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Add mt patterns
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@vwmaus
vwmaus committed Oct 22, 2019
1 parent 63d98f2 commit 42b09e0
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Expand Up @@ -39,7 +39,8 @@ Imports:
caret,
mgcv,
xtable,
Rdpack
Rdpack,
data.table
Suggests:
knitr,
rmarkdown,
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16 changes: 9 additions & 7 deletions R/twdtw_reduce_time.R
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Expand Up @@ -38,8 +38,10 @@
px <- x[,names(x)!="date",drop=FALSE]
tx <- as.Date(x$date)

## Basic use case

# Comput TWDTW alignments for all patterns
aligs <- do.call("rbind", lapply(seq_along(y), function(l){
aligs <- lapply(seq_along(y), function(l){

# Split pattern time series from dates
py <- y[[l]][,names(y[[l]])!="date",drop=FALSE]
Expand All @@ -55,7 +57,6 @@
cm <- proxy::dist(py, px, method = dist.method)

if(!is.null(weight.fun)){

# Get day of the year for pattern and time series
doyy <- as.numeric(format(ty, "%j"))
doyx <- as.numeric(format(tx, "%j"))
Expand All @@ -65,9 +66,7 @@

# Apply time-weight to local cost matrix
cm <- w * cm

}

# Compute accumulated DTW cost matrix
internals <- .computecost(cm = cm, step.matrix = step.matrix)

Expand Down Expand Up @@ -107,11 +106,14 @@
distance = candidates$d[I],
label = l
)

tictoc::toc()
return(res)

}))
})

# Bind rows
aligs <- data.table::rbindlist(aligs)

# Create classification intervals
breaks <- seq(as.Date(from), as.Date(to), by = by)
# Find best macthes for the intervals
Expand All @@ -123,7 +125,7 @@
breaks = breaks,
overlap = overlap,
fill = 99999)$IM

