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assaforon / cir

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Documentation surrounding ordering of x's #1

Open adw96 opened 1 year ago

adw96 commented 1 year ago

Dear @assaforon ,

First of all, thank you for your excellent R package. We have been enjoying using it with with much success for reweighting-based estimators.

It took me some time to debug the following issue:

my_df <- structure(list(x = c(49.0046744288143, 74.6004805025514, 14.0424434314875, 
                              15.0093007827047, 8.73911971302957), y = c(1225.32722130527, 
                                                                         2362.0066919363, 121.935555430898, 4.03728696991483, 32.9374863651358
                              ), wt = c(1, 1, 1, 1, 1)), row.names = 2:6, class = "data.frame")

my_df %>% cirPAVA # fails
my_df[order(my_df$x), ] %>% cirPAVA() # runs

... because (as I understand it) I didn't realize that the inputs needed to be pre-ordered by x.

I therefore write only with the request that this be included (perhaps more prominently) in the documentation, or that an error message can alert me to the relevant issue.

Thank you for considering, and thank you again for the excellent package.

Sincerely,

Amy

assaforon commented 1 year ago

Hi Amy!

Thank you so much for your kind words and for the excellent point.

I'll have to go back and figure out why I didn't have an auto-ordering step there, possibly with un-ordering before return.

I think some of the functions do have a heads-up either in documentation or in error messages. Whatever route I take I will make sure it is self-consistent across the package.

I'm curious what is your use case for cir and what you're working on in general?

Feel free to also write me directly at @.***

Cheers, Assaf

On Mon, Jun 5, 2023 at 1:22 PM AmyW @.***> wrote:

Dear @assaforon https://github.com/assaforon ,

First of all, thank you for your excellent R package. We have been enjoying using it with with much success for reweighting-based estimators.

It took me some time to debug the following issue:

my_df <- structure(list(x = c(49.0046744288143, 74.6004805025514, 14.0424434314875, 15.0093007827047, 8.73911971302957), y = c(1225.32722130527, 2362.0066919363, 121.935555430898, 4.03728696991483, 32.9374863651358 ), wt = c(1, 1, 1, 1, 1)), row.names = 2:6, class = "data.frame")

my_df %>% cirPAVA # fails my_df[order(my_df$x), ] %>% cirPAVA() # runs

... because I didn't realize that the inputs needed to be pre-ordered by x.

I therefore write only with the request that this be included (perhaps more prominently) in the documentation.

Thank you for considering, and thank you again for the excellent package.

Sincerely,

Amy

— Reply to this email directly, view it on GitHub https://github.com/assaforon/cir/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABLQQDKCPVFOITJKEG4YP2DXJY5YFANCNFSM6AAAAAAY3OTAEQ . You are receiving this because you were mentioned.Message ID: @.***>

adw96 commented 1 year ago

Thanks so much for getting back to me so quickly, Assaf! Here is the full issue that I am continuing to try to understand. I apologize that these are such large vectors.

Regarding what we're doing, we use cir in tinyvamp (with preprint here arxiv.org/pdf/2204.12733.pdf) to help us estimate the empirical mean-variance relationship under a monotonicity constraint in our (usually microbiome) data, which we then use as weights in a weighted maximum likelihood estimator. The overall goal is to remove contamination and estimate distortion effects in high-throughput sequencing. I'd be happy to give more details if you're interested! (Or buy you a coffee, since we possibly work in the same building!

