inst/colourPickerTest/RSdump.R

In professorbeautiful/NNTbiomarkerHome: Calculate Design Parameters for Biomarker Validation Studies

RSsample <-
c(0.0341477327446855, 0.0434267846175871, 0.122475117841134, 
0.182294061841282, 0.192681563411215, 0.196168133750553, 0.239084210359342, 
0.317410132805927, 0.36346540642838, 0.400755617527035, 0.486746673937461, 
0.492640541572243, 0.592058786518414, 0.59327242368905, 0.602354220648288, 
0.717309126151143, 0.72107378119997, 0.828425157179304, 0.866343873794311, 
0.896840705665947, 0.902065478586641, 0.921847873244524, 0.933937296584508, 
0.943385773060858, 0.944608186870699, 1.05180708024565, 1.06285088815048, 
1.11195255460657, 1.13406722629253, 1.16609120617758, 1.18246511792937, 
1.19847922048171, 1.22536421832188, 1.26674461596734, 1.27702348144409, 
1.35634050093798, 1.40815702793248, 1.54111185856969, 1.55887162794174, 
1.56542369274271, 1.58174047094992, 1.5883547143239, 1.63167850072722, 
1.68015044762902, 1.76771906064991, 1.79428808367315, 1.9012892880433, 
1.95656145207205, 1.95819821023701, 1.99937205662989, 2.02160095896671, 
2.05722880105258, 2.06519995238409, 2.07369230898459, 2.09267977523432, 
2.09347391691965, 2.11596439580438, 2.12819460683443, 2.15094251268261, 
2.17102598777817, 2.17585298199312, 2.18102177277896, 2.21407502647239, 
2.26589174310792, 2.33199256240874, 2.33828057315566, 2.38180993772886, 
2.40102312448257, 2.41967757761256, 2.45004800119997, 2.45193119943092, 
2.46142343073572, 2.46686061997886, 2.47149399369995, 2.47263837666566, 
2.58262766138424, 2.62871598946335, 2.67619111752464, 2.75169751442052, 
2.80714720372381, 2.82158209209055, 2.94215623599418, 2.96160320150829, 
2.96977260530965, 2.97468012571051, 3.011642954468, 3.07353263724009, 
3.09501538809952, 3.09688490374525, 3.10014389396888, 3.22717423328359, 
3.24391248193194, 3.37358448112006, 3.38980891241806, 3.39922657648873, 
3.41667443974023, 3.4266331367435, 3.48038504981574, 3.4853130232816, 
3.48774016155644, 3.5262263032854, 3.54346288918679, 3.55985586539102, 
3.66765375432324, 3.682168149817, 3.70546441401538, 3.73082705463517, 
3.75077857749658, 3.98372449302496, 3.98875955497809, 3.99861165207326, 
4.03083106712154, 4.03685173444297, 4.03817997655771, 4.09296580993323, 
4.16869517087572, 4.20433134121992, 4.26138189519321, 4.32348061501641, 
4.36839154241773, 4.42262399690031, 4.60601765740197, 4.67851538020822, 
4.68361188762772, 4.70986724353626, 4.71060326078892, 4.72061062817377, 
4.76387080379195, 4.79814911128349, 4.87210404089241, 4.91242876232232, 
5.01343553356024, 5.05025536652832, 5.1536727670442, 5.15711241278617, 
5.2119105519999, 5.23741029176829, 5.24890974961723, 5.26383341834806, 
5.26869312790317, 5.31707206985449, 5.42127941482298, 5.4341355672172, 
5.49171373782584, 5.52130990563674, 5.53883575223372, 5.57667503659875, 
5.59384474844229, 5.6142756951096, 5.70917171090641, 5.76347213425427, 
5.81517538747954, 5.9162925772001, 5.93596846529695, 5.95157991402346, 
5.985400473196, 6.00607930442887, 6.01207623801839, 6.03504005722835, 
6.0377786655783, 6.10906615169685, 6.1878847600389, 6.34594585871555, 
6.37697545807322, 6.41343846296895, 6.41521195401068, 6.42627723521425, 
6.43787443601022, 6.50738116175108, 6.52029992625987, 6.53499336999086, 
6.64680430430774, 6.68072865693963, 6.78503447317246, 6.81192481956445, 
6.82306285898829, 6.85913624320828, 6.96784655019383, 6.97555480045629, 
6.98760946263211, 7.00558069051283, 7.00665895030296, 7.04256921018401, 
7.06261061763004, 7.07179980423385, 7.13320369814931, 7.19849306972402, 
7.23839839005749, 7.24134794264097, 7.31287254523737, 7.48667537170394, 
7.49061980299522, 7.49882816744727, 7.51076401917222, 7.53241429896336, 
7.53985300941635, 7.56594171419779, 7.57422235690461, 7.57575026333954, 
