HMM适用于不同长度的多个时间序列

时间:2017-05-29 15:46:28

标签: r hidden-markov-models

我为每组实验设置了一组多个时间序列,我想要比较,我想描述粒子'行为是他们所处状态的函数。

使用depmixS4软件包,我可以很容易地适应单个时间序列,但它们太短并且包含的​​变化太小而无法提供任何有用的描述性统计信息(例如,整个跟踪可能只有1或2个状态转换)。

enter image description here

是否有可能以某种方式(虽然也在统计上有效)将HMM应用于不同长度的多个序列(如提供的示例),以描述组'行为?

示例数据:

    track_id   frame steplength condition
      <fctr> <int>      <dbl>    <fctr>
  1   21015A     1 0.00000000    pH 7.8
  2   21015A     2 0.95475173    pH 7.8
  3   21015A     3 0.22495888    pH 7.8
  4   21015A     4 0.22377790    pH 7.8
  5   21015A     5 0.17043093    pH 7.8
  6   21015A     6 0.05642755    pH 7.8
  7   21015A     7 0.17542212    pH 7.8
  8   21015A     8 0.13407864    pH 7.8
  9   21015A     9 0.07291593    pH 7.8
 10   21015A    10 0.06758305    pH 7.8
 11   21015A    11 0.09533805    pH 7.8
 12   21015A    12 0.16611745    pH 7.8
 13   21015A    13 0.10443396    pH 7.8
 14   21015A    14 0.02220178    pH 7.8
 15   21015A    15 0.12547629    pH 7.8
 16   21015A    16 0.10354815    pH 7.8
 17   21015A    17 0.26636457    pH 7.8
 18   21015A    18 0.31292069    pH 7.8
 19   28159A     1 0.00000000    pH 7.8
 20   28159A     2 0.95900496    pH 7.8
 21   28159A     3 0.23238272    pH 7.8
 22   28159A     4 0.09977546    pH 7.8
 23   28159A     5 0.81910999    pH 7.8
 24   28159A     6 0.25688508    pH 7.8
 25   28159A     7 0.78828766    pH 7.8
 26   28159A     8 0.92156411    pH 7.8
 27   28159A     9 0.12172240    pH 7.8
 28   28159A    10 0.26770810    pH 7.8
 29   28159A    11 0.40067941    pH 7.8
 30   28159A    12 0.20093836    pH 7.8
 31   28159A    13 0.94831115    pH 7.8
 32   28159A    14 0.73296074    pH 7.8
 33   28159A    15 0.21240673    pH 7.8
 34   28159A    16 0.90103120    pH 7.8
 35   28159A    17 0.92942744    pH 7.8
 36   28159A    18 0.53607093    pH 7.8
 37   28159A    19 0.90858258    pH 7.8
 38   13600B     1 0.00000000    pH 7.8
 39   13600B     2 0.87908538    pH 7.8
 40   13600B     3 0.62942457    pH 7.8
 41   13600B     4 0.66744765    pH 7.8
 42   13600B     5 0.71691440    pH 7.8
 43   13600B     6 0.64046385    pH 7.8
 44   13600B     7 0.25856434    pH 7.8
 45   13600B     8 0.28124370    pH 7.8
 46   13600B     9 0.40112227    pH 7.8
 47   13600B    10 0.67924165    pH 7.8
 48   13600B    11 0.60165390    pH 7.8
 49   13600B    12 0.87197611    pH 7.8
 50   13600B    13 0.89870192    pH 7.8
 51   13600B    14 0.35304406    pH 7.8
 52   13600B    15 0.68034008    pH 7.8
 53   13600B    16 0.24958022    pH 7.8
 54   13600B    17 0.24944000    pH 7.8
 55   13600B    18 0.68230732    pH 7.8
 56   13600B    19 0.82468295    pH 7.8
 57   13600B    20 0.95994077    pH 7.8
 58   17251B     1 0.00000000    pH 7.8
 59   17251B     2 0.49783219    pH 7.8
 60   17251B     3 0.36760485    pH 7.8
 61   17251B     4 0.48471362    pH 7.8
 62   17251B     5 0.82246223    pH 7.8
 63   17251B     6 0.45872818    pH 7.8
 64   17251B     7 0.85831869    pH 7.8
 65   17251B     8 0.75879929    pH 7.8
 66   17251B     9 0.21361300    pH 7.8
 67   17251B    10 0.16443686    pH 7.8
 68   17251B    11 0.12069282    pH 7.8
 69   17251B    12 0.79570678    pH 7.8
 70   17251B    13 0.62048202    pH 7.8
 71   17251B    14 0.20564776    pH 7.8
 72   17251B    15 0.58574733    pH 7.8
 73   17251B    16 0.87558161    pH 7.8
 74   20992B     1 0.00000000    pH 7.8
 75   20992B     2 0.67524054    pH 7.8
 76   20992B     3 0.48413085    pH 7.8
 77   20992B     4 0.60150589    pH 7.8
