y}|} \end{equation}
This can only be resolved if the numerator in the term $\frac{\frac{\partial T_{ij}}{\partial y_i}}{|\mathbf{x}-\mathbf{y}|}$ is given a different interpretation...Just try showing this:
Let $t-|\mathbf{x}-\mathbf{y}|/c = \phi(t,\mathbf{x}, \mathbf{y})$
\begin{array}{lcl} \frac{\partial}{\partial x_i} \frac{T_{ij}(\mathbf{y},\phi)}{|\mathbf{x}-\mathbf{y}|} & = & \frac{1}{|\mathbf{x}-\mathbf{y}|} \frac{\partial}{\partial x_i}T_{ij}(\mathbf{y},\phi) + T_{ij}(\mathbf{y},\phi) \frac{\partial}{\partial x_i} \frac{1}{|\mathbf{x}-\mathbf{y}|} \\ & = & \frac{1}{|\mathbf{x}-\mathbf{y}|} (\frac{\partial T_{ij}}{\partial \phi}\frac{\partial \phi}{\partial x_i}) + T_{ij}(\mathbf{y},\phi) \frac{\partial}{\partial x_i} \frac{1}{|\mathbf{x}-\mathbf{y}|}\\ & = & -\frac{1}{|\mathbf{x}-\mathbf{y}|} (\frac{\partial T_{ij}}{\partial \phi}\frac{\partial \phi}{\partial y_i}) + T_{ij}(\mathbf{y},\phi) \frac{\partial}{\partial x_i} \frac{1}{|\mathbf{x}-\mathbf{y}|} \end{array}
\begin{array}{lcl} \frac{\partial}{\partial y_i} \frac{T_{ij}(\mathbf{y},\phi)}{|\mathbf{x}-\mathbf{y}|} & = & \frac{1}{|\mathbf{x}-\mathbf{y}|} \frac{\partial}{\partial y_i}T_{ij}(\mathbf{y},\phi) + T_{ij}(\mathbf{y},\phi) \frac{\partial}{\partial y_i} \frac{1}{|\mathbf{x}-\mathbf{y}|} \\ & = & \frac{1}{|\mathbf{x}-\mathbf{y}|} ( \frac{\partial}{\partial y_i}T_{ij} +\frac{\partial T_{ij}}{\partial \phi}\frac{\partial \phi}{\partial y_i}) - T_{ij}(\mathbf{y},\phi) \frac{\partial}{\partial x_i} \frac{1}{|\mathbf{x}-\mathbf{y}|} \end{array}
Adding up the last line from each expression gives the result.
Let's use a different notation: for a function of two variables $f$, denote by $\partial_1f$ and $\partial_2f$ the first-order derivatives of $f$ with respect to the first and second variable respectively, namely: \begin{align*} \partial_1f(x,y)&=\lim_{h\to0}\frac{f(x+h,y)-f(x,y)}h,& \partial_2f(x,y)&=\lim_{h\to0}\frac{f(x,y)-f(x,y+h)}h. \end{align*} Now, from the chain rule, $$\frac{\mathrm{d}}{\mathrm{d}y}\Bigl(f\bigl(y,\phi(y,x)\bigr)\Bigr) =\partial_1f\bigl(y,\phi(y,x)\bigr)+\partial_1\phi(y,x)\partial_2f\bigl(x,\phi(y,x)\bigr),$$ where $$\frac{\mathrm{d}}{\mathrm{d}y}\Bigl(f\bigl(y,\phi(y,x)\bigr)\Bigr)=\lim_{h\to0}\frac{f\bigl(y+h,\phi(y+h,x)\bigr)-f\bigl(y,\phi(y,x)\bigr)}{h}.$$
In fact, I try to always be careful to what I'm writing and what I really mean. First, I'm careful to never say the function f(x), but the function $f$ (unless $f$ is a function with codomain a set of functions). At best, $f(x)$ is an expression that depends on $x$.
Then I use symbols like $\partial_1$, $\partial_2$, etc. for functions, and things like $\dfrac{\mathrm{d}}{\mathrm{d}x}$ or $\dfrac{\partial}{\partial x}$ for expressions (though, in fact, it's slightly more complicated).
(Hence, I hate when people say something like [something] is a function of $x$. Heck, what does it mean to be a function of $x$? you're a function or you're not, you can't be a function of $x$; at best, you're an expression that depends on $x$).
Then there's something I like to do: take a function $f$ of two variables and define the function $g$ by $$g(y,x)=f(x,y).$$
Then I like to ask this question: with your notation, what sense do you give to $$\frac{\partial g}{\partial x}?$$ or to any other variation on the theme: $$\frac{\partial g(x,y)}{\partial x},\ \frac{\partial g}{\partial x}(x,y),\ \ldots$$