7.60717977831174, 7.70747642498279, 7.76114451717311, 7.80599102985215, 
7.81177818207471, 7.86014810042903, 7.86512634011402, 7.97247879116271, 
7.98066679126956, 8.04460637729926, 8.10488302705703, 8.26393511568869, 
8.27150893749226, 8.40685194529842, 8.40900417079808, 8.56180749785761, 
8.63764734856617, 8.64690729455643, 8.68774727017403, 8.70016762172242, 
8.72273244759894, 8.73064352638122, 8.74125984144036, 8.78507974830619, 
8.81380592079225, 8.867408023662, 8.92360193734212, 8.95443385996259, 
9.00227240931364, 9.07605470885867, 9.11911314425033, 9.13972434130476, 
9.28032675316419, 9.29371049044041, 9.43212018603767, 9.45978251481222, 
9.46407579954791, 9.47193782998033, 9.56082614837424, 9.56871911985071, 
9.72183573241826, 9.78945548107044, 9.85711700519455, 9.90958548888946, 
10.0287840363745, 10.0546259438082, 10.1347119717291, 10.1392408359888, 
10.2522433370879, 10.2594482046827, 10.2702812925933, 10.328904122964, 
10.3305157455137, 10.3469672677896, 10.4099110300457, 10.4776426514445, 
10.5563843215218, 10.5761138398854, 10.7059070851821, 10.7211876218486, 
10.8231061409992, 10.8876596443749, 10.897657170799, 10.927078402309, 
10.9402658955207, 11.043473737625, 11.051145580293, 11.1799470796189, 
11.2199315048975, 11.3530599506612, 11.5411334754435, 11.7537977655783, 
11.775886332345, 11.855285253111, 11.9671646652666, 12.0269225325383, 
12.0452121382799, 12.2328145234718, 12.2678940848781, 12.2779383307273, 
12.3284381640582, 12.4072649080027, 12.4103749968588, 12.4126911544335, 
12.4728671734637, 12.4911363765063, 12.5742126368188, 12.5804479830203, 
12.5856114981596, 12.605293636322, 12.6094760972739, 12.6255472528729, 
12.6718143629445, 12.6746369725896, 12.7886036178016, 12.9038161726016, 
12.9904682913458, 13.0489429478982, 13.0640633824173, 13.1492173745064, 
13.4590087246729, 13.4853558601909, 13.4867582241559, 13.5013840580923, 
13.5196899109861, 13.5397157932962, 13.5457054809365, 13.5638393589427, 
13.6737162043565, 13.739043940557, 13.8498815529706, 13.8815335472661, 
13.8940498255597, 13.9277118449904, 14.0014084148607, 14.0435418605607, 
14.069299893108, 14.0940251364921, 14.14563265321, 14.2226810612011, 
14.2688725983784, 14.2735196055651, 14.3243435030832, 14.3641567891639, 
14.4158675730722, 14.499363097711, 14.5426173578614, 14.578718711757, 
14.7100075460193, 14.7702836140333, 14.8638795109421, 14.8745556985403, 
14.9861215633889, 14.9977233310513, 15.0606266997687, 15.163468478719, 
15.1902346603422, 15.2964924196811, 15.453029932844, 15.4910097818103, 
15.5118621450185, 15.5774811987606, 15.699692082273, 15.7126242529847, 
15.7424301824042, 15.7561330409683, 15.7708278327994, 15.9280013349827, 
15.9325394502859, 15.9927072869078, 16.0145948036237, 16.0587779908969, 
16.1032908177916, 16.1673103872845, 16.2311366795365, 16.4459966052106, 
16.6630658507743, 16.8661328831567, 16.992414846693, 17.0588911801901, 
17.074541261527, 17.2076570976103, 17.4464338686092, 17.4622985130222, 
17.6043725068418, 17.6073088433151, 17.7247411350355, 17.7426299268678, 
17.7502968607418, 17.7698754459318, 17.8172645226011, 17.8889119246895, 
17.9480827561874, 17.976124077956, 18.068840097994, 18.1399586310636, 
18.2008556238003, 18.2037190030355, 18.238050553591, 18.2655609406009, 
18.3533010464072, 18.3917282714179, 18.400446841338, 18.4388226903446, 
18.5658772853487, 18.6524646212116, 18.7782175620178, 18.839694662586, 
18.8408716178113, 18.9923366816472, 19.1313257579504, 19.2764582728232, 
19.333185853825, 19.3789776745755, 19.4107366086349, 19.4139248237554, 
19.5095810108948, 19.5582507335466, 19.5810734106592, 19.6049066537581, 
19.9630986901175, 20.1705481853298, 20.2142205783627, 20.3952231127109, 
20.4626871554925, 20.5771913738259, 20.5790663308174, 20.584159184068, 