 78   20992B     5 0.85905918    pH 7.8
 79   20992B     6 0.31254149    pH 7.8
 80   20992B     7 0.71813937    pH 7.8
 81   20992B     8 0.14237898    pH 7.8
 82   20992B     9 0.18548305    pH 7.8
 83   20992B    10 0.26960475    pH 7.8
 84   20992B    11 0.39545306    pH 7.8
 85   20992B    12 0.13345209    pH 7.8
 86   20992B    13 0.09430367    pH 7.8
 87   20992B    14 0.07466136    pH 7.8
 88   20992B    15 0.21563522    pH 7.8
 89   20992B    16 0.10843926    pH 7.8
 90   20992B    17 0.04246758    pH 7.8
 91   20992B    18 0.12772479    pH 7.8
 92   20992B    19 0.26755821    pH 7.8
 93   20992B    20 0.13206399    pH 7.8
 94   20992B    21 0.05596412    pH 7.8
 95   20992B    22 0.10777590    pH 7.8
 96   20992B    23 0.08224530    pH 7.8
 97   20992B    24 0.39681568    pH 7.8
 98   20992B    25 0.55013082    pH 7.8
 99   20992B    26 0.23321302    pH 7.8
100   20992B    27 0.25409129    pH 7.8
101   20992B    28 0.16079712    pH 7.8
102   20992B    29 0.10654253    pH 7.8
103   20992B    30 0.10887321    pH 7.8
104   20992B    31 0.10310689    pH 7.8
105   20992B    32 0.04918907    pH 7.8
106   20992B    33 0.08857568    pH 7.8
107   20992B    34 0.05057029    pH 7.8
108   20992B    35 0.09314572    pH 7.8
109   20992B    36 0.10941719    pH 7.8
110   20992B    37 0.14745186    pH 7.8
111   20992B    38 0.08173773    pH 7.8
112   20992B    39 0.06002999    pH 7.8
113   20992B    40 0.13886600    pH 7.8
114   20992B    41 0.20743972    pH 7.8
115   20992B    42 0.16996468    pH 7.8
116   20992B    43 0.24178652    pH 7.8
117   20992B    44 0.43204626    pH 7.8
118   21051B     1 0.00000000    pH 7.8
119   21051B     2 0.15856285    pH 7.8
120   21051B     3 0.18664926    pH 7.8
121   21051B     4 0.69785503    pH 7.8
122   21051B     5 0.75580210    pH 7.8
123   21051B     6 0.41164971    pH 7.8
124   21051B     7 0.52517229    pH 7.8
125   21051B     8 0.64111855    pH 7.8
126   21051B     9 0.21459416    pH 7.8
127   21051B    10 0.50414805    pH 7.8
128   21051B    11 0.60942178    pH 7.8
129   21051B    12 0.79580454    pH 7.8
130   21051B    13 0.24508781    pH 7.8
131   21051B    14 0.94284153    pH 7.8
132   21051B    15 0.57121663    pH 7.8
133   21051B    16 0.26585843    pH 7.8
134   21051B    17 0.56708164    pH 7.8
135   22878B     1 0.00000000    pH 7.8
136   22878B     2 0.88523396    pH 7.8
137   22878B     3 0.15809572    pH 7.8
138   22878B     4 0.05604665    pH 7.8
139   22878B     5 0.05199143    pH 7.8
140   22878B     6 0.05623043    pH 7.8
141   22878B     7 0.26054153    pH 7.8
142   22878B     8 0.22959704    pH 7.8
143   22878B     9 0.22572947    pH 7.8
144   22878B    10 0.23783136    pH 7.8
145   22878B    11 0.06596497    pH 7.8
146   22878B    12 0.06748562    pH 7.8
147   22878B    13 0.16013917    pH 7.8
148   22878B    14 0.06314859    pH 7.8
149   22878B    15 0.82603830    pH 7.8
150   22878B    16 0.84796499    pH 7.8
151   15613C     1 0.00000000    pH 7.8
152   15613C     2 0.45651425    pH 7.8
153   15613C     3 0.30087472    pH 7.8
154   15613C     4 0.49968861    pH 7.8
155   15613C     5 0.47793610    pH 7.8
156   15613C     6 0.88761604    pH 7.8
157   15613C     7 0.14207819    pH 7.8
158   15613C     8 0.02262178    pH 7.8
159   15613C     9 0.25745317    pH 7.8
160   15613C    10 0.22933344    pH 7.8
161   15613C    11 0.04626455    pH 7.8
162   15613C    12 0.11803396    pH 7.8
163   15613C    13 0.14175595    pH 7.8
164   15613C    14 0.24253581    pH 7.8