# Build output
out <- as.data.frame(best_matches[,c(1,3)])
names(out) <- c("label", "Alig.N")
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1 change: 1 addition & 0 deletions R/zzz.R
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Expand Up @@ -49,6 +49,7 @@
#' @importFrom xtable xtable print.xtable
#' @importFrom utils packageDescription flush.console
#' @importFrom Rdpack reprompt
#' @importFrom data.table rbindlist
#' @useDynLib dtwSat, .registration = TRUE
#'
NULL
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45 changes: 45 additions & 0 deletions inst/lucc_MT/patterns/araguaia.csv
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date,mir,blue,nir,red,evi,ndvi
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2003-09-06,0.157352603470522,0.03283999361940011,0.15760991443727204,0.06761722512983084,0.16909019940948328,0.3908705414590904
2003-09-14,0.166365304317564,0.03228892645263741,0.15600700391187805,0.06796599367343695,0.165777889375191,0.38518743214636003
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2004-04-17,0.06750530445765626,0.025283589122385597,0.17689735557291725,0.04928881980244361,0.24560086162138384,0.5644413565528826
2004-04-25,0.07193885743704981,0.025388340767777292,0.1787289661726774,0.04953572252460384,0.2482334205190675,0.5678333279597554
2004-05-03,0.07652401889659972,0.025123786950867012,0.17990969657064151,0.04942245547914148,0.25067122875850845,0.5709203051114895
2004-05-11,0.08089285332226885,0.024503818559083825,0.1803383460858965,0.048942656930490394,0.25268186615664284,0.5736069511722656
2004-05-19,0.0848243279340348,0.023669082108743834,0.18013614753072504,0.04823050089515993,0.25410666903781187,0.5756679601621144
2004-05-27,0.08832644259444705,0.022927565149191385,0.17971794456725929,0.04760996684017513,0.25487986252944683,0.5766693645222478
2004-06-04,0.09154106927142404,0.022548973710341917,0.17942378032528716,0.04738633769974419,0.2548682601400938,0.5760070091751255
2004-06-12,0.09479248965629977,0.022711410984285214,0.17942076954594297,0.0478017787147809,0.2538124568906927,0.5728324226775636
2004-06-20,0.0984198696396643,0.023462461310021228,0.17966074341709878,0.04897223769212221,0.2513813984720936,0.566315060103165
2004-06-28,0.1027556609381923,0.024650478844696903,0.1797715878616486,0.05081646083978328,0.24714983138853244,0.5556991999607237
2004-07-06,0.10802579349893218,0.026074293497807193,0.17935598215516363,0.05318057685840513,0.24081307365893567,0.5405610759148308
2004-07-14,0.11428102096408499,0.02748518394086073,0.1780312768437244,0.055824490845978,0.23228331147694947,0.5210151521251677
2004-07-22,0.12144745459042529,0.028710461348427935,0.1756200556110752,0.058551267752860674,0.22171866188868067,0.4975866164133348
2004-07-30,0.12927541277095625,0.029710329749120672,0.17227961390656615,0.06124927716924343,0.20964499520251292,0.47138565636258273
2004-08-07,0.13750509358429996,0.03051311873502884,0.16828041463943977,0.06387106940984308,0.19663102641092445,0.4435262266159805
45 changes: 45 additions & 0 deletions inst/lucc_MT/patterns/campo_cerrado.csv
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date,mir,blue,nir,red,evi,ndvi
2003-09-14,0.21413687134018405,0.048672053929892906,0.23336044543861054,0.1139625352737606,0.19341421281796733,0.3526594875417768
2003-09-22,0.21362667186245604,0.04973961018982551,0.23980984777402398,0.11416749095994455,0.20381472473003215,0.36598947241844165
2003-09-30,0.2125613235486052,0.050830033007930805,0.24634028525910143,0.11428666631525122,0.21461004873753484,0.3796537727110462
2003-10-08,0.21039223926835268,0.05196241889045884,0.2530048478727791,0.11422943037340932,0.22615806302942137,0.3939635085287554
2003-10-16,0.2067682713656191,0.05313141232071317,0.2597020779348156,0.11390835980778735,0.23852587643222545,0.4090211893469124
2003-10-24,0.2014899247357263,0.05431796822255233,0.2662563789206229,0.11324866649057108,0.251607884563542,0.424792240154226
2003-11-01,0.19478702532232584,0.0554738602697076,0.27236634053893816,0.11223053692047544,0.2649049100078465,0.4408972494582877
2003-11-09,0.18707552357501578,0.056541963536654825,0.27771477745723155,0.11086720491950054,0.277789123924952,0.45682005715733787
2003-11-17,0.17903023010487965,0.057465267520634286,0.28209174181575386,0.10924857335536704,0.2895936307710538,0.4718967720582977
2003-11-25,0.17137898957685568,0.058192682621602126,0.2853732750293922,0.10749557016255464,0.29971440579030567,0.48545835998629744