20.7761751301662, 20.798118167693, 20.8809648176424, 20.9015634426278, 
20.9962791899401, 21.0536957780197, 21.1410898712017, 21.361127043596, 
21.4182438225995, 21.5019916230266, 21.514207875639, 21.7221756919149, 
21.736100006765, 21.7637508756224, 21.7970903570768, 21.8110213332487, 
21.897841029167, 22.3347229067408, 22.4562186077826, 22.6377475185799, 
22.8444553126927, 23.0450785355883, 23.1241593367011, 23.175602968719, 
23.204463286455, 23.2807488747474, 23.4736737690131, 23.5362116648609, 
23.5502602445824, 23.6797622721097, 23.7307324677975, 23.7449112890575, 
23.7640121561234, 23.8617449681814, 23.8678985597702, 23.8834683775715, 
23.9425372183559, 23.9471087351823, 23.9532986334893, 24.0509560598034, 
24.2112314738392, 24.3166186095571, 24.3465964206131, 24.3561771843555, 
24.4566373246497, 24.7467276462071, 24.8610916330268, 24.888395930881, 
24.9512577033682, 24.9635168707328, 25.0708587257086, 25.1115580007945, 
25.364753645327, 25.5798267000411, 25.613896798195, 25.731617377588, 
25.8843879468047, 26.0515110797759, 26.213603883139, 26.2321205739521, 
26.3167765807096, 26.3360943027734, 26.466037934823, 26.5263840966309, 
26.6912589563496, 26.7489063355321, 27.0493246573102, 27.1043563130532, 
27.1948298414358, 27.296107637546, 27.3316003844669, 27.3488508401201, 
27.6033034140655, 27.6314229916636, 27.7357891714667, 28.076104288549, 
28.1493648677492, 28.2128441001655, 28.3082658149017, 28.3160701942996, 
28.968865826598, 29.2689595485349, 29.3129286997718, 29.3670149513731, 
30.0357336470291, 30.0495940866852, 30.0934654930863, 30.1582974701517, 
30.1669383885581, 30.279072875669, 30.3266938372358, 30.361990455642, 
30.7007433564885, 30.729294006949, 30.7912726111272, 30.8372519076782, 
30.8591541259839, 30.9377723653265, 30.949282536861, 31.0759266356764, 
31.1875292378366, 31.3035045513525, 31.5632085610105, 31.7839092669357, 
31.885690676628, 31.9615780669872, 31.9875964452163, 32.0688868058347, 
32.177833650086, 32.2204861644342, 32.2594336841693, 32.3449432784243, 
32.4049906565306, 32.4704602241781, 32.6959474803825, 32.8054330997729, 
33.1045776603925, 33.2610068982771, 33.300728816971, 33.4685489472713, 
33.5579780816322, 34.007621551503, 34.0415289067815, 34.0598452448206, 
34.1964450602895, 34.364758723444, 34.4892162978846, 34.5003127245506, 
35.0221698624073, 35.4771095713397, 35.6210510793235, 35.629504952441, 
35.679377825725, 35.8533191380412, 35.9720074014349, 36.4281697365238, 
36.5451330406705, 37.1750808218197, 37.3045664995735, 37.3128613150438, 
37.5259189507991, 37.6890402944452, 37.7895431776007, 37.8166932420868, 
38.1570398144645, 38.6260665224492, 38.6523262049951, 38.6551915117573, 
38.6735650097902, 38.734953138291, 38.8684621156155, 39.0129336225806, 
39.0179984581546, 39.4169219663787, 39.5602682216372, 40.383658523618, 
40.75977669517, 40.9191354246815, 41.3735512552149, 41.6776266199116, 
41.7147928487964, 41.7796447616898, 41.895496657111, 42.0047991494133, 
42.0832767714447, 42.0960311652639, 42.3702153085449, 42.4522329386294, 
42.7628969900881, 43.1077259856007, 43.462348907423, 43.5401898503539, 
43.7020121089972, 43.8891128223004, 44.078382513414, 44.1130326770007, 
44.1422470927616, 44.1635795194299, 44.2274406911608, 44.3202958138567, 
44.6004808914196, 44.7094778282708, 44.7382971220235, 44.7529860136203, 
44.9550111318195, 46.2161467110393, 46.275781943277, 46.8438038139098, 
47.0284557299465, 47.5207510213894, 49.4016173238031, 49.4703713024605, 
49.4997269266138, 49.8416272459904, 49.9434091884013)
RSsampleBtoT <-
c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L)
smartBarPlot <-
function (the.split, groupNames, groupOrder = groupNames, groupColors, 
    ylim., pointcol = "blue", col = "grey", round = TRUE, squeeze = 1, 
    na.rm = TRUE, ...) 