165   15613C    15 0.28807616    pH 7.8
166   15613C    16 0.31963949    pH 7.8
167   15613C    17 0.21889348    pH 7.8
168   15613C    18 0.46647481    pH 7.8
169   15613C    19 0.16754681    pH 7.8
170   15613C    20 0.13843759    pH 7.8
171   15613C    21 0.21332824    pH 7.8
172   15613C    22 0.22492601    pH 7.8
173   15613C    23 0.22119060    pH 7.8
174   15613C    24 0.17748138    pH 7.8
175   15613C    25 0.41248344    pH 7.8
176   17012C     1 0.00000000    pH 7.8
177   17012C     2 0.35007721    pH 7.8
178   17012C     3 0.83836238    pH 7.8
179   17012C     4 0.12498104    pH 7.8
180   17012C     5 0.60547775    pH 7.8
181   17012C     6 0.64549343    pH 7.8
182   17012C     7 0.80107605    pH 7.8
183   17012C     8 0.37467350    pH 7.8
184   17012C     9 0.18249931    pH 7.8
185   17012C    10 0.29221793    pH 7.8
186   17012C    11 0.90794044    pH 7.8
187   17012C    12 0.80162778    pH 7.8
188   17012C    13 0.22684907    pH 7.8
189   17012C    14 0.63475637    pH 7.8
190   17012C    15 0.77960353    pH 7.8
191   17012C    16 0.21149525    pH 7.8
192   17012C    17 0.59882314    pH 7.8
193   17012C    18 0.64282854    pH 7.8
194   17012C    19 0.27128529    pH 7.8
195   17012C    20 0.37947076    pH 7.8
196   17012C    21 0.32288263    pH 7.8
197   17012C    22 0.23507265    pH 7.8
198   17012C    23 0.66999674    pH 7.8
199   16205E     1 0.00000000    pH 7.8
200   16205E     2 0.09530848    pH 7.8
201   16205E     3 0.17581441    pH 7.8
202   16205E     4 0.16373008    pH 7.8
203   16205E     5 0.19333740    pH 7.8
204   16205E     6 0.56345662    pH 7.8
205   16205E     7 0.35314371    pH 7.8
206   16205E     8 0.10429839    pH 7.8
207   16205E     9 0.28600095    pH 7.8
208   16205E    10 0.20532890    pH 7.8
209   16205E    11 0.24797560    pH 7.8
210   16205E    12 0.42435678    pH 7.8
211   16205E    13 0.23010161    pH 7.8
212   16205E    14 0.09550116    pH 7.8
213   16205E    15 0.27402161    pH 7.8
214   16205E    16 0.32397273    pH 7.8
215   16205E    17 0.44268867    pH 7.8
216   16205E    18 0.23834322    pH 7.8
217   16205E    19 0.37878350    pH 7.8
218   16205E    20 0.37576286    pH 7.8
219   16205E    21 0.50450438    pH 7.8
220   16205E    22 0.17414906    pH 7.8
221   16205E    23 0.24941509    pH 7.8
222   16205E    24 0.18587707    pH 7.8
223   16205E    25 0.75289268    pH 7.8
224   16205E    26 0.77726300    pH 7.8
225   16205E    27 0.39877986    pH 7.8
226   16205E    28 0.58319069    pH 7.8
227   16205E    29 0.64957893    pH 7.8
228   16205E    30 0.13684108    pH 7.8
229   16205E    31 0.00988737    pH 7.8
230   16205E    32 0.10749816    pH 7.8
231   16205E    33 0.21750341    pH 7.8
232   16205E    34 0.25509511    pH 7.8
233   16205E    35 0.08930492    pH 7.8
234   16205E    36 0.16768898    pH 7.8
235   16205E    37 0.22072275    pH 7.8
236   16205E    38 0.10166999    pH 7.8
237   16205E    39 0.17357192    pH 7.8
238   16205E    40 0.20035468    pH 7.8
239   16205E    41 0.38443699    pH 7.8
240   15677A     1 0.00000000      pH 9
241   15677A     2 0.74719242      pH 9
242   15677A     3 0.71441746      pH 9
243   15677A     4 0.80413896      pH 9
244   15677A     5 0.63581502      pH 9
245   15677A     6 0.45302006      pH 9
246   15677A     7 0.20097245      pH 9
247   15677A     8 0.42753395      pH 9
248   15677A     9 0.87014812      pH 9
249   15677A    10 0.60552091      pH 9
250   15677A    11 0.57297228      pH 9
251   15677A    12 0.64725567      pH 9
