-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathdvc.lock
375 lines (375 loc) · 9.99 KB
/
dvc.lock
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
schema: '2.0'
stages:
join:
cmd: "lyscripts data join --inputs data/2023-isb-multisite.csv data/2023-clb-multisite.csv
--output data/joined.csv\n"
deps:
- path: data/2023-clb-multisite.csv
hash: md5
md5: 9d72ee96af2c51033a2fb0bb8551e318
size: 123938
- path: data/2023-isb-multisite.csv
hash: md5
md5: 569984943168f3a56d6ca58d0813dee2
size: 204323
outs:
- path: data/joined.csv
hash: md5
md5: d1c58d1bd8e9e9f39e322fac3d81553d
size: 385761
enhance:
cmd: "lyscripts data enhance data/joined.csv data/enhanced.csv --modalities CT
MRI PET FNA diagnostic_consensus pathology pCT\n"
deps:
- path: data/joined.csv
hash: md5
md5: d1c58d1bd8e9e9f39e322fac3d81553d
size: 385761
params:
params.yaml:
modalities:
CT:
- 0.76
- 0.81
MRI:
- 0.63
- 0.81
PET:
- 0.86
- 0.79
FNA:
- 0.98
- 0.8
diagnostic_consensus:
- 0.86
- 0.81
pathology:
- 1.0
- 1.0
pCT:
- 0.86
- 0.81
max_llh:
- 1.0
- 1.0
outs:
- path: data/enhanced.csv
hash: md5
md5: 810d9a11d0b6028cdd198aec16510770
size: 482794
statistics:
cmd: ".venv/bin/python scripts/statistics.py\n"
deps:
- path: data/enhanced.csv
md5: c11857f2f4ebfa770ee2ff5628d69f0d
size: 458572
- path: scripts/statistics.py
md5: fc53b4a142364b88da3ace48d55e2aeb
size: 11756
outs:
- path: figures/statistics.png
md5: 8ee419375b8fd843aa66d538dfae271b
size: 224157
copy:
cmd: "bash copy.sh\n"
deps:
- path: copy.sh
hash: md5
md5: 8f2f11ed8419c435154e665ba6f6d00a
size: 794
- path: figures
hash: md5
md5: 8a3d590bde843e678f1a82f3149c70ba.dir
size: 905301
nfiles: 8
- path: tables
hash: md5
md5: a71483712242f3d06069c5d17c5ea83a.dir
size: 2428
nfiles: 5
contra-involvement-table:
cmd: ".venv/bin/python scripts/contra_involvement.py\n"
deps:
- path: data/enhanced.csv
md5: c11857f2f4ebfa770ee2ff5628d69f0d
size: 458572
- path: scripts/contra_involvement.py
md5: 6a369719f0b729e82bf223388ec1eeb8
size: 2116
outs:
- path: tables/contra_involvement.csv
md5: 8b92ff1820277cf6247c7be0b271a4d7
size: 639
tables@contra_involvement:
cmd: "python scripts/contra_involvement.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 810d9a11d0b6028cdd198aec16510770
size: 482794
- path: scripts/contra_involvement.py
hash: md5
md5: 2117e407183da5ed4adb6c6742654219
size: 1809
- path: scripts/shared.py
hash: md5
md5: 35bf09255dfb9f9f1dd8f9027e73abc9
size: 2343
outs:
- path: tables/contra_involvement.csv
hash: md5
md5: 73a448dba414ee9d8420afb40ad48793
size: 833
figures@statistics:
cmd: "python scripts/statistics.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: f3b752be16fb194b4566e16951f13bf1
size: 460298
- path: scripts/statistics.py
hash: md5
md5: a6f04e8371cde2665ddd0598ecab9227
size: 10914
outs:
- path: figures/statistics.png
hash: md5
md5: 12b60eafb5964d874afa2ee61b8af3d0
size: 221932
figures@venn_diagram:
cmd: "python scripts/venn_diagram.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: f3b752be16fb194b4566e16951f13bf1
size: 460298
- path: scripts/venn_diagram.py
hash: md5
md5: 70f7fffb093619080a8f7f469e397f1f
size: 1911
outs:
- path: figures/venn_diagram.png
hash: md5
md5: c6260bb1a69b06445f8759afa496e905
size: 77280
tables@ece_data:
cmd: "python scripts/ece_data.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: f3b752be16fb194b4566e16951f13bf1
size: 460298
- path: scripts/ece_data.py
hash: md5
md5: 3fe6b4d1ee3bad3a594b695a22554303
size: 1381
outs:
- path: tables/ece_data.csv
hash: md5
md5: 4bcfb44a048a115afe61582b9f0319f7
size: 225
logistic-regression:
cmd: ".venv/bin/python scripts/logistic_regression.py\n"
deps:
- path: data/lymph_nodes_invest_OC.csv
md5: bbe7e3def57cbb40358e4cc01197963e
size: 25487
- path: scripts/logistic_regression.py
md5: 978d1404475e4dca7766d2e76932d1b6
size: 5229
outs:
- path: figures/Log_ROC.svg
md5: 140ab8a0f46e750c83d8beedc2f60931
size: 30934
- path: figures/confusion_matrix.png
md5: a1b25fc36b98479173504356ffdf5c7b
size: 30271
- path: figures/confusionmat_lymphsize_hist.png
md5: f13f2be6a0bd64cf081e07465befc5b1
size: 53804
figures@ece_stacked_bar:
cmd: "python scripts/ece_stacked_bar.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: f3b752be16fb194b4566e16951f13bf1
