Nothing
tests/testthat/test_CovarianceWithMissing.R
In FastImputation: Learn from Training Data then Quickly Fill in Missing Data
context("CovarianceWithMissing")
miss <-
c(1755L, 1010L, 3612L, 2651L, 2603L, 1824L, 1898L, 154L, 4674L,
667L, 2904L, 4334L, 173L, 1934L, 3223L, 1975L, 2187L, 3783L,
2159L, 59L, 4931L, 3181L, 4114L, 1261L, 1370L, 3678L, 4516L,
1772L, 3627L, 2631L, 1456L, 1490L, 1534L, 3474L, 2959L, 4481L,
1285L, 4036L, 2285L, 1598L, 4030L, 4705L, 2906L, 244L, 1927L,
1939L, 1054L, 3320L, 2209L, 3490L, 1637L, 2275L, 4605L, 2186L,
573L, 1566L, 2985L, 520L, 1546L, 4891L, 2658L, 2442L, 628L, 1567L,
2561L, 4411L, 3558L, 4803L, 3284L, 4677L, 4141L, 4412L, 2169L,
2008L, 4825L, 3214L, 1203L, 2242L, 1756L, 300L, 222L, 3638L,
2041L, 3043L, 1212L, 3311L, 620L, 4880L, 1426L, 4212L, 2883L,
4562L, 2921L, 1718L, 4912L, 2536L, 3532L, 4235L, 3235L, 1280L,
4420L, 3617L, 229L, 400L, 2258L, 4165L, 2189L, 2367L, 2526L,
1372L, 635L, 2632L, 4706L, 2483L, 4370L, 655L, 1362L, 213L, 951L,
2857L, 3000L, 1600L, 1968L, 2704L, 1524L, 1260L, 2450L, 4104L,
2377L, 4432L, 1052L, 3803L, 466L, 4157L, 3132L, 374L, 3764L,
328L, 1980L, 4392L, 2975L, 600L, 1098L, 2781L, 1284L, 4629L,
3239L, 2777L, 1626L, 759L, 1840L, 4149L, 1263L, 1991L, 1483L,
982L, 4546L, 4876L, 2040L, 2061L, 2465L, 1207L, 2099L, 4269L,
938L, 2855L, 4082L, 4248L, 3848L, 1185L, 4073L, 1634L, 949L,
4393L, 4670L, 1239L, 1374L, 752L, 789L, 166L, 20L, 3513L, 3220L,
3879L, 3545L, 4660L, 1194L, 802L, 3823L, 4576L, 3827L, 2128L,
4260L, 2426L, 3951L, 1436L, 1411L, 768L, 1105L, 1706L, 905L,
1903L, 2175L, 1581L, 2936L, 3718L, 164L, 4080L, 3672L, 2590L,
4633L, 839L, 3476L, 4380L, 88L, 2288L, 1045L, 548L, 4572L, 1778L,
2028L, 843L, 2706L, 2409L, 3966L, 2022L, 2030L, 968L, 1553L,
2204L, 305L, 182L, 3630L, 3838L, 195L, 1459L, 4159L, 4940L, 3897L,
3190L, 1236L, 792L, 3109L, 351L, 3775L, 1453L, 3234L, 2191L,
2860L, 1861L, 3709L, 873L, 3812L, 3299L, 3128L, 1074L, 1083L,
279L, 4725L, 1183L, 1469L, 4192L, 1336L, 3307L, 1555L, 760L,
2618L, 3511L, 4979L, 1663L, 1246L, 1681L, 3289L, 1941L, 4117L,
58L, 2765L, 2396L, 4977L, 4995L, 1565L, 2499L, 1076L, 2001L,
1254L, 895L, 1672L, 2923L, 140L, 4476L, 2628L, 1657L, 859L, 2225L,
3650L, 4878L, 2914L, 4965L, 3686L, 4533L, 1379L, 1403L, 4942L,
1431L, 1494L, 3956L, 1107L, 1106L, 2226L, 1390L, 3232L, 4990L,
2506L, 2711L, 513L, 3590L, 957L, 4950L, 4985L, 2510L, 3386L,
2559L, 186L, 2467L, 2890L, 4255L, 2192L, 143L, 2570L, 1190L,
1082L, 4771L, 746L, 3443L, 636L, 1316L, 886L, 1342L, 3505L, 2274L,
2598L, 4197L, 2394L, 1335L, 1854L, 998L, 4132L, 1359L, 3904L,
1674L, 3837L, 735L, 3573L, 2405L, 1376L, 2114L, 3264L, 2249L,
793L, 4713L, 4150L, 333L, 2120L, 1389L, 732L, 4989L, 4004L, 3354L,
1406L, 3472L, 1949L, 3310L, 4902L, 2786L, 419L, 4489L, 1206L,
2449L, 304L, 3349L, 434L, 4415L, 3169L, 4506L, 4218L, 1416L,
2503L, 1504L, 1558L, 4622L, 2866L, 4962L, 3615L, 483L, 3522L,
2885L, 2731L, 2576L, 4586L, 840L, 457L, 233L, 1166L, 3095L, 1599L,
4401L, 3433L, 2986L, 1425L, 916L, 3914L, 2989L, 318L, 2889L,
4709L, 4071L, 1733L, 3195L, 1678L, 3040L, 2444L, 4174L, 1679L,
4699L, 3123L, 291L, 1650L, 176L, 4346L, 3834L, 239L, 113L, 4015L,
2092L, 335L, 4487L, 907L, 1808L, 2216L, 555L, 3910L, 1113L, 2272L,
923L, 439L, 862L, 3364L, 4596L, 4898L, 1745L, 4035L, 259L, 4920L,
3367L, 420L, 4653L, 2929L, 1420L, 4984L, 1966L, 2086L, 1864L,
2034L, 602L, 4527L, 925L, 1275L, 2858L, 334L, 1300L, 3346L, 1666L,
4075L, 976L, 196L, 646L, 1112L, 1025L, 4062L, 403L, 3358L, 1805L,
3892L, 4866L, 2389L, 882L, 3697L, 102L, 501L, 854L, 1811L, 863L,
2150L, 4383L, 1219L, 3776L, 4502L, 3935L, 4726L, 2540L, 2408L,
1557L, 3822L, 4475L, 2032L, 956L, 3669L, 1150L, 4007L, 2118L,
298L, 2537L, 131L, 1852L, 2533L, 238L, 1993L, 3644L, 701L, 4992L,
203L, 1470L, 2684L, 1394L, 1548L, 858L, 4534L, 3357L, 46L, 2241L,
738L, 490L, 1320L, 3727L, 4845L, 801L, 3417L, 1917L, 4529L, 2243L,
4391L, 3304L, 510L, 2998L, 2733L, 2881L, 4524L, 4671L, 4615L,
2398L, 1099L, 417L, 970L, 4560L, 3856L, 3799L, 3120L, 4322L,
917L, 3230L, 4679L, 754L, 2493L, 2863L, 2412L, 3035L, 2214L,
1894L, 3507L, 440L, 1817L, 3390L, 4168L, 2091L, 2574L, 1873L,
1289L, 1647L, 2349L, 990L, 1547L, 1660L, 3674L, 1639L, 706L,
4296L, 144L, 3584L, 2336L, 2492L, 911L, 4033L, 1520L, 4640L,
4122L, 3524L, 3409L, 4711L, 1172L, 626L, 3820L, 607L, 4685L,
474L, 2489L, 4050L, 4018L, 391L, 2740L, 187L, 382L, 1944L, 60L,
532L, 2991L, 1224L, 2758L, 3939L, 747L, 861L, 3489L, 3715L, 3982L,
1407L, 687L, 2521L, 825L, 866L, 876L, 2718L, 4051L, 3130L, 625L,
13L, 2420L, 2597L, 2222L, 2725L, 1510L, 906L, 3186L, 3018L, 4098L,
3296L, 1232L, 4597L, 4652L, 2095L, 660L, 850L, 2260L, 3407L,
1839L, 2625L, 557L, 4525L, 574L, 2763L, 4910L, 492L, 257L, 2109L,
27L, 2355L, 1948L, 679L, 627L, 3839L, 559L, 4946L, 587L, 2157L,
1692L, 2075L, 4740L, 2218L, 4829L, 2262L, 4810L, 4120L, 4474L,
4584L, 2606L, 4185L, 3339L, 2732L, 944L, 4903L, 3400L, 4125L,
1358L, 2671L, 3710L, 3251L, 215L, 1021L, 950L, 1593L, 3204L,
2605L, 1645L, 2504L, 3900L, 2515L, 4807L, 197L, 3414L, 4016L,
3536L, 4583L, 2581L, 4327L, 3928L, 4207L, 2884L, 449L, 4108L,
1042L, 4720L, 4191L, 3899L, 1015L, 4480L, 3595L, 4900L, 2747L,
4186L, 1447L, 4906L, 1646L, 2888L, 2378L, 1977L, 2604L, 4116L,
4665L, 2077L, 4310L, 1325L, 1936L, 4490L, 3588L, 1175L, 1687L,
254L, 1276L, 1381L, 1028L, 4608L, 3972L, 230L, 1020L, 4376L,
1122L, 78L, 4628L, 3661L, 1515L, 885L, 3952L, 4522L, 4167L, 1800L,
3088L, 4594L, 181L, 1737L, 937L, 4413L, 3395L, 2197L, 2847L,
265L, 2749L, 148L, 2328L, 4779L, 3492L, 2188L, 4793L, 3819L,
3855L, 536L, 165L, 1030L, 3303L, 611L, 797L, 2256L, 2784L, 3309L,
