Create multiClust class and implement related fixes

[nsh87]

The major commit here is https://github.com/nsh87/receptormarker/commit/3d58920d11f0dfac3250ab148e5e80986492cda1. It creates an actual multiClust class and moves the documentation around. The rest of the commits are around:

• Fixing function calls to use the new multiClust class
• Updating/fixing unit tests for the same
• Modifying unit tests either for more coverage or to reduce redundancy

@catterbu: If you can take a look at all of these that would be great. This PR is going to fail. I've split up most of the unit tests to be more atomic so it's more obvious what is failing. I think you'll have to address those failing ones yourself - I've done most of what I feel comfortable doing.

[nsh87]

@catterbu: actually, it might just be some stupid thing that causes this to fail. If so I can fix it, but if you can take a look at these commits all the same that would be awesome. I still have to test this on the site tonight once this is merged into dev.

[nsh87]

@catterbu: never mind, it's not a stupid typo or anything. You're going to have to check out these failed tests to see what's going on:

1. Error: the 'clust_model' slot in the pre-generated multiClust validates -----
argument "FUN" is missing, with no default
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: lapply(expect_is(f_clust@clust_model[[1]], "kmeans")) at test_multi_clustering.R:47
5: match.fun(FUN)

2. Error: multi_clust() correctly handles contrived boolean data ---------------
more cluster centers than distinct data points.
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: multi_clust(contrived_bool, krange = 2:7) at test_multi_clustering.R:81
5: stats::kmeans(d, k, iter.max = iter.max, nstart = runs, ...) at /home/travis/build/nsh87/receptormarker/R/multi_clustering.R:88
6: stop("more cluster centers than distinct data points.")

3. Failure (at test_multi_clustering.R#92): multi_clust() correctly handles non-boolean iris data 
k_best is not identical to 3. Differences: 
Mean relative difference: 0.3333333

*** grep results from unit tests ********************

27:3. Failure (at test_multi_clustering.R#92): multi_clust() correctly handles non-boolean iris data 
10:1. Error: the 'clust_model' slot in the pre-generated multiClust validates -----
18:2. Error: multi_clust() correctly handles contrived boolean data ---------------

ERROR, WARNING, or Failure found in unit tests. See grep results above.

[catterbu]

@nsh87 will do this evening. Just got back from a meeting with Bill. My guess was absolutely correct. You set up everything perfectly, now he is jut waiting on the money and data I say "go."

On Mar 14, 2016, at 3:44 PM, Nikhil Haas notifications@github.com wrote:

@catterbu: never mind, it's not a stupid typo or anything. You're going to have to check out these failed tests to see what's going on:

1. Error: the 'clust_model' slot in the pre-generated multiClust validates ----- argument "FUN" is missing, with no default 1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage")) 2: eval(code, new_test_environment) 3: eval(expr, envir, enclos) 4: lapply(expect_is(f_clust@clust_model[[1]], "kmeans")) at test_multi_clustering.R:47 5: match.fun(FUN)
2. Error: multi_clust() correctly handles contrived boolean data --------------- more cluster centers than distinct data points. 1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage")) 2: eval(code, new_test_environment) 3: eval(expr, envir, enclos) 4: multi_clust(contrived_bool, krange = 2:7) at test_multi_clustering.R:81 5: stats::kmeans(d, k, iter.max = iter.max, nstart = runs, ...) at /home/travis/build/nsh87/receptormarker/R/multi_clustering.R:88 6: stop("more cluster centers than distinct data points.")
3. Failure (at test_multi_clustering.R#92): multi_clust() correctly handles non-boolean iris data k_best is not identical to 3. Differences: Mean relative difference: 0.3333333

* grep results from unit tests **

27:3. Failure (at test_multi_clustering.R#92): multi_clust() correctly handles non-boolean iris data 10:1. Error: the 'clust_model' slot in the pre-generated multiClust validates ----- 18:2. Error: multi_clust() correctly handles contrived boolean data ---------------

ERROR, WARNING, or Failure found in unit tests. See grep results above. — Reply to this email directly or view it on GitHub.

[nsh87]

@catterbu: I fixed the first error - that one was dumb.