252   15677A    13 0.38703559      pH 9
253   15677A    14 0.76490806      pH 9
254   15677A    15 0.81037376      pH 9
255   15677A    16 0.35965996      pH 9
256   15677A    17 0.15057120      pH 9
257   30107A     1 0.00000000      pH 9
258   30107A     2 0.40986829      pH 9
259   30107A     3 0.33081624      pH 9
260   30107A     4 0.27757424      pH 9
261   30107A     5 0.44207100      pH 9
262   30107A     6 0.13499497      pH 9
263   30107A     7 0.22253359      pH 9
264   30107A     8 0.12261432      pH 9
265   30107A     9 0.24577569      pH 9
266   30107A    10 0.47248811      pH 9
267   30107A    11 0.25905970      pH 9
268   30107A    12 0.29059163      pH 9
269   30107A    13 0.47722354      pH 9
270   30107A    14 0.76536020      pH 9
271   30107A    15 0.22788593      pH 9
272   30107A    16 0.28258634      pH 9
273   30107A    17 0.24756205      pH 9
274   12058B     1 0.00000000      pH 9
275   12058B     2 0.69424034      pH 9
276   12058B     3 0.59369383      pH 9
277   12058B     4 0.87034777      pH 9
278   12058B     5 0.31016502      pH 9
279   12058B     6 0.55551818      pH 9
280   12058B     7 0.53941741      pH 9
281   12058B     8 0.81313682      pH 9
282   12058B     9 0.46162957      pH 9
283   12058B    10 0.44886047      pH 9
284   12058B    11 0.58591678      pH 9
285   12058B    12 0.95242265      pH 9
286   12058B    13 0.71509873      pH 9
287   12058B    14 0.43981576      pH 9
288   12058B    15 0.48502996      pH 9
289   12058B    16 0.28299509      pH 9
290   12058B    17 0.80351370      pH 9
291   12058B    18 0.29462494      pH 9
292   32683B     1 0.00000000      pH 9
293   32683B     2 0.51535572      pH 9
294   32683B     3 0.84273169      pH 9
295   32683B     4 0.94923571      pH 9
296   32683B     5 0.70697780      pH 9
297   32683B     6 0.71657686      pH 9
298   32683B     7 0.21957302      pH 9
299   32683B     8 0.30260669      pH 9
300   32683B     9 0.89397219      pH 9
301   32683B    10 0.51712813      pH 9
302   32683B    11 0.34476385      pH 9
303   32683B    12 0.46081555      pH 9
304   32683B    13 0.27992732      pH 9
305   32683B    14 0.43642920      pH 9
306   32683B    15 0.50387904      pH 9
307   32683B    16 0.62153897      pH 9
308   32683B    17 0.55935740      pH 9
309   34868B     1 0.00000000      pH 9
310   34868B     2 0.65033330      pH 9
311   34868B     3 0.11056894      pH 9
312   34868B     4 0.33683853      pH 9
313   34868B     5 0.76494063      pH 9
314   34868B     6 0.78233805      pH 9
315   34868B     7 0.18280291      pH 9
316   34868B     8 0.57439957      pH 9
317   34868B     9 0.36011108      pH 9
318   34868B    10 0.76025755      pH 9
319   34868B    11 0.73095309      pH 9
320   34868B    12 0.91688957      pH 9
321   34868B    13 0.24354734      pH 9
322   34868B    14 0.77688990      pH 9
323   34868B    15 0.95106263      pH 9
324   34868B    16 0.54385432      pH 9
325    5692C     1 0.00000000      pH 9
326    5692C     2 0.77917762      pH 9
327    5692C     3 0.51222728      pH 9
328    5692C     4 0.82213710      pH 9
329    5692C     5 0.54802370      pH 9
330    5692C     6 0.20234740      pH 9
331    5692C     7 0.24018563      pH 9
332    5692C     8 0.14765969      pH 9
333    5692C     9 0.08492065      pH 9
334    5692C    10 0.02011456      pH 9
335    5692C    11 0.05562570      pH 9
336    5692C    12 0.01094203      pH 9
337    5692C    13 0.05361751      pH 9
338    5692C    14 0.07530542      pH 9