2003-12-03,0.16472711634690618,0.058700782496924786,0.2876856916943161,0.10576485920332387,0.30789931016585986,0.49702419413127974
2003-12-11,0.1595593616033224,0.05897937017289364,0.2892534005433843,0.10421252966775993,0.3140824945531364,0.5062524174322326
2003-12-19,0.15596900508610945,0.05904067494274494,0.2904020104026127,0.10294036395510205,0.3185685594619343,0.5131838609203984
2003-12-27,0.15385942443839642,0.05890240101101236,0.2914497352522534,0.10200912466008208,0.32178434505232173,0.5180373353385004
2004-01-04,0.15280211762151288,0.05857560334278675,0.29253213490403185,0.10136368153295455,0.3241978143747844,0.5213201617658131
2004-01-12,0.15222856918029656,0.05805811541555839,0.2935892316005838,0.10086588412051482,0.32617741221594343,0.5236568234625288
2004-01-20,0.15151003626426734,0.05732940985160185,0.2943320219893709,0.10030002603593136,0.32790586374665287,0.5257168044516656
2004-01-28,0.15015715766522272,0.05636341968646091,0.2944173595151486,0.09945740416636709,0.32941985570672544,0.5280484220868996
2004-02-05,0.14792173541505171,0.05512824054181848,0.29345261374737486,0.09815449523317178,0.3305468024361334,0.530991348857883
2004-02-13,0.14477139574729558,0.053605575466021384,0.2911665781217506,0.09628074176968703,0.3310820276562491,0.5346877548971765
2004-02-21,0.14098966703352853,0.051800770318743736,0.2874974442989778,0.09384220553213161,0.3308032151599817,0.5389879105818669
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2004-03-08,0.13320114927659948,0.0475058094052369,0.27670409636373805,0.08772162469178323,0.3273453755696549,0.548062679757431
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2004-06-12,0.14445015097051325,0.0346652192318844,0.21635855183617747,0.07821267593515466,0.24393153357447386,0.4798609883857846
2004-06-20,0.1492993497833582,0.03558792986834457,0.21469439573139848,0.08083506786508972,0.23526489778673165,0.46435244429886124
2004-06-28,0.1549424642057409,0.03671841981720148,0.21418824244663487,0.08390694443236946,0.22740258843044076,0.4486073283496693
2004-07-06,0.16119377997026402,0.03800770968265471,0.21473817496418934,0.08732684992908879,0.22043947988233856,0.43302419408322324
2004-07-14,0.16772658233295445,0.03940338407208868,0.21604275630271502,0.09095109640301441,0.2142994761861164,0.41795154648488675
2004-07-22,0.1742272114558916,0.04085836946513127,0.21777417069815358,0.0946439420452857,0.20884274821303928,0.4036378235188046
2004-07-30,0.18042803380413525,0.04233509005663477,0.21959528236540543,0.0982902019916366,0.20385306451610746,0.3901736805790519
2004-08-07,0.18617760277820739,0.04380753278623462,0.22126961874909412,0.10181818265503631,0.19913652766424364,0.377530319422114
2004-08-15,0.19150815580995495,0.045267194285248086,0.22272800597390977,0.10522444392198034,0.19454868124450575,0.3655084331883162
2004-08-23,0.19652345751709577,0.04671297880911857,0.22398367861536944,0.10853332033349779,0.18999413127918283,0.35388173097518827
45 changes: 45 additions & 0 deletions inst/lucc_MT/patterns/cerradao.csv
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date,mir,blue,nir,red,evi,ndvi
2014-09-14,0.10486548793474104,0.02457024257294535,0.26807279429696595,0.051281688200426126,0.3927871893841736,0.6721307221483572
2014-09-22,0.10684493006770285,0.025910671316964035,0.27898527858272343,0.052437852960509276,0.40706022514662993,0.6790892506196199
2014-09-30,0.1083414479858966,0.027348504408938115,0.2898025361620075,0.053580585930292315,0.4213713259407666,0.686318924363666
2014-10-08,0.10891567868653959,0.028970691032589077,0.30038598097289004,0.054695249708194435,0.43568064589072425,0.6940187867482321
2014-10-16,0.10827463976018523,0.0308292333335144,0.31045515077594166,0.05576340350368547,0.4496919005388834,0.7021489094178377
2014-10-24,0.10629918596164378,0.032941383418332984,0.31968797561678874,0.05677170359459448,0.4629789475797468,0.7104930673707655
2014-11-01,0.10333571082188467,0.03523528395415447,0.32772522785770236,0.05772612697397507,0.47487000147345704,0.7184257945871666
2014-11-09,0.09987590007277256,0.03761230620507549,0.334257723440106,0.05864315876327113,0.4846992946348014,0.7252502961321585
2014-11-17,0.09656265715832044,0.039948232577996005,0.33916638714223313,0.059560208482194225,0.4919925309561932,0.7303219311146
2014-11-25,0.09397210103156939,0.042130906269543494,0.3424606742803833,0.06051810816771808,0.4964823086593536,0.7331734992532681