831L, 354L, 2039L, 2390L, 4378L, 4813L, 3646L, 2079L, 3500L,
2451L, 1031L, 2155L, 3142L, 519L, 761L, 3037L, 2126L, 1872L,
3448L, 50L, 1851L, 4059L, 3173L, 2093L, 4053L, 3991L, 3512L,
3372L, 2911L, 2056L, 277L, 1527L, 57L, 2544L, 3188L, 3569L, 4381L,
748L, 2037L, 826L, 180L, 634L, 1272L, 4860L, 1981L, 12L, 4798L,
3808L, 1235L, 3523L, 824L, 2438L, 160L, 2455L, 2694L, 2298L,
2459L, 658L, 3057L, 4930L, 581L, 3337L, 375L, 2048L, 2479L, 2313L,
1796L, 2287L, 4842L, 1273L, 621L, 2569L, 1252L, 178L, 4083L,
2245L, 1227L, 1843L, 4222L, 2123L, 1970L, 433L, 2789L, 202L,
2637L, 4403L, 1244L, 565L, 171L, 2154L, 4883L, 74L, 2861L, 4056L,
4020L, 3636L, 4639L, 1378L, 4775L, 3577L, 1003L, 3074L, 1299L,
2917L, 3949L, 2995L, 3867L, 3067L, 2966L, 4619L, 4512L, 117L,
3765L, 2516L, 156L, 4867L, 920L, 1827L, 2283L, 3541L, 2687L,
3759L, 3981L, 3200L, 2424L, 4201L, 696L, 3789L, 2769L, 1836L,
3719L, 331L, 2017L, 1159L, 1005L, 4993L, 2265L, 1798L, 640L,
4046L, 3736L, 1291L, 2988L, 2281L, 3978L, 4944L, 779L, 2937L,
597L, 1802L, 2908L, 2200L, 4145L, 2446L, 4288L, 3495L, 24L, 4275L,
377L, 2329L, 1419L, 775L, 2415L, 2027L, 4333L, 468L, 3548L, 3118L,
3967L, 4914L, 1611L, 3416L, 4202L, 2645L, 81L, 4307L, 4661L,
476L, 4313L, 1877L, 4888L, 3713L, 4044L, 1180L, 2599L, 1559L,
1034L, 4749L, 4762L, 903L, 2926L, 1452L, 1428L, 1667L, 3859L,
899L, 4171L, 111L, 3145L, 2776L, 3961L, 2968L, 1760L, 1521L,
1011L, 1354L, 595L, 127L, 2062L, 4134L, 4452L, 214L, 3184L, 4418L,
1495L, 4823L, 2770L, 758L, 3086L, 2647L, 268L, 4882L, 1823L,
3735L, 3068L, 1442L, 3344L, 2130L, 2428L, 2650L, 306L, 1535L,
4495L, 810L, 267L, 2462L, 4999L, 1356L, 3150L, 4570L, 3442L,
3061L, 411L, 1522L, 2748L, 4460L, 2482L, 82L, 2181L, 3231L, 3761L,
3496L, 3989L, 4538L, 1363L, 3539L, 4684L, 985L, 2843L, 3437L,
4861L, 4361L, 1804L, 1279L, 836L, 3731L, 809L, 1148L, 1301L,
975L, 392L, 1391L, 3805L, 3228L, 2657L, 1628L, 674L, 3540L, 4929L,
4250L, 3787L, 3467L, 3700L, 3980L, 4837L, 4176L, 999L, 4835L,
4355L, 1424L, 4961L, 497L, 3240L, 1315L, 3270L, 2517L, 3642L,
4194L, 814L, 4451L, 3960L, 3458L, 4220L, 509L, 3675L, 2850L,
4341L, 3350L, 3272L, 796L, 1923L, 955L, 4885L, 3918L, 869L, 642L,
4668L, 632L, 1264L, 1282L, 327L, 3689L, 4089L, 1382L, 1153L,
788L, 70L, 1474L, 2762L, 4283L, 4938L, 4446L, 4573L, 1930L, 1467L,
1912L, 3420L, 993L, 1801L, 4886L, 892L, 355L, 4505L, 4657L, 2484L,
3083L, 282L, 1067L, 2913L, 4869L, 4473L, 1699L, 4491L, 1488L,
2010L, 1069L, 1051L, 1126L, 578L, 352L, 4302L, 2916L, 2280L,
4812L, 4911L, 1705L, 1785L, 585L, 4027L, 1019L, 2529L, 2572L,
4736L, 3104L, 220L, 1552L, 708L, 4486L, 4613L, 692L, 1795L, 1893L,
68L, 379L, 841L, 169L, 3263L, 4264L, 1543L, 724L, 2567L, 3148L,
2264L, 2591L, 3335L, 1117L, 936L, 1450L, 3236L, 2413L, 1711L,
1904L, 309L, 228L, 1913L, 952L, 2964L, 3990L, 1767L, 3655L, 1954L,
2156L, 803L, 3192L, 2575L, 1445L, 1413L, 1696L, 2752L, 1799L,
4759L, 142L, 3306L, 2307L, 2494L, 877L, 4792L, 248L, 699L, 4634L,
1759L, 1916L, 3800L, 856L, 888L, 1781L, 3108L, 97L, 2085L, 4581L,
2522L, 3211L, 4874L, 2812L, 4569L, 1739L, 4294L, 1306L, 2379L,
1164L, 3620L, 4295L, 2578L, 4009L, 1151L, 1889L, 2289L, 4708L,
292L, 37L, 3869L, 1454L, 545L, 4111L, 2683L, 4925L, 3383L, 2696L,
2406L, 4559L, 3036L, 930L, 842L, 3737L, 4066L, 4225L, 3465L,
1174L, 4166L, 2326L, 4095L, 1688L, 3292L, 921L, 484L, 3302L,
208L, 966L, 2656L, 3667L, 3692L, 3487L, 1111L, 833L, 1792L, 2853L,
2624L, 4344L, 1266L, 3135L, 3498L, 2960L, 1465L, 2825L, 1297L,
4574L, 3887L, 1092L, 629L, 4737L, 4641L, 2113L, 1911L, 1184L,
3831L, 2722L, 3203L, 954L, 1773L, 3600L, 1549L, 1643L, 3226L,
2741L, 3215L, 4901L, 1976L, 1726L, 4766L, 2901L, 1763L, 4738L,
1103L, 3113L, 1983L, 2805L, 3225L, 313L, 386L, 414L, 2158L, 3038L,
1708L, 4301L, 1670L, 4323L, 608L, 2595L, 2707L, 221L, 1830L,
4635L, 2060L, 2L, 1868L, 1110L, 2735L, 1853L, 742L, 1463L, 2314L,
237L, 4450L, 1493L, 1146L, 3009L, 4817L, 4228L, 3394L, 3355L,
3608L, 51L, 1518L, 4681L, 3008L, 4658L, 3772L, 2673L, 1457L,
2724L, 2862L, 3639L, 1850L, 939L, 4328L, 3041L, 2562L, 1355L,
3919L, 1570L, 2044L, 1690L, 28L, 3459L, 613L, 4856L, 1523L, 2478L,
1278L, 2938L, 3253L, 1764L, 4504L, 2560L, 2721L, 3632L, 1295L,
1812L, 2717L, 1061L, 4733L, 4443L, 4691L, 791L, 242L, 3351L,
2180L, 4158L, 1238L, 3424L, 3218L, 1393L, 1508L, 4881L, 2880L,
1100L, 274L, 3097L, 3102L, 1400L, 1636L, 1652L, 3001L, 2182L,
4436L, 109L, 118L, 485L, 410L, 1697L, 1368L, 3368L, 2117L, 4675L,
2147L, 3419L, 2488L, 3126L, 853L, 654L, 2633L, 1017L, 4983L,
1118L, 933L, 325L, 1724L, 3927L, 2728L, 2045L, 4363L, 2925L,
529L, 2065L, 2208L, 1188L, 4022L, 4423L, 2865L, 1680L, 3752L,
4010L, 3599L, 1344L, 575L, 522L, 3022L, 4632L, 4770L, 2082L,
3858L, 922L, 4190L, 3771L, 896L, 1157L, 4662L, 3865L, 4760L,
4184L, 1624L, 447L, 4135L, 2646L, 240L, 617L, 2552L, 3872L, 3801L,
1247L, 1810L, 2410L, 1758L, 4309L, 25L, 3267L, 2166L, 4388L,
1330L, 4892L, 3587L, 4110L, 2793L, 4254L, 580L, 2014L, 4588L,
368L, 1538L, 4298L, 429L, 1492L, 258L, 2703L, 4801L, 4778L, 2556L,
2193L, 472L, 1147L, 353L, 2555L, 3359L, 1959L, 2839L, 4003L,
1952L, 1617L, 405L, 4899L, 1712L, 757L, 3434L, 4102L, 245L, 93L,
1675L, 319L, 365L, 262L, 2539L, 1152L, 3360L, 3784L, 387L, 794L,
898L, 4045L, 1644L, 3105L, 4767L, 718L, 2356L, 4673L, 1528L,
4532L, 1132L, 730L, 1434L, 4173L, 4305L, 2571L, 3527L, 4741L,
808L, 42L, 2437L, 1392L, 4462L, 4276L, 962L, 4002L, 1135L, 2112L,
4819L, 3249L, 3578L, 3780L, 1128L, 4846L, 3457L, 332L, 3868L,
1899L, 1729L, 4284L, 4092L, 3365L, 3079L, 689L, 3729L, 887L,
669L, 1108L, 3377L, 3015L, 3060L, 3343L, 4311L, 2363L, 3609L,
