Create unit test for join for Vignette 2

[hmhummel]

See issue #2.

I have been able to create join unit tests for Vignettes 1 and #3 because join is called by simplify. However, I have not been able to create the join unit test for Vignette 2 because simplify does not iterate all the way through, although the unit test passes the test_that test.

I created the unit tests for 1 and 3 by running simplify with breakpoints on each vignette (e.g. simplify(P_3_s1 (or s2), topo_3, G_3.unobs, G_3, G_3.obs)) using the browser() function. I added print statements after step 5 in simplify, and printed the J, D, vari, cond, S, M, and O that result after this step. Note that: P$children[[k]]$var = var, P$children[[k]]$cond: = cond, P$sumset[j] = S.

step <- step + 1
    cat("Step", step, "- After topological sorting\n")
    cat("M:", M, "\n")
    cat("O:", O, "\n")
    browser()  # Breakpoint 5: After topological sorting
    
    while (k <= i) {
      step <- step + 1
      cat("Step", step, "- Inside nested while loop before join operation\n")
      cat("P$children[[k]]$var:", P$children[[k]]$var, "\n")
      cat("P$children[[k]]$cond:", P$children[[k]]$cond, "\n")
      cat("P$sumset[j]:", P$sumset[j], "\n")
      browser()  # Breakpoint 6: Before join operation

When I attempt to similarly run simplify with breakpoints for Vignette 2, it only iterates through the first step and skips to step 8 (the last step).

[hmhummel]

To address this, I plan to:

• re-visit the output from causal.effect using expr = FALSE to ensure that the correct input is being used for parse.expression, which calls simplify.
• update the parse.expression unit test using this input.
• Then, I can use the output from parse.expression to input into simplify, and update the simplify unit test.
• I will see if this new input not only passes the test_that unit test, but also iterates correctly through simplify so that I can obtain the inputs for join.