{
    if (na.rm) 
        the.split = lapply(the.split, remove.missing)
    if (missing(groupNames)) 
        groupNames = names(the.split)
    if (missing(ylim.)) 
        ylim. = range(unlist(the.split))
    boxplotdata = lapply(the.split, boxplotdataJitter, round = round)
    for (element in 1:length(boxplotdata)) rownames(boxplotdata[[element]]) = NULL
    names(boxplotdata) = groupNames
    maxcircles = max(sapply(boxplotdata, function(group) max(rle(group[, 
        2])$lengths)))
    for (group in groupNames) {
        boxplotdata[[group]][, "x"] = boxplotdata[[group]][, 
            "x"]/squeeze
        boxplotdata[[group]][, "x"] = boxplotdata[[group]][, 
            "x"] + (which(group == groupNames))
    }
    boxplotdataMatrix = boxplotdata[[1]]
    for (group in 2:length(boxplotdata)) boxplotdataMatrix = rbind(boxplotdataMatrix, 
        boxplotdata[[group]])
    if (missing(groupColors)) 
        boxcol = "black"
    else {
        print(groupColors)
        if (length(groupColors) == length(groupNames)) {
            boxcol = groupColors
            pointsPerBox = unlist(sapply(boxplotdata, nrow))
            catn("pointsPerBox = ", pointsPerBox)
            pointcol = rep(groupColors, times = pointsPerBox)
        }
        else if (length(groupColors) == 1) {
            pointcol = groupColors
            boxcol = groupColors
        }
        else warning("groupColors ignored;  length = " %&% length(groupColors) %&% 
            " with " %&% length(groupNames) %&% "groups")
    }
    print(pointcol)
    plot(boxplotdataMatrix, col = pointcol, axes = F, xlab = "", 
        ylab = "", xlim = c(1/2, length(boxplotdata) + 1/2), 
        ylim = ylim.)
    boxplot(the.split, boxwex = 0.5, xlim = c(1 - 0.4, length(the.split) + 
        0.4), ylim = ylim., border = boxcol, names = groupNames, 
        cex.lab = 1.5, cex.axis = 1.5, staplewex = 1, add = TRUE, 
        ...)
    return(invisible(boxplotdata))
}
boxplotdataJitter <-
function (y, round = TRUE, nCirclesPerInch = 11.48936, print = FALSE) 
{
    nCirclesPerInch = 11.48936
    linesPerYAxis = nCirclesPerInch * par("pin")[2]
    if (print) 
        catn("linesPerYAxis ", linesPerYAxis)
    if (length(y) == 0) {
        return(cbind(x = numeric(0), y = numeric(0)))
    }
    y = sort(y)
    if (round & (max(y) > min(y))) 
        ygroup = round(linesPerYAxis * (y - min(y))/(max(y) - 
            min(y)))
    else ygroup = y
    ty = table(ygroup)
    maxEqual = max(ty)
    if (print) 
        catn("maxEqual ", maxEqual)
    x = unlist(lapply(ty, function(n) cumsum((0:(n - 1)) * (-1)^(1:n))))
    xUserPerInch = (par("usr")[2] - par("usr")[1])/par("pin")[1]
    circleWidthUser = xUserPerInch/nCirclesPerInch
    if (print) 
        catn("circleWidthUser ", circleWidthUser)
    xoffset = min(circleWidthUser, 2/3/maxEqual)
    if (print) 
        catn("xoffset ", xoffset)
    x = x * xoffset
    return(data.frame(x = x, y = y))
}
remove.missing <-
function (x) 
{
    if (is.factor(x) || is.character(x)) 
        return(x[!is.element(x, c("", " ", "NA", NA))])
    else return(x[!is.na(x)])
}