3096L, 170L, 2514L, 583L, 3807L, 847L, 3294L, 3435L, 3325L, 3894L,
2893L, 3042L, 137L, 2194L, 4530L, 1461L, 3544L, 855L, 4238L,
4445L, 4069L, 3986L, 2543L, 4908L, 1009L, 3911L, 4396L, 39L,
564L, 4364L, 4356L, 1776L, 1486L, 362L, 4614L, 4337L, 3255L,
4279L, 9L, 1137L, 1318L, 3308L, 1070L, 3943L, 3456L, 4710L, 2611L,
2124L, 3004L, 4127L, 2374L, 1205L, 1576L, 2691L, 4461L, 1689L,
2501L, 556L, 2944L, 361L, 3478L, 206L, 3168L, 3885L, 2832L, 21L,
4826L, 3777L, 943L, 2661L, 4958L, 2879L, 2012L, 2816L, 2350L,
1848L, 4427L, 3796L, 753L, 834L, 3121L, 3515L, 1095L, 4650L,
3987L, 868L, 1310L, 1256L, 2331L, 390L, 1380L, 3485L, 1694L,
4515L, 2286L, 370L, 4057L, 4440L, 4267L, 1905L, 1519L, 4126L,
1961L, 2616L, 1065L, 4895L, 1047L, 4320L, 2161L, 3746L, 1987L,
1143L, 1387L, 2295L, 1439L, 2441L, 99L, 2452L, 2919L, 2143L,
526L, 3373L, 572L, 1462L, 4179L, 891L, 2319L, 715L, 1819L, 145L,
848L, 2359L, 2739L, 3657L, 659L, 1618L, 3103L, 2491L, 2388L,
100L, 1985L, 4400L, 3683L, 647L, 1170L, 4847L, 3305L, 606L, 3704L,
3716L, 442L, 2952L, 1791L, 4585L, 3691L, 1938L, 4857L, 1531L,
455L, 3062L, 1233L, 4773L, 1719L, 3535L, 4821L, 1023L, 2644L,
4047L, 1847L, 4933L, 3594L, 3179L, 1229L, 2498L, 2477L, 3874L,
1807L, 1039L, 3039L, 1698L, 4163L, 2534L, 4567L, 818L, 1427L,
3570L, 398L, 3742L, 3242L, 879L, 3469L, 524L, 3950L, 430L, 3013L,
3379L, 4564L, 4539L, 2854L, 614L, 4085L, 3504L, 1879L, 3574L,
4739L, 2699L, 288L, 1217L, 255L, 3212L, 3862L, 1947L, 1541L,
4048L, 2674L, 3571L, 4170L, 3641L, 1230L, 3701L, 3098L, 1710L,
133L, 1797L, 2635L, 4128L, 4648L, 1421L, 1686L, 2206L, 3888L,
4271L, 4672L, 3361L, 1418L, 3370L, 4966L, 2078L, 1866L, 4025L,
1749L, 126L, 1834L, 4067L, 1262L, 286L, 2667L, 3647L, 591L, 3089L,
1591L, 2434L, 2253L, 2915L, 4017L, 3677L, 2535L, 4156L, 3714L,
1602L, 4919L, 3723L, 2435L, 1029L, 4049L, 822L, 2947L, 722L,
3384L, 3930L, 2587L, 435L, 4325L, 2682L, 1703L, 774L, 4913L,
453L, 4278L, 3564L, 3555L, 4205L, 4666L, 3778L, 4031L, 38L, 2300L,
172L, 552L, 2141L, 4488L, 3276L, 3406L, 1195L, 2525L, 609L, 4265L,
4335L, 3147L, 2481L, 2757L, 4224L, 3758L, 2891L, 3143L, 4193L,
1286L, 2557L, 77L, 225L, 2830L, 924L, 2612L, 3438L, 3902L, 2196L,
4579L, 4402L, 3028L, 739L, 467L, 3010L, 2185L, 345L, 4257L, 2898L,
3399L, 1955L, 2419L, 3139L, 1182L, 4354L, 3436L, 2545L, 1144L,
372L, 4107L, 1664L, 76L, 3994L, 1156L, 648L, 1730L, 3941L, 1360L,
4732L, 1422L, 3426L, 1058L, 3493L, 811L, 992L, 2554L, 570L, 838L,
138L, 1121L, 1908L, 1027L, 531L, 1999L, 2971L, 2902L, 3589L,
401L, 2588L, 3932L, 2167L, 2471L, 3679L, 3165L, 124L, 2129L,
2453L, 4169L, 1223L, 110L, 702L, 750L, 4607L, 3363L, 1863L, 3056L,
2238L, 4794L, 4728L, 4918L, 104L, 3851L, 1339L, 945L, 2083L,
2136L, 3658L, 4724L, 2607L, 2392L, 3295L, 1398L, 4948L, 3604L,
4543L, 3983L, 3877L, 2151L, 469L, 4702L, 3445L, 4477L, 777L,
1876L, 4556L, 677L, 2301L, 3282L, 4843L, 712L, 4868L, 1735L,
67L, 2531L, 134L, 2237L, 4704L, 2701L, 2924L, 2652L, 1582L, 296L,
2110L, 4312L, 3392L, 2305L, 1116L, 1742L, 4189L, 2785L, 2984L,
3998L, 3112L, 189L, 3279L, 3921L, 1783L, 1294L, 1226L, 1089L,
3045L, 676L, 586L, 3471L, 530L, 1994L, 1935L, 3330L, 3381L, 4410L,
4941L, 671L, 4996L, 4782L, 3453L, 2790L, 1662L, 978L, 4042L,
1967L, 1635L, 663L, 2794L, 348L, 3648L, 114L, 3621L, 3640L, 2090L,
1606L, 3210L, 4818L, 653L, 1353L, 1114L, 3396L, 3779L, 2425L,
1338L, 2273L, 4055L, 8L, 2439L, 383L, 4626L, 3073L, 4144L, 947L,
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2173L, 537L, 4580L, 3092L, 721L, 276L, 3659L, 3550L, 2910L, 4974L,
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4213L, 4086L, 4223L, 2304L, 1651L, 3878L, 709L, 3863L, 3946L,
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3526L, 2679L, 168L, 3452L, 2622L, 4676L, 350L, 184L, 1700L, 2142L,
2021L, 819L, 3653L, 3687L, 281L, 2387L, 2965L, 4853L, 3428L,
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3853L, 4781L)
x.full <-
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2.24047484947906, 4.851568682903, -0.612209743388409, 4.64053613094402,
6.37300197942863, 4.77667216762443, 3.01157674673919, 2.39003037546731,
3.98705124445537, 5.24539482580431, 0.952077238990415, -1.25929043147384,
8.83518683163742, 9.67905990597786, 3.77467506964309, 3.3267630303517,
5.9051270202224, 5.19298219743963, 5.3047665192004, 2.39988966946043,
1.3240218748845, 3.7988517665392, 2.49088415614328, 2.5854728930113,
0.941738443671879, 1.39471689690284, 4.64843034400783, 3.76583715347816,
4.68507470387495, 11.4215301122455, 4.03345755772288, 1.9926244388882,
5.46343005552307, 3.1374082952857, 0.78965319442547, 7.65396985619888,
8.51483148204832, 5.30262052457091, 8.79511112335617, 5.10369946732517,
9.54663477268045, 2.00145675367386, 3.42923690403028, 5.55280464488671,
1.875447793798, 5.84695920120575, 2.40733362624327, 5.56821724976872,
4.92583614502899, 2.01280784526801, 5.8741859092085, 5.90286534889309,
3.81465154370379, 3.17248112337878, 5.90470267626223, 2.75198358014593,
0.0101110262182553, 10.5133374543899, 8.73554359017231, 6.33124618877542,
10.1571926498543, 4.11614074956542, -0.235594488084464, 6.55466823669685,
2.58173261084099, 4.1757115711121, 3.5064735629459, 7.01983794792461,
4.52657486447694, 3.82200809252202, 0.972370738212325, 8.37390568295937,
6.57382695393214, 6.83696041119528, 9.46731696802275, 7.50161713462025,
7.07943760569842, 5.45080249416059, 1.85640575587286, 2.77841117897263,
1.29721444694327, 4.38131398678851, 4.90575300941273, 5.89256018636704,
1.61162501702381, 10.0640045903002, 4.21281419015664, 2.73931718209816,
8.19930461987559, 1.71959115245854, 3.92673172685605, 5.16435507069159,