Thanks again, Assaf!

cc @ailurophilia, who is the mastermind behind tinyvamp.

xx <- c(81.0174173691156, 49.0046744288143, 74.6004805025514, 14.0424434314875, 
  15.0093007827047, 8.73911971302957, 8.73624170281569, 9.07291486562561, 
  7.17085440206417, 11.0613025626149, 18.9774416647036, 10.8972814682676, 
  6.16946763123808, 12.3878526896459, 52.9008776200101, 5.1047737845675, 
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  5.56518219366086, 6.55793713049063, 6.53779346783918, 11.2023022848657, 
  4.25301920883538, 6.03422241261011, 10.3678130730815, 5.76085541196832, 
  3.25450953995888, 3.25163224215958, 3.41853001902598, 3.08473415320403, 
  13.1014850266424, 3.01567268675989, 2.72504067132127, 2.65022385424565, 
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  6.63850827451625, 3.37536688323216, 2.54950999490934, 10.6555674811033, 
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  291.745538774801, 942.305059893746, 3659.25644694897, 459.249891174836
)
yy <- c(59845426.5310337, 1225.32722130527, 2362.0066919363, 121.935555430898, 
        4.03728696991483, 32.9374863651358, 59.8494310589034, 50.0261228995168, 
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        16.7574424336913, 15.839403534932, 2429.60940141094, 14.0809064894212, 
        13.2404483426698, 10.874235406431, 10.874235406431, 10.1372182623566, 
        9.42606136895154, 9.42606136895158, 8.74076472621569, 7.44775219275191, 
        314.203482957226, 4.18936060842306, 4.18936060842306, 3.73680622171072, 
        3.73680622171072, 3.73680622171072, 3.31011208566765, 2.53430456558934, 
        2.18519118155409, 2.1851911815541, 2.1851911815541, 1.56454516549144, 
        1.29301253346402, 1.04734015210588, 0.633576141397425, 0.46548451204711, 
        0.465484512047112, 0.206882005354306, 0.206882005354306, 129669.127327428, 
        2972824.42762482, 1122993.84025579, 136.970364539146, 29403.2307832616, 
        87998.0957279982, 126813.333901614, 9894297.18911188, 11287384.5582114, 
        23567.8963242288, 1817621.8204871, 1779.91956291354, 26660.310970961, 
        54225.4902515257, 53239.6911941509, 1258.43506217747, 35335.7393003647, 
        61437.0507836797, 34069.5897078185, 2987.76275663571, 22798.6846063035, 
        1080.21389525614, 3969426.09345137, 56536.5073189035, 9871.68253928722, 
        677255.744575069, 111.966001022743, 221334.374226138, 6170.22179812149, 
        7046.6372045717, 21659.2972603895, 622.084747663738, 11840.2279696325, 
        11652.8276816142, 7156.54638074337, 10394.9960203535, 2495.35330641784, 
        950.311066983739, 22547.4445085391, 18359.2111279043, 11560.6535200957, 
        1058.67783017799, 767.107565339355, 13551.3856844027, 39165.9473646466, 
        8157.67739325489, 13434.8794622807, 5781.43686284325, 25152.3195952591, 
        20374.0995564742, 12540.9919547787, 11673.3318640984, 5847.77936201798, 
        2489.6557367817, 9502.72862280965, 29146.5359593265, 2974.3680391483, 
        126483.345164156, 9010.40515300348, 812.742769941142, 11542.5641497888, 
        13817.5276583423, 996.910348136158, 13877.0217882991, 11898.3307394796, 
        9474.26520974375, 75243.5388190039, 12597.6743320845, 6401.35430673316, 
        5713.03406258971, 55423.976747569, 1588.9443093084, 2540.54124322039, 
        7284.27341002247, 3717.73337729609, 81353.8767122612, 3163.62112908225, 
        15218.2278028362, 38323.9700145195, 2252.32411171521, 8536.88044518379, 
        6401.35430673315, 1974.07497363074, 2334.37142721803, 2685.54329907197, 
        2177.37359215984, 2222.70644649961, 2071.48863925211, 472.592032739302, 