2014-12-03,0.09235712265771621,0.04410528672630091,0.34443846913592396,0.06155429377713925,0.4984451455675524,0.7338819520540345
2014-12-11,0.09178423886897982,0.04584503584851089,0.3454824939168496,0.06269436741522366,0.4983727740024509,0.7327706613969387
2014-12-19,0.09193543893887912,0.04737781911563496,0.3460522197661012,0.0639274590651133,0.4970825809843745,0.730590486451149
2014-12-27,0.09240328673965761,0.04873388603968766,0.3465458736662347,0.06521728774481261,0.4953878983702356,0.7281455353952043
2015-01-04,0.09275972236745157,0.04991256244793424,0.3471005597125128,0.06646840185060705,0.49385252376802274,0.726109681025306
2015-01-12,0.09271949320168124,0.05085432789424521,0.34758133250650863,0.06753709096901994,0.49268491860280844,0.7248937968834501
2015-01-20,0.09217553469118167,0.05143677809984666,0.34759558429411513,0.06823715211081396,0.49173199194230494,0.7246280786973067
2015-01-28,0.09114468466699603,0.05150593898856005,0.34669553786219875,0.06837361293041361,0.4907096679360583,0.7253579104751444
2015-02-05,0.0897742229791679,0.05087718828375527,0.34439501319403737,0.06774612122019073,0.48921367743552224,0.7270557408783634
2015-02-13,0.08815676840615733,0.049416605877531015,0.3404131914018668,0.06620490788459055,0.48703433454083966,0.7298548543186222
2015-02-21,0.08630758341264651,0.04705628071713094,0.33472301927782966,0.0636640389405455,0.4842071727086752,0.7340843121240666
2015-03-01,0.08414812844501042,0.043840639263868476,0.3275546539593694,0.06014547406623669,0.48097337718907335,0.7401058772773447
2015-03-09,0.08149851372656607,0.03994448140204279,0.31942349861346314,0.0557973937162853,0.4777928443994194,0.7482903970391883
2015-03-17,0.07826487513469702,0.035626716260357905,0.31088366456203126,0.050876286892618125,0.4749902538877112,0.7586067392085017
2015-03-25,0.07447012657496685,0.03123499882184307,0.3025066495860907,0.045757671032954784,0.4727019328664949,0.770530606568934
2015-04-02,0.07035491437204436,0.027099726598480294,0.294668099043091,0.04084008489006129,0.4707079635734086,0.7830092349568474
2015-04-10,0.0664092423277786,0.02352069694656215,0.28750563937869894,0.03653672929773383,0.4683803665826403,0.7944053399993192
2015-04-18,0.0631726124428744,0.02069332516466418,0.280980485040056,0.03315912439417543,0.46501202988812634,0.8031072053118702
2015-04-26,0.06121439050963985,0.018688685569265846,0.274865974425115,0.030892191093367022,0.4598486880582345,0.8076045266410968
2015-05-04,0.06083312405809231,0.01747285808584342,0.2689905543259659,0.029758740222167353,0.45256630202567033,0.8071584364002172
2015-05-12,0.06199463184367691,0.01689653954938422,0.2632684074394348,0.029596904149479106,0.44336921183765815,0.8019595575372646
2015-05-20,0.06434007069234274,0.0167826918674132,0.25780694769941614,0.03015534599121155,0.43297329688755015,0.7930014924140224
2015-05-28,0.06715479971911041,0.016932061929615407,0.25293616527256585,0.031093473049914888,0.42265476539269814,0.782150426701038
2015-06-05,0.06976808559181613,0.01719935273003564,0.24903170091199645,0.03213774233466209,0.41362155768628883,0.7711738087177733
2015-06-13,0.07160381368407212,0.017507021685280733,0.24649842150504553,0.03310605123705532,0.4069334787331696,0.761620836868981
2015-06-21,0.07254291062514376,0.017851501992067333,0.2455225330309055,0.033981563705372114,0.40292538956205515,0.7540048751163599
2015-06-29,0.07301140270872195,0.01831223539038236,0.24602122114691177,0.03493881042023697,0.40106611961297195,0.7476039643669076
2015-07-07,0.07382919794995524,0.01899574123354671,0.2476482589727907,0.036253436452359046,0.4001644926960537,0.7407953417022393
2015-07-15,0.07623324192993793,0.020032909154659873,0.24976744566398235,0.03830316111097278,0.3983232012989928,0.7309989883676266
2015-07-23,0.08129216583204041,0.021516311610222515,0.25174379194757396,0.04138882683194642,0.39382260845547157,0.7159473490986479
2015-07-31,0.08982264742476251,0.023489274215923305,0.2529755007632126,0.0457062539410117,0.38523738469301494,0.6938594302839713
2015-08-08,0.10200601774813328,0.025929171676227096,0.25314519296614413,0.05125702150961883,0.372053969491603,0.6642818668996597
2015-08-16,0.11728040134336662,0.028738362610052116,0.25227599118918304,0.05781809429461421,0.3548321818109576,0.6283180915606503
2015-08-24,0.1346931383533912,0.03179047033672381,0.250620219415458,0.0650618916875826,0.3347454617079458,0.5879125327441632
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