-0.443013779889997, 8.99372610324204, 0.498656462636761, 6.72382687073463,
4.41316843476709, 6.02206429903555, -1.38715357187282, 8.12418916887016,
5.50180276653606, 2.20076750694192, 7.45887371224926, 1.12423497329095,
8.32672064993794, 5.76662583459337, 3.01581497863461, 8.03867753850363,
4.59793890091132, 7.20198721934907, 2.53647190630645, 1.43984520623409,
4.9588997046061, 5.39648812175142, 0.689047355568849, 5.64883831247181,
6.42127033572805, 5.82205639874631, 3.86788862110194, 3.97491916872919,
7.67148194340246, 3.11135756732789, 6.76700401245109, 3.347286789324,
3.72041919195097, 7.71913371949239, 2.41035792540298, 1.75315471398838,
1.23177034323375, 3.28931854730963, 8.79899724845982, -0.00189056685984657,
7.20207517756466, 1.22106195868106, 6.72528030728377, 2.33649667877263,
1.13036886382528, 2.71265161603589, 3.7020155505672, 2.95627766273871,
2.74167389011769, 3.39793470118529, 5.15267979825199, 6.95144469693794,
1.28892907008833, 3.6747193374802, 5.63111261375112, 2.34505493977553,
3.99841953197836, 8.05108391905124, 7.84309886502793, 1.20882158780534,
5.78524623473018, 5.53027106398681, 4.27193051023528, 6.87128285087747,
4.47726179181244, 6.01514480816364, 7.08053784072589, 3.96019002647998,
5.26834227218323, 6.20477658663633, 4.31675683804794, 1.93099802695233,
4.94354624684112, 3.93343407240841, 2.85171975276596, 6.93524515833713,
6.36243395328599, 6.7243558150464, 5.08527643213477, 1.54658110274774,
5.26917063072746, 6.06181308176647, 3.65787586066713, 5.38619859378501,
5.61463704446218, 3.49091763637435, 6.24445483387337, 7.06610674626727,
1.99568579843186, 2.61940770587604, 6.55817113157641, 5.77676147106923,
2.43683763661187, 0.899174496332188, 5.62622263123913, 4.54389005705384,
2.89773241855398, 4.24362192046509, 6.59238744314388, 8.63063174629931,
2.59467436185943, 3.30422174136898, 2.64431320437896, 9.00716612313614,
8.23589027653903, 6.11704980692414, 2.19888589267801, 2.35520063938938,
6.35995964827307, 4.49913022577282, 7.28993163244222, 7.75140182332863,
7.28595594188508, 8.06633111054202, -1.88861319270814, 2.16030122120576,
5.15908143134282, 4.30427478714882, 3.91752933378457, 6.18689437185545,
-0.0909572463896851, 8.51449051346567, 3.26218500404479, -0.499656374016631,
3.59407829657458, 0.872623759840229, 2.53322285772215, 7.68839811717404,
5.92920871677031, 2.6288624125951, -0.488039877224844, 4.58096232060246,
1.39811021104076, 1.97148538899507, 3.11458269256954, -1.47721303048256,
4.18594436235417, 3.72182100955478, 6.53220291088728, 3.45463319209468,
5.73113205290402, 3.62876681721106, 1.64827719351671, 3.24609479733808,
11.921281006227, 2.67786427287998, 4.582040185562, 5.40756115346143,
7.0469116145243, 2.17857036566385, 7.05124699446184, 2.74566921590146,
4.48908869492447, 3.34571499039664, 3.57161865451065, 5.16747642773435,
9.49847536697945, 7.14923380434398, 4.61470881727973, 3.03706680977709,
10.9801555700036, 3.86869652318769, 5.62225267167554, 6.43350839453757,
8.39844008563752, 2.2646573525206, 3.41490841854915, 5.67805702655872,
-0.809393495885701, 4.41008441225406, 7.05635228677153, 9.14784402640491,
2.04194032863614, 5.11169891262685, 3.18925722111377, 5.36323249015687,
3.60724863752236, 7.33997947708907, 0.40240767440875, 6.77899709763861,
3.01577394940177, 6.20475510881418, -0.572333813375631, 5.42322562145073,
2.06305986033774, 2.20906574002165, 1.09265760829026, 3.37888894762875,
6.64520917000146, 5.90361658257861, 3.96066402532801, 8.26564580206152,
2.25256203679789, -1.18241058400835, 4.37837737457062, 5.12603855756102,
4.42803491640459, 1.1518648413664, 5.55749375246577, 0.230097439482677,
6.86153235906733, 7.25187928826696, 5.95130098381689, 1.64811040956296,
6.21784040655025, 2.02060687762526, 0.845496529456125, 5.90047567548973,
4.05017497589272, 2.96572113174928, 3.22932821829479, 0.762116171884792,
9.10512926651492, 2.32404943725825, 2.22356921283681, 6.98805649323141,
6.24681459758109, 5.5654724846077, 6.43752643408256, 3.30817214100794,
1.3570853077758, 5.61186201669309, 7.5799219662882, 1.74808829059628,
4.35081453647544, 5.60458103719858, 4.46024578536714, 5.31152218347951,
5.54931483435023, 4.53311259509895, 9.85661494243682, 1.62181793533198,
-1.24870896406228, 3.44200922130121, 7.0299327977222, 8.42076247812042,
4.58269299347816, 0.230497829109535, 2.26641155589679, 4.68940803869865,
6.80178704287899, 9.69696237753812, 5.9153266548654, 4.60520880274873,
-1.32382254038878, 6.15872018789166, -0.458597838486124, 3.74462132324235,
7.21142305359308, 0.16268033748901, 5.90487553108412, 5.11375731589594,
2.42493479936202, 3.44754134300746, 8.32933299662675, 5.3777981078863,
5.97748021299252, 4.65991096529264, 5.45544896313774, 2.04795689131482,
4.83092007945016, 5.1810433313885, 4.74921805283506, 4.1230228580566,
3.10639763068901, 1.72494827071261, 4.61405298852966, 1.41089522203996,
3.88393466694468, -0.309016465366817, -0.401219941282472, 2.22986306386453,
6.83730747158862, 7.1762083707765, 3.04262691177725, 3.72473625021332,
1.99601708574019, 7.30771727392297, 4.86263872395864, 4.96568209165822,
10.3076195914808, 3.7836708815514, 1.55833016312973, -2.37253450063571,
4.83860610659918, 9.20114447476412, 2.44513659078818, 2.08913542533366,
8.25775752008983, 2.93913798623585, 2.70927803606851, 5.90983797236913,
8.55575843777914, 4.65967586094405, 5.62678405566949, 0.718458712797539,
3.03866539031414, 0.534743007333415, 6.25505782511016, 3.81500943091501,
4.71688493190289, 3.55442719830069, 0.573106774998025, 3.64437107819603,