        3395.20730197545, 7745.1818479928, 6081.83696002622, 3064.87429308247, 
        1636.83214685016, 2798.11874549336, 21016.0704527921, 413.021184262975, 
        6566.28577539164, 9010.4051530035, 7396.53987435312, 5693.94290112396, 
        1380.89006899812, 12371.7116644933, 2294.7895599167, 2506.38945544337, 
        6319.2928553287, 31860.1008941933, 1147.45069549403, 1063.4176333101, 
        2818.14299795536, 958.951436804255, 10233.2352644561, 4187.97776675741, 
        6269.33965061088, 823.22046792314, 745.37006639799, 4671.56249619229, 
        6965.0554408261, 2467.45673407714, 1071.12306722643, 1495.91631381263, 
        651.879290751535, 10820.9182463838, 2940.21460026475, 601.267743033154, 
        588.934373450266, 1399.37587112525, 12597.6743320845, 951.13923767727, 
        564.651055100536, 21459.4384500603, 3499.09836725722, 523.385389773334, 
        5246.1865300739, 1766.77804630932, 467.15033675291, 21722.732958396, 
        440.231000292846, 429.686927851518, 424.46281923286, 6344.09997484492, 
        364.265751113269, 335.892610725691, 19.2476441138935, 2198.9343559046, 
        2818.14299795535, 261.748610422341, 257.674764251828, 1625.72023591233, 
        253.632869815985, 230.052489629011, 1845.46832268693, 222.447976777386, 
        10093.1151709617, 200.401279854605, 196.838661438823, 9234.53259498197, 
        7991.913817747, 388.788707473028, 179.504845379971, 5129.47821139015, 
        7221.81203562383, 8096.62448761684, 7116.68252642582, 156.579475753747, 
        6722.75539939594, 135.219741126386, 393.789153948992, 123.717116644936, 
        120.92133986125, 97.4174582518451, 118.157514812235, 115.42564149789, 
        5095.49886424422, 112.725719918216, 104.817665587219, 104.817665587219, 
        308.669732786258, 97.1971768682582, 245.644936148311, 104.817665587219, 
        94.7209174312795, 89.8642537613335, 4034.83158320165, 89.8642537613335, 
        67.4980394918464, 120.92133986125, 63.4082174539971, 63.4082174539971, 
        59.4462023548311, 57.5131224072535, 57.5131224072535, 55.6119941943474, 
        55.6119941943474, 53.7428177161116, 2368.67649552837, 53.7428177161116, 
        156.579475753746, 2479.58647942945, 44.8762113449936, 44.8762113449936, 
        2063.65092039927, 39.9396683383709, 299.851054017146, 39.9396683383711, 
        135.219741126386, 456.286746964873, 1758.37711560648, 35.2906909437847, 
        33.8049352815972, 33.8049352815972, 32.3511313540806, 30.9292791612347, 
        30.9292791612347, 29.5393787030594, 25.5613877365577, 23.0691524322433, 
        989.087127528643, 19.5704374858021, 55.6119941943474, 831.107933548373, 
        16.3592881513971, 13.4357044290283, 13.4357044290284, 598.336657393869, 
        11.6464072874694, 556.361509234859, 10.7996863186959, 9.20209958516108, 
        6.39034693413972, 5.17618101665324, 5.17618101665324, 191.857777003797, 
        4.61702565991604, 220.560323962789, 4.08982203784953, 3.1312699977286, 
        2.69992157967418, 2.69992157967419, 128.978182524952, 92.3453259498175, 
        1.59758673353509, 47.0930676687192, 0.782817499432262, 0.57513122407271, 
        0.575131224072712, 0.255613877365692, 0.255613877365692, 6.74833539942245, 
        23958.2881012806, 28714.2452084544, 7361.13273040593, 71960.4563406274, 
        4529.97096103939, 3320618.55597668, 432635.205931402)
cir::cirPAVA(y = yy, x = xx)
adw96 commented 1 year ago

Hi @assaforon -- I was wondering if you have any estimate regarding when this issue may be fixed. Our tinyvamp tests are failing and we are debating whether we should re-write our tests or wait for a cir fix.

I apologize for bothering you again.

Best wishes,

Amy