339    5692C    15 0.05207479      pH 9
340    5692C    16 0.05136302      pH 9
341    5692C    17 0.01164088      pH 9
342    5692C    18 0.03289228      pH 9
343    5692C    19 0.00220202      pH 9
344    5692C    20 0.06196600      pH 9
345   54413C     1 0.00000000      pH 9
346   54413C     2 0.81489124      pH 9
347   54413C     3 0.50065140      pH 9
348   54413C     4 0.47126512      pH 9
349   54413C     5 0.52694021      pH 9
350   54413C     6 0.79088585      pH 9
351   54413C     7 0.50507849      pH 9
352   54413C     8 0.56040159      pH 9
353   54413C     9 0.83034350      pH 9
354   54413C    10 0.48197041      pH 9
355   54413C    11 0.75997088      pH 9
356   54413C    12 0.41635746      pH 9
357   54413C    13 0.66789980      pH 9
358   54413C    14 0.55000497      pH 9
359   54413C    15 0.71769196      pH 9
360   54413C    16 0.37110810      pH 9
361   54413C    17 0.30916870      pH 9
362   54413C    18 0.43760609      pH 9
363    5274D     1 0.00000000      pH 9
364    5274D     2 0.59553117      pH 9
365    5274D     3 0.59543134      pH 9
366    5274D     4 0.76713324      pH 9
367    5274D     5 0.91305342      pH 9
368    5274D     6 0.74629559      pH 9
369    5274D     7 0.57896386      pH 9
370    5274D     8 0.79990968      pH 9
371    5274D     9 0.68832108      pH 9
372    5274D    10 0.31907597      pH 9
373    5274D    11 0.54530503      pH 9
374    5274D    12 0.63859079      pH 9
375    5274D    13 0.18348335      pH 9
376    5274D    14 0.76970163      pH 9
377    5274D    15 0.25392009      pH 9
378    5274D    16 0.64914459      pH 9
379    5274D    17 0.61852933      pH 9
380    5274D    18 0.55929106      pH 9
381    5274D    19 0.47499277      pH 9
382    5274D    20 0.79403146      pH 9
383    5274D    21 0.90888779      pH 9
384    5274D    22 0.14803973      pH 9
385    5274D    23 0.52374221      pH 9
386    5274D    24 0.22724479      pH 9
387   27324D     1 0.00000000      pH 9
388   27324D     2 0.64467962      pH 9
389   27324D     3 0.48257792      pH 9
390   27324D     4 0.92754743      pH 9
391   27324D     5 0.68940088      pH 9
392   27324D     6 0.91497501      pH 9
393   27324D     7 0.38496064      pH 9
394   27324D     8 0.17318844      pH 9
395   27324D     9 0.50268424      pH 9
396   27324D    10 0.21927692      pH 9
397   27324D    11 0.19539169      pH 9
398   27324D    12 0.56253043      pH 9
399   27324D    13 0.08783290      pH 9
400   27324D    14 0.60487929      pH 9
401   27324D    15 0.12009344      pH 9
402   27324D    16 0.07259841      pH 9
403   27324D    17 0.48625488      pH 9
404   27324D    18 0.62431128      pH 9
405   27324D    19 0.17160649      pH 9
406   43194E     1 0.00000000      pH 9
407   43194E     2 0.78005602      pH 9
408   43194E     3 0.32841336      pH 9
409   43194E     4 0.32223727      pH 9
410   43194E     5 0.32956133      pH 9
411   43194E     6 0.57378270      pH 9
412   43194E     7 0.54780965      pH 9
413   43194E     8 0.18664611      pH 9
414   43194E     9 0.50469749      pH 9
415   43194E    10 0.78256829      pH 9
416   43194E    11 0.70882117      pH 9
417   43194E    12 0.38050106      pH 9
418   43194E    13 0.14883783      pH 9
419   43194E    14 0.43105548      pH 9
420   43194E    15 0.50089813      pH 9
421   43194E    16 0.24204920      pH 9
422   43194E    17 0.48649130      pH 9
423   43194E    18 0.90926207      pH 9
424   43194E    19 0.58333722      pH 9

0 个答案:

没有答案