4.7181539472855, 4.26803626318181, 4.62865978274796, 7.58898022563777,
7.28054265491218, 5.83790209700189, 6.09378454993791, -0.241602104530848,
2.35983503332862, 10.4759249427807, 5.30180774473196, 2.98082345120828,
5.30478282787459, 6.60074465588181, 1.60827344025758, 4.32440880773869,
6.67140556987472, 8.40080539316999, 2.01178775649063, 6.75856695792377,
1.59340838388762, 6.09011935588765, 3.89132371573187, 8.41447414276382,
2.50849884779586, 3.3728892707509, 5.15946499944911, 1.11304789176458,
8.29780487001974, 3.95310264590947, 2.23146637924962, 7.35785573579783,
3.48713491318771, 9.71686625243746, 5.01014222812169, 7.39502643961673,
8.01052007877, 4.18590208146441, 7.11533307902753, 8.08843954548832,
1.94512616458512, 2.13502742268915, 8.98344026010025, 3.42953965956949,
8.73507412119494, 8.10529044365727, 0.84119471363463, 4.73201965827815,
3.93259084518863, 3.82413294282592, 2.78118033828502, 3.4729981092777,
7.24706556767089, 1.27300933719095, -2.96945948662342, 5.56959913635448,
3.70832716625335, 5.44120572900449, 6.57391456144965, 6.15807897671651,
4.66486100506104, 2.38195351163393, 4.90397534145485, 0.327044182105048,
5.82701567995983, 1.84171316429545, 6.88137315740556, 6.56178385431594,
6.47526515473959), .Dim = c(1000L, 5L))
MeanRelativeError <- function(est, base) mean(abs((est-base)/base))
test_that("CovarianceWithMissing catches bad input", {
bad.df <- data.frame(a=1:3, b=letters[24:26])
bad.character <- letters
bad.numeric <- 4:10
bad.char.matrix <- matrix(letters, nrow=13)
bad.3d.array <- array(1:27, dim=c(3,3,3))
expect_error(CovarianceWithMissing(x=bad.df))
expect_error(CovarianceWithMissing(x=bad.character))
expect_error(CovarianceWithMissing(x=bad.numeric))
expect_error(CovarianceWithMissing(x=bad.char.matrix))
expect_error(CovarianceWithMissing(x=bad.3d.array))
})
test_that("CovarianceWithMissing returns correct types", {
good.full <- x.full
good.missing <- x.full
good.missing[miss] <- NA
out.full <- CovarianceWithMissing(x=good.full)
out.missing <- CovarianceWithMissing(x=good.missing)
expect_true( is.matrix(out.full) )
expect_true( is.numeric(out.full) )
expect_true( identical(c(5L, 5L), dim(out.full)))
expect_true( is.matrix(out.missing) )
expect_true( is.numeric(out.missing) )
expect_true( identical(c(5L, 5L), dim(out.missing)))
})
test_that("CovarianceWithMissing returns correct values", {
good.full <- x.full
good.missing <- x.full
good.missing[miss] <- NA
cov.full <- var(good.full)
out.missing <- CovarianceWithMissing(x=good.missing)
out.var <- var(good.missing, na.rm=TRUE)
expect_true( MeanRelativeError(out.missing, cov.full) < MeanRelativeError(out.var, cov.full) )
expect_true( det(out.missing) > 0 )
})
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FastImputation documentation built on Sept. 25, 2023, 5:06 p.m.
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context("CovarianceWithMissing")
miss <-
c(1755L, 1010L, 3612L, 2651L, 2603L, 1824L, 1898L, 154L, 4674L,
667L, 2904L, 4334L, 173L, 1934L, 3223L, 1975L, 2187L, 3783L,
2159L, 59L, 4931L, 3181L, 4114L, 1261L, 1370L, 3678L, 4516L,
1772L, 3627L, 2631L, 1456L, 1490L, 1534L, 3474L, 2959L, 4481L,
1285L, 4036L, 2285L, 1598L, 4030L, 4705L, 2906L, 244L, 1927L,
1939L, 1054L, 3320L, 2209L, 3490L, 1637L, 2275L, 4605L, 2186L,
573L, 1566L, 2985L, 520L, 1546L, 4891L, 2658L, 2442L, 628L, 1567L,
2561L, 4411L, 3558L, 4803L, 3284L, 4677L, 4141L, 4412L, 2169L,
2008L, 4825L, 3214L, 1203L, 2242L, 1756L, 300L, 222L, 3638L,
2041L, 3043L, 1212L, 3311L, 620L, 4880L, 1426L, 4212L, 2883L,
4562L, 2921L, 1718L, 4912L, 2536L, 3532L, 4235L, 3235L, 1280L,
4420L, 3617L, 229L, 400L, 2258L, 4165L, 2189L, 2367L, 2526L,
1372L, 635L, 2632L, 4706L, 2483L, 4370L, 655L, 1362L, 213L, 951L,
2857L, 3000L, 1600L, 1968L, 2704L, 1524L, 1260L, 2450L, 4104L,
2377L, 4432L, 1052L, 3803L, 466L, 4157L, 3132L, 374L, 3764L,
328L, 1980L, 4392L, 2975L, 600L, 1098L, 2781L, 1284L, 4629L,
3239L, 2777L, 1626L, 759L, 1840L, 4149L, 1263L, 1991L, 1483L,
982L, 4546L, 4876L, 2040L, 2061L, 2465L, 1207L, 2099L, 4269L,
938L, 2855L, 4082L, 4248L, 3848L, 1185L, 4073L, 1634L, 949L,
4393L, 4670L, 1239L, 1374L, 752L, 789L, 166L, 20L, 3513L, 3220L,
3879L, 3545L, 4660L, 1194L, 802L, 3823L, 4576L, 3827L, 2128L,
4260L, 2426L, 3951L, 1436L, 1411L, 768L, 1105L, 1706L, 905L,
1903L, 2175L, 1581L, 2936L, 3718L, 164L, 4080L, 3672L, 2590L,
4633L, 839L, 3476L, 4380L, 88L, 2288L, 1045L, 548L, 4572L, 1778L,
2028L, 843L, 2706L, 2409L, 3966L, 2022L, 2030L, 968L, 1553L,
2204L, 305L, 182L, 3630L, 3838L, 195L, 1459L, 4159L, 4940L, 3897L,
3190L, 1236L, 792L, 3109L, 351L, 3775L, 1453L, 3234L, 2191L,
2860L, 1861L, 3709L, 873L, 3812L, 3299L, 3128L, 1074L, 1083L,
279L, 4725L, 1183L, 1469L, 4192L, 1336L, 3307L, 1555L, 760L,
2618L, 3511L, 4979L, 1663L, 1246L, 1681L, 3289L, 1941L, 4117L,
58L, 2765L, 2396L, 4977L, 4995L, 1565L, 2499L, 1076L, 2001L,
1254L, 895L, 1672L, 2923L, 140L, 4476L, 2628L, 1657L, 859L, 2225L,
3650L, 4878L, 2914L, 4965L, 3686L, 4533L, 1379L, 1403L, 4942L,
1431L, 1494L, 3956L, 1107L, 1106L, 2226L, 1390L, 3232L, 4990L,
2506L, 2711L, 513L, 3590L, 957L, 4950L, 4985L, 2510L, 3386L,
2559L, 186L, 2467L, 2890L, 4255L, 2192L, 143L, 2570L, 1190L,
1082L, 4771L, 746L, 3443L, 636L, 1316L, 886L, 1342L, 3505L, 2274L,
2598L, 4197L, 2394L, 1335L, 1854L, 998L, 4132L, 1359L, 3904L,
1674L, 3837L, 735L, 3573L, 2405L, 1376L, 2114L, 3264L, 2249L,
793L, 4713L, 4150L, 333L, 2120L, 1389L, 732L, 4989L, 4004L, 3354L,
1406L, 3472L, 1949L, 3310L, 4902L, 2786L, 419L, 4489L, 1206L,
2449L, 304L, 3349L, 434L, 4415L, 3169L, 4506L, 4218L, 1416L,