size: 460298
- path: scripts/ece_stacked_bar.py
hash: md5
md5: ff54d09dd918a689231f990aec110d95
size: 4581
outs:
- path: figures/ece_stacked_bar.png
hash: md5
md5: b13f4577b0fae2af30ec34b374cde76d
size: 77888
figures_lymph_invest@lymph_invest:
cmd: "python scripts/lymph_invest.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: c4a74afa0a1b2248763b911e48fa2133
size: 456854
- path: scripts/lymph_invest.py
hash: md5
md5: eeef01bed4035a81c67bb3272f1a8da2
size: 26589
pvalues_lymph_invest@lymph_invest_pvalues:
cmd: "python scripts/lymph_invest_pvalues.py\n"
deps:
- path: scripts/lymph_invest_pvalues.py
hash: md5
md5: c8928e42307025aedc9fe9f421955056
size: 2702
tables@prevalence_overall:
cmd: "python scripts/prevalence_overall.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: f3b752be16fb194b4566e16951f13bf1
size: 460298
- path: scripts/prevalence_overall.py
hash: md5
md5: 7ea22e383aad72f66dea53235183966d
size: 1867
outs:
- path: tables/prevalence_overall.csv
hash: md5
md5: 52ccf1b4fed49c7195730f11688eb1d3
size: 392
tables@prevalence_by_subsite:
cmd: "python scripts/prevalence_by_subsite.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: f3b752be16fb194b4566e16951f13bf1
size: 460298
- path: scripts/prevalence_by_subsite.py
hash: md5
md5: ee39d3fe8989bb2a6c7aac2eafa1156d
size: 1692
outs:
- path: tables/prevalence_by_subsite.csv
hash: md5
md5: e5125f4bac4325d57f2e668a1403563b
size: 274
tables@involvement_combinations:
cmd: "python scripts/involvement_combinations.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 810d9a11d0b6028cdd198aec16510770
size: 482794
- path: scripts/involvement_combinations.py
hash: md5
md5: f82d3e7eb1abd4267c805b3f4493902e
size: 2942
- path: scripts/shared.py
hash: md5
md5: 35bf09255dfb9f9f1dd8f9027e73abc9
size: 2343
outs:
- path: tables/involvement_combinations.csv
hash: md5
md5: b8ca3ac3f19707ce6b1752da7d8f3263
size: 446
tables@prevalence_stratified:
cmd: "python scripts/prevalence_stratified.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 810d9a11d0b6028cdd198aec16510770
size: 482794
- path: scripts/prevalence_stratified.py
hash: md5
md5: 0cdf789ce85e18b7c39fc223f5948aca
size: 2411
- path: scripts/shared.py
hash: md5
md5: 35bf09255dfb9f9f1dd8f9027e73abc9
size: 2343
outs:
- path: tables/prevalence_stratified.csv
hash: md5
md5: c458845231e25b5e232d0eb29abf4af6
size: 778
figures@multi_panel_statistics:
cmd: "python scripts/multi_panel_statistics.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 810d9a11d0b6028cdd198aec16510770
size: 482794
- path: scripts/multi_panel_statistics.py
hash: md5
md5: 77c709cb30d01041215ac88446c967fe
size: 11015
- path: scripts/shared.py
hash: md5
md5: 35bf09255dfb9f9f1dd8f9027e73abc9
size: 2343
outs:
- path: figures/multi_panel_statistics.png
hash: md5
md5: 24def62f204c4f1e86d09cbd5ea1acdb
size: 218072
figures@venn_and_stacked_ece:
cmd: "python scripts/venn_and_stacked_ece.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 810d9a11d0b6028cdd198aec16510770
size: 482794
- path: scripts/shared.py
hash: md5
md5: 35bf09255dfb9f9f1dd8f9027e73abc9
size: 2343
- path: scripts/venn_and_stacked_ece.py
hash: md5
md5: 285456666b9d56d095cc64aa358ca959
size: 6471
outs:
- path: figures/venn_and_stacked_ece.png
hash: md5
md5: 9ecb6c6e55cb31ca335a9879f089590a
size: 138828
figures@dissected_vs_positive:
cmd: "python scripts/dissected_vs_positive.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 810d9a11d0b6028cdd198aec16510770
size: 482794
- path: scripts/dissected_vs_positive.py
hash: md5
md5: 1739860ac5847bf653023d53341e4045
size: 3787
- path: scripts/shared.py
hash: md5
md5: 35bf09255dfb9f9f1dd8f9027e73abc9
size: 2343
outs:
- path: figures/dissected_vs_positive.png
hash: md5
md5: 06db6be383131a0ffe273bf5396495bd
size: 139771
figures@contra_by_subsite:
cmd: "python scripts/contra_by_subsite.py\n"
deps:
- path: data/enhanced.csv
hash: md5
md5: 810d9a11d0b6028cdd198aec16510770
size: 482794
- path: scripts/contra_by_subsite.py
hash: md5
md5: 17a720be7b79d6b42bd4dc0374be687f
size: 3108
- path: scripts/shared.py
hash: md5
md5: 35bf09255dfb9f9f1dd8f9027e73abc9
size: 2343
outs:
- path: figures/contra_by_subsite.png
hash: md5
md5: 85cc98bd72cfa2fb86f2deba5819ea9c
size: 49525