2503L, 1504L, 1558L, 4622L, 2866L, 4962L, 3615L, 483L, 3522L,
2885L, 2731L, 2576L, 4586L, 840L, 457L, 233L, 1166L, 3095L, 1599L,
4401L, 3433L, 2986L, 1425L, 916L, 3914L, 2989L, 318L, 2889L,
4709L, 4071L, 1733L, 3195L, 1678L, 3040L, 2444L, 4174L, 1679L,
4699L, 3123L, 291L, 1650L, 176L, 4346L, 3834L, 239L, 113L, 4015L,
2092L, 335L, 4487L, 907L, 1808L, 2216L, 555L, 3910L, 1113L, 2272L,
923L, 439L, 862L, 3364L, 4596L, 4898L, 1745L, 4035L, 259L, 4920L,
3367L, 420L, 4653L, 2929L, 1420L, 4984L, 1966L, 2086L, 1864L,
2034L, 602L, 4527L, 925L, 1275L, 2858L, 334L, 1300L, 3346L, 1666L,
4075L, 976L, 196L, 646L, 1112L, 1025L, 4062L, 403L, 3358L, 1805L,
3892L, 4866L, 2389L, 882L, 3697L, 102L, 501L, 854L, 1811L, 863L,
2150L, 4383L, 1219L, 3776L, 4502L, 3935L, 4726L, 2540L, 2408L,
1557L, 3822L, 4475L, 2032L, 956L, 3669L, 1150L, 4007L, 2118L,
298L, 2537L, 131L, 1852L, 2533L, 238L, 1993L, 3644L, 701L, 4992L,
203L, 1470L, 2684L, 1394L, 1548L, 858L, 4534L, 3357L, 46L, 2241L,
738L, 490L, 1320L, 3727L, 4845L, 801L, 3417L, 1917L, 4529L, 2243L,
4391L, 3304L, 510L, 2998L, 2733L, 2881L, 4524L, 4671L, 4615L,
2398L, 1099L, 417L, 970L, 4560L, 3856L, 3799L, 3120L, 4322L,
917L, 3230L, 4679L, 754L, 2493L, 2863L, 2412L, 3035L, 2214L,
1894L, 3507L, 440L, 1817L, 3390L, 4168L, 2091L, 2574L, 1873L,
1289L, 1647L, 2349L, 990L, 1547L, 1660L, 3674L, 1639L, 706L,
4296L, 144L, 3584L, 2336L, 2492L, 911L, 4033L, 1520L, 4640L,
4122L, 3524L, 3409L, 4711L, 1172L, 626L, 3820L, 607L, 4685L,
474L, 2489L, 4050L, 4018L, 391L, 2740L, 187L, 382L, 1944L, 60L,
532L, 2991L, 1224L, 2758L, 3939L, 747L, 861L, 3489L, 3715L, 3982L,
1407L, 687L, 2521L, 825L, 866L, 876L, 2718L, 4051L, 3130L, 625L,
13L, 2420L, 2597L, 2222L, 2725L, 1510L, 906L, 3186L, 3018L, 4098L,
3296L, 1232L, 4597L, 4652L, 2095L, 660L, 850L, 2260L, 3407L,
1839L, 2625L, 557L, 4525L, 574L, 2763L, 4910L, 492L, 257L, 2109L,
27L, 2355L, 1948L, 679L, 627L, 3839L, 559L, 4946L, 587L, 2157L,
1692L, 2075L, 4740L, 2218L, 4829L, 2262L, 4810L, 4120L, 4474L,
4584L, 2606L, 4185L, 3339L, 2732L, 944L, 4903L, 3400L, 4125L,
1358L, 2671L, 3710L, 3251L, 215L, 1021L, 950L, 1593L, 3204L,
2605L, 1645L, 2504L, 3900L, 2515L, 4807L, 197L, 3414L, 4016L,
3536L, 4583L, 2581L, 4327L, 3928L, 4207L, 2884L, 449L, 4108L,
1042L, 4720L, 4191L, 3899L, 1015L, 4480L, 3595L, 4900L, 2747L,
4186L, 1447L, 4906L, 1646L, 2888L, 2378L, 1977L, 2604L, 4116L,
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3719L, 331L, 2017L, 1159L, 1005L, 4993L, 2265L, 1798L, 640L,
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377L, 2329L, 1419L, 775L, 2415L, 2027L, 4333L, 468L, 3548L, 3118L,
3967L, 4914L, 1611L, 3416L, 4202L, 2645L, 81L, 4307L, 4661L,
476L, 4313L, 1877L, 4888L, 3713L, 4044L, 1180L, 2599L, 1559L,
1034L, 4749L, 4762L, 903L, 2926L, 1452L, 1428L, 1667L, 3859L,
899L, 4171L, 111L, 3145L, 2776L, 3961L, 2968L, 1760L, 1521L,
1011L, 1354L, 595L, 127L, 2062L, 4134L, 4452L, 214L, 3184L, 4418L,
1495L, 4823L, 2770L, 758L, 3086L, 2647L, 268L, 4882L, 1823L,
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4861L, 4361L, 1804L, 1279L, 836L, 3731L, 809L, 1148L, 1301L,
975L, 392L, 1391L, 3805L, 3228L, 2657L, 1628L, 674L, 3540L, 4929L,
4250L, 3787L, 3467L, 3700L, 3980L, 4837L, 4176L, 999L, 4835L,
4355L, 1424L, 4961L, 497L, 3240L, 1315L, 3270L, 2517L, 3642L,
4194L, 814L, 4451L, 3960L, 3458L, 4220L, 509L, 3675L, 2850L,
4341L, 3350L, 3272L, 796L, 1923L, 955L, 4885L, 3918L, 869L, 642L,
4668L, 632L, 1264L, 1282L, 327L, 3689L, 4089L, 1382L, 1153L,
788L, 70L, 1474L, 2762L, 4283L, 4938L, 4446L, 4573L, 1930L, 1467L,
1912L, 3420L, 993L, 1801L, 4886L, 892L, 355L, 4505L, 4657L, 2484L,
3083L, 282L, 1067L, 2913L, 4869L, 4473L, 1699L, 4491L, 1488L,
2010L, 1069L, 1051L, 1126L, 578L, 352L, 4302L, 2916L, 2280L,
4812L, 4911L, 1705L, 1785L, 585L, 4027L, 1019L, 2529L, 2572L,
4736L, 3104L, 220L, 1552L, 708L, 4486L, 4613L, 692L, 1795L, 1893L,
68L, 379L, 841L, 169L, 3263L, 4264L, 1543L, 724L, 2567L, 3148L,
2264L, 2591L, 3335L, 1117L, 936L, 1450L, 3236L, 2413L, 1711L,
1904L, 309L, 228L, 1913L, 952L, 2964L, 3990L, 1767L, 3655L, 1954L,
2156L, 803L, 3192L, 2575L, 1445L, 1413L, 1696L, 2752L, 1799L,
4759L, 142L, 3306L, 2307L, 2494L, 877L, 4792L, 248L, 699L, 4634L,
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2522L, 3211L, 4874L, 2812L, 4569L, 1739L, 4294L, 1306L, 2379L,
1164L, 3620L, 4295L, 2578L, 4009L, 1151L, 1889L, 2289L, 4708L,
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1103L, 3113L, 1983L, 2805L, 3225L, 313L, 386L, 414L, 2158L, 3038L,
1708L, 4301L, 1670L, 4323L, 608L, 2595L, 2707L, 221L, 1830L,
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2724L, 2862L, 3639L, 1850L, 939L, 4328L, 3041L, 2562L, 1355L,
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4436L, 109L, 118L, 485L, 410L, 1697L, 1368L, 3368L, 2117L, 4675L,
2147L, 3419L, 2488L, 3126L, 853L, 654L, 2633L, 1017L, 4983L,
1118L, 933L, 325L, 1724L, 3927L, 2728L, 2045L, 4363L, 2925L,
529L, 2065L, 2208L, 1188L, 4022L, 4423L, 2865L, 1680L, 3752L,
4010L, 3599L, 1344L, 575L, 522L, 3022L, 4632L, 4770L, 2082L,
3858L, 922L, 4190L, 3771L, 896L, 1157L, 4662L, 3865L, 4760L,
4184L, 1624L, 447L, 4135L, 2646L, 240L, 617L, 2552L, 3872L, 3801L,
1247L, 1810L, 2410L, 1758L, 4309L, 25L, 3267L, 2166L, 4388L,
1330L, 4892L, 3587L, 4110L, 2793L, 4254L, 580L, 2014L, 4588L,
368L, 1538L, 4298L, 429L, 1492L, 258L, 2703L, 4801L, 4778L, 2556L,
2193L, 472L, 1147L, 353L, 2555L, 3359L, 1959L, 2839L, 4003L,
1952L, 1617L, 405L, 4899L, 1712L, 757L, 3434L, 4102L, 245L, 93L,
1675L, 319L, 365L, 262L, 2539L, 1152L, 3360L, 3784L, 387L, 794L,
898L, 4045L, 1644L, 3105L, 4767L, 718L, 2356L, 4673L, 1528L,
4532L, 1132L, 730L, 1434L, 4173L, 4305L, 2571L, 3527L, 4741L,
808L, 42L, 2437L, 1392L, 4462L, 4276L, 962L, 4002L, 1135L, 2112L,
4819L, 3249L, 3578L, 3780L, 1128L, 4846L, 3457L, 332L, 3868L,
1899L, 1729L, 4284L, 4092L, 3365L, 3079L, 689L, 3729L, 887L,
669L, 1108L, 3377L, 3015L, 3060L, 3343L, 4311L, 2363L, 3609L,
3096L, 170L, 2514L, 583L, 3807L, 847L, 3294L, 3435L, 3325L, 3894L,
2893L, 3042L, 137L, 2194L, 4530L, 1461L, 3544L, 855L, 4238L,
4445L, 4069L, 3986L, 2543L, 4908L, 1009L, 3911L, 4396L, 39L,
564L, 4364L, 4356L, 1776L, 1486L, 362L, 4614L, 4337L, 3255L,
4279L, 9L, 1137L, 1318L, 3308L, 1070L, 3943L, 3456L, 4710L, 2611L,
2124L, 3004L, 4127L, 2374L, 1205L, 1576L, 2691L, 4461L, 1689L,
2501L, 556L, 2944L, 361L, 3478L, 206L, 3168L, 3885L, 2832L, 21L,
4826L, 3777L, 943L, 2661L, 4958L, 2879L, 2012L, 2816L, 2350L,
1848L, 4427L, 3796L, 753L, 834L, 3121L, 3515L, 1095L, 4650L,
3987L, 868L, 1310L, 1256L, 2331L, 390L, 1380L, 3485L, 1694L,
4515L, 2286L, 370L, 4057L, 4440L, 4267L, 1905L, 1519L, 4126L,
1961L, 2616L, 1065L, 4895L, 1047L, 4320L, 2161L, 3746L, 1987L,
1143L, 1387L, 2295L, 1439L, 2441L, 99L, 2452L, 2919L, 2143L,
526L, 3373L, 572L, 1462L, 4179L, 891L, 2319L, 715L, 1819L, 145L,
848L, 2359L, 2739L, 3657L, 659L, 1618L, 3103L, 2491L, 2388L,
100L, 1985L, 4400L, 3683L, 647L, 1170L, 4847L, 3305L, 606L, 3704L,
3716L, 442L, 2952L, 1791L, 4585L, 3691L, 1938L, 4857L, 1531L,
455L, 3062L, 1233L, 4773L, 1719L, 3535L, 4821L, 1023L, 2644L,
4047L, 1847L, 4933L, 3594L, 3179L, 1229L, 2498L, 2477L, 3874L,
1807L, 1039L, 3039L, 1698L, 4163L, 2534L, 4567L, 818L, 1427L,
3570L, 398L, 3742L, 3242L, 879L, 3469L, 524L, 3950L, 430L, 3013L,
3379L, 4564L, 4539L, 2854L, 614L, 4085L, 3504L, 1879L, 3574L,
4739L, 2699L, 288L, 1217L, 255L, 3212L, 3862L, 1947L, 1541L,
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133L, 1797L, 2635L, 4128L, 4648L, 1421L, 1686L, 2206L, 3888L,
4271L, 4672L, 3361L, 1418L, 3370L, 4966L, 2078L, 1866L, 4025L,
1749L, 126L, 1834L, 4067L, 1262L, 286L, 2667L, 3647L, 591L, 3089L,
1591L, 2434L, 2253L, 2915L, 4017L, 3677L, 2535L, 4156L, 3714L,
1602L, 4919L, 3723L, 2435L, 1029L, 4049L, 822L, 2947L, 722L,
3384L, 3930L, 2587L, 435L, 4325L, 2682L, 1703L, 774L, 4913L,
453L, 4278L, 3564L, 3555L, 4205L, 4666L, 3778L, 4031L, 38L, 2300L,
172L, 552L, 2141L, 4488L, 3276L, 3406L, 1195L, 2525L, 609L, 4265L,
4335L, 3147L, 2481L, 2757L, 4224L, 3758L, 2891L, 3143L, 4193L,
1286L, 2557L, 77L, 225L, 2830L, 924L, 2612L, 3438L, 3902L, 2196L,
4579L, 4402L, 3028L, 739L, 467L, 3010L, 2185L, 345L, 4257L, 2898L,
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372L, 4107L, 1664L, 76L, 3994L, 1156L, 648L, 1730L, 3941L, 1360L,
4732L, 1422L, 3426L, 1058L, 3493L, 811L, 992L, 2554L, 570L, 838L,
138L, 1121L, 1908L, 1027L, 531L, 1999L, 2971L, 2902L, 3589L,
401L, 2588L, 3932L, 2167L, 2471L, 3679L, 3165L, 124L, 2129L,
2453L, 4169L, 1223L, 110L, 702L, 750L, 4607L, 3363L, 1863L, 3056L,
2238L, 4794L, 4728L, 4918L, 104L, 3851L, 1339L, 945L, 2083L,
2136L, 3658L, 4724L, 2607L, 2392L, 3295L, 1398L, 4948L, 3604L,
4543L, 3983L, 3877L, 2151L, 469L, 4702L, 3445L, 4477L, 777L,
1876L, 4556L, 677L, 2301L, 3282L, 4843L, 712L, 4868L, 1735L,
67L, 2531L, 134L, 2237L, 4704L, 2701L, 2924L, 2652L, 1582L, 296L,
2110L, 4312L, 3392L, 2305L, 1116L, 1742L, 4189L, 2785L, 2984L,
3998L, 3112L, 189L, 3279L, 3921L, 1783L, 1294L, 1226L, 1089L,
3045L, 676L, 586L, 3471L, 530L, 1994L, 1935L, 3330L, 3381L, 4410L,
4941L, 671L, 4996L, 4782L, 3453L, 2790L, 1662L, 978L, 4042L,
1967L, 1635L, 663L, 2794L, 348L, 3648L, 114L, 3621L, 3640L, 2090L,
1606L, 3210L, 4818L, 653L, 1353L, 1114L, 3396L, 3779L, 2425L,
1338L, 2273L, 4055L, 8L, 2439L, 383L, 4626L, 3073L, 4144L, 947L,
2528L, 2550L, 3172L, 2495L, 1564L, 1192L, 4001L, 6L, 4405L, 3319L,
380L, 631L, 4318L, 3066L, 1402L, 2967L, 2080L, 3743L, 707L, 915L,
3071L, 2659L, 893L, 2400L, 618L, 2783L, 3913L, 2067L, 1595L,
1584L, 4215L, 1693L, 829L, 3656L, 2011L, 934L, 4521L, 1482L,
2173L, 537L, 4580L, 3092L, 721L, 276L, 3659L, 3550L, 2910L, 4974L,
776L, 3733L, 3975L, 1978L, 762L, 4240L, 3466L, 3898L, 2761L,
1347L, 4435L, 958L, 3146L, 4375L, 4617L, 1691L, 741L, 1171L,
1312L, 289L, 2871L, 3748L, 1060L, 4060L, 1590L, 2344L, 4565L,
216L, 73L, 4028L, 136L, 1526L, 3624L, 711L, 913L, 3781L, 2101L,
2474L, 2365L, 516L, 686L, 3732L, 4227L, 4497L, 639L, 3962L, 725L,
4438L, 4131L, 4013L, 1351L, 3895L, 4058L, 3965L, 2341L, 4389L,
3871L, 2987L, 827L, 3271L, 2508L, 3945L, 1684L, 2734L, 389L,
2511L, 3473L, 3565L, 251L, 2807L, 633L, 1738L, 90L, 1472L, 2074L,
3491L, 3788L, 2458L, 4289L, 1131L, 670L, 2897L, 488L, 3288L,
1324L, 3556L, 4982L, 310L, 1496L, 3745L, 4317L, 4308L, 889L,
3747L, 3418L, 544L, 2087L, 3262L, 2063L, 4466L, 1833L, 619L,
1202L, 3082L, 1437L, 541L, 3006L, 4471L, 2229L, 935L, 4909L,
2693L, 1638L, 4409L, 769L, 3182L, 3660L, 2103L, 1658L, 1277L,
3069L, 1875L, 4211L, 3583L, 2841L, 340L, 2767L, 2401L, 4106L,
1480L, 4519L, 3890L, 3432L, 521L, 1237L, 4465L, 3825L, 3814L,
4213L, 4086L, 4223L, 2304L, 1651L, 3878L, 709L, 3863L, 3946L,
4659L, 1761L, 4012L, 610L, 1619L, 2315L, 2655L, 2905L, 1160L,
4382L, 3833L, 4101L, 316L, 2098L, 3974L, 396L, 4563L, 346L, 4200L,
1973L, 2641L, 1907L, 563L, 2485L, 590L, 1323L, 3724L, 132L, 1958L,
2974L, 902L, 1627L, 2433L, 4232L, 4256L, 546L, 4105L, 2029L,
2312L, 1243L, 1433L, 56L, 3693L, 4609L, 2969L, 4971L, 4282L,
1725L, 4379L, 1625L, 1578L, 4735L, 820L, 2232L, 1998L, 4449L,
2583L, 2818L, 1430L, 4776L, 2558L, 543L, 2547L, 3884L, 576L,
421L, 4894L, 4226L, 2094L, 4844L, 3501L, 1641L, 1162L, 4655L,
4414L, 2586L, 1914L, 2296L, 4338L, 3064L, 4593L, 3125L, 3722L,
3526L, 2679L, 168L, 3452L, 2622L, 4676L, 350L, 184L, 1700L, 2142L,
2021L, 819L, 3653L, 3687L, 281L, 2387L, 2965L, 4853L, 3428L,
1846L, 3219L, 2369L, 3287L, 3444L, 4478L, 4177L, 4090L, 1062L,
1177L, 598L, 1078L, 2049L, 3290L, 3562L, 3773L, 3427L, 3940L,
3185L, 1589L, 3183L, 4268L, 3750L, 518L, 471L, 4023L, 3034L,
1265L, 3984L, 4281L, 3464L, 1270L, 1240L, 2760L, 3269L, 1828L,
3391L, 601L, 3854L, 406L, 1049L, 894L, 4147L, 4864L, 953L, 4137L,
1349L, 2978L, 4182L, 4304L, 2636L, 3947L, 4499L, 4479L, 3721L,
981L, 2942L, 4121L, 2385L, 1377L, 1888L, 179L, 149L, 983L, 1199L,
3533L, 4969L, 4029L, 4557L, 2617L, 4578L, 4964L, 3100L, 302L,
2745L, 798L, 4329L, 972L, 3954L, 3633L, 940L, 3207L, 3070L, 1307L,
2507L, 408L, 3047L, 765L, 15L, 4459L, 3187L, 218L, 857L, 3509L,
2836L, 3353L, 388L, 4786L, 517L, 3846L, 1012L, 256L, 1723L, 558L,
3853L, 4781L)
x.full <-
structure(c(-5.17167858626162, -6.0021845664732, -8.74033081580247,
-6.2104313642886, -4.9201389353668, -8.20299620447974, -7.52571034201535,
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9.10512926651492, 2.32404943725825, 2.22356921283681, 6.98805649323141,
6.24681459758109, 5.5654724846077, 6.43752643408256, 3.30817214100794,
1.3570853077758, 5.61186201669309, 7.5799219662882, 1.74808829059628,
4.35081453647544, 5.60458103719858, 4.46024578536714, 5.31152218347951,
5.54931483435023, 4.53311259509895, 9.85661494243682, 1.62181793533198,
-1.24870896406228, 3.44200922130121, 7.0299327977222, 8.42076247812042,
4.58269299347816, 0.230497829109535, 2.26641155589679, 4.68940803869865,
6.80178704287899, 9.69696237753812, 5.9153266548654, 4.60520880274873,
-1.32382254038878, 6.15872018789166, -0.458597838486124, 3.74462132324235,
7.21142305359308, 0.16268033748901, 5.90487553108412, 5.11375731589594,
2.42493479936202, 3.44754134300746, 8.32933299662675, 5.3777981078863,
5.97748021299252, 4.65991096529264, 5.45544896313774, 2.04795689131482,
4.83092007945016, 5.1810433313885, 4.74921805283506, 4.1230228580566,
3.10639763068901, 1.72494827071261, 4.61405298852966, 1.41089522203996,
3.88393466694468, -0.309016465366817, -0.401219941282472, 2.22986306386453,
6.83730747158862, 7.1762083707765, 3.04262691177725, 3.72473625021332,
1.99601708574019, 7.30771727392297, 4.86263872395864, 4.96568209165822,
10.3076195914808, 3.7836708815514, 1.55833016312973, -2.37253450063571,
4.83860610659918, 9.20114447476412, 2.44513659078818, 2.08913542533366,
8.25775752008983, 2.93913798623585, 2.70927803606851, 5.90983797236913,
8.55575843777914, 4.65967586094405, 5.62678405566949, 0.718458712797539,
3.03866539031414, 0.534743007333415, 6.25505782511016, 3.81500943091501,
4.71688493190289, 3.55442719830069, 0.573106774998025, 3.64437107819603,
4.7181539472855, 4.26803626318181, 4.62865978274796, 7.58898022563777,
7.28054265491218, 5.83790209700189, 6.09378454993791, -0.241602104530848,
2.35983503332862, 10.4759249427807, 5.30180774473196, 2.98082345120828,
5.30478282787459, 6.60074465588181, 1.60827344025758, 4.32440880773869,
6.67140556987472, 8.40080539316999, 2.01178775649063, 6.75856695792377,
1.59340838388762, 6.09011935588765, 3.89132371573187, 8.41447414276382,
2.50849884779586, 3.3728892707509, 5.15946499944911, 1.11304789176458,
8.29780487001974, 3.95310264590947, 2.23146637924962, 7.35785573579783,
3.48713491318771, 9.71686625243746, 5.01014222812169, 7.39502643961673,
8.01052007877, 4.18590208146441, 7.11533307902753, 8.08843954548832,
1.94512616458512, 2.13502742268915, 8.98344026010025, 3.42953965956949,
8.73507412119494, 8.10529044365727, 0.84119471363463, 4.73201965827815,
3.93259084518863, 3.82413294282592, 2.78118033828502, 3.4729981092777,
7.24706556767089, 1.27300933719095, -2.96945948662342, 5.56959913635448,
3.70832716625335, 5.44120572900449, 6.57391456144965, 6.15807897671651,
4.66486100506104, 2.38195351163393, 4.90397534145485, 0.327044182105048,
5.82701567995983, 1.84171316429545, 6.88137315740556, 6.56178385431594,
6.47526515473959), .Dim = c(1000L, 5L))
MeanRelativeError <- function(est, base) mean(abs((est-base)/base))
test_that("CovarianceWithMissing catches bad input", {
bad.df <- data.frame(a=1:3, b=letters[24:26])
bad.character <- letters
bad.numeric <- 4:10
bad.char.matrix <- matrix(letters, nrow=13)
bad.3d.array <- array(1:27, dim=c(3,3,3))
expect_error(CovarianceWithMissing(x=bad.df))
expect_error(CovarianceWithMissing(x=bad.character))
expect_error(CovarianceWithMissing(x=bad.numeric))
expect_error(CovarianceWithMissing(x=bad.char.matrix))
expect_error(CovarianceWithMissing(x=bad.3d.array))
})
test_that("CovarianceWithMissing returns correct types", {
good.full <- x.full
good.missing <- x.full
good.missing[miss] <- NA
out.full <- CovarianceWithMissing(x=good.full)
out.missing <- CovarianceWithMissing(x=good.missing)
expect_true( is.matrix(out.full) )
expect_true( is.numeric(out.full) )
expect_true( identical(c(5L, 5L), dim(out.full)))
expect_true( is.matrix(out.missing) )
expect_true( is.numeric(out.missing) )
expect_true( identical(c(5L, 5L), dim(out.missing)))
})
test_that("CovarianceWithMissing returns correct values", {
good.full <- x.full
good.missing <- x.full
good.missing[miss] <- NA
cov.full <- var(good.full)
out.missing <- CovarianceWithMissing(x=good.missing)
out.var <- var(good.missing, na.rm=TRUE)
expect_true( MeanRelativeError(out.missing, cov.full) < MeanRelativeError(out.var, cov.full) )
expect_true( det(out.missing) > 0 )
})
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