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Merge pull request #5 from PharmCat/dev
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Dev
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@PharmCat
PharmCat committed Aug 21, 2023
2 parents a03f72f + c59e88f commit 9a9ef27
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Showing 10 changed files with 3,950 additions and 4 deletions.
2 changes: 1 addition & 1 deletion Project.toml
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Expand Up @@ -3,7 +3,7 @@ uuid = "00e1d80e-504f-4d7b-946f-0aea2e7abfe3"
keywords = ["bioequivalence"]
desc = "Bioequivalence"
authors = ["Vladimir Arnautov <mail@pharmcat.net>"]
version = "0.2.1"
version = "0.2.2"

[deps]
CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
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2 changes: 1 addition & 1 deletion src/bioequivalence.jl
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Expand Up @@ -489,7 +489,7 @@ function estimate(be; estimator = "auto", method = "auto", supresswarn = false,
# If GLM used
if estimator == "glm"

results = [fit(LinearModel, m, be.data; contrasts = Dict(be.formulation => DummyCoding(base = be.reference))) for m in models]
results = [fit(LinearModel, m, be.data; contrasts = Dict(be.formulation => DummyCoding(base = be.reference)), dropcollinear = true) for m in models]

df = DataFrame(Parameter = String[], Metric = String[], PE = Float64[], SE = Float64[], DF = Float64[], lnLCI = Float64[], lnUCI = Float64[], GMR = Float64[], LCI = Float64[], UCI = Float64[], level = Float64[])
for i in results
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37 changes: 37 additions & 0 deletions test/csv/2x2rds2.csv
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ObsNumber Subj Seq Per Trt Var
1 1 TR 1 T 2.52
2 2 TR 1 T 8.87
3 3 TR 1 T 0.79
4 4 TR 1 T 1.68
5 5 TR 1 T 6.95
6 6 TR 1 T 1.05
7 7 TR 1 T 0.99
8 8 TR 1 T 5.6
9 9 TR 1 T 3.16
10 1 TR 2 R 5.47
11 2 TR 2 R 4.84
12 3 TR 2 R 2.25
13 4 TR 2 R 1.82
14 5 TR 2 R 7.87
15 6 TR 2 R 3.25
16 7 TR 2 R 12.39
17 8 TR 2 R 4.77
18 9 TR 2 R 1.88
19 10 RT 1 R 4.98
20 11 RT 1 R 7.14
21 12 RT 1 R 1.81
22 13 RT 1 R 7.34
23 14 RT 1 R 4.25
24 15 RT 1 R 6.66
25 16 RT 1 R 4.76
26 17 RT 1 R 7.16
27 18 RT 1 R 5.52
28 10 RT 2 T 3.19
29 11 RT 2 T 9.83
30 12 RT 2 T 2.91
31 13 RT 2 T 4.58
32 14 RT 2 T 7.05
33 15 RT 2 T 3.41
34 16 RT 2 T 2.49
35 17 RT 2 T 6.18
36 18 RT 2 T 2.85
27 changes: 27 additions & 0 deletions test/csv/2x2rds3.csv
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ObsNumber Subj Seq Per Trt Var
1 1 TR 1 T 2.52
10 1 TR 2 R 5.47
4 4 TR 1 T 1.68
13 4 TR 2 R 1.82
5 5 TR 1 T 6.95
14 5 TR 2 R 7.87
7 7 TR 1 T 0.99
16 7 TR 2 R 12.39
19 10 RT 1 R 4.98
28 10 RT 2 T 3.19
20 11 RT 1 R 7.14
29 11 RT 2 T 9.83
21 12 RT 1 R 1.81
30 12 RT 2 T 2.91
22 13 RT 1 R 7.34
31 13 RT 2 T 4.58
23 14 RT 1 R 4.25
32 14 RT 2 T 7.05
24 15 RT 1 R 6.66
33 15 RT 2 T 3.41
25 16 RT 1 R 4.76
34 16 RT 2 T 2.49
26 17 RT 1 R 7.16
35 17 RT 2 T 6.18
27 18 RT 1 R 5.52
36 18 RT 2 T 2.85
37 changes: 37 additions & 0 deletions test/csv/2x2rds4.csv
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@@ -0,0 +1,37 @@
ObsNumber Subj Seq Per Trt Var
1 1 TR 1 T 2.52
10 1 TR 2 R 5.47
2 2 TR 1 T 8.87
11 2 TR 2 R 4.84
3 3 TR 1 T 0.79
12 3 TR 2 R 2.25
4 4 TR 1 T 1680000
13 4 TR 2 R 1820000
5 5 TR 1 T 6.95
14 5 TR 2 R 7.87
6 6 TR 1 T 1.05
15 6 TR 2 R 3.25
7 7 TR 1 T 0.99
16 7 TR 2 R 12.39
8 8 TR 1 T 5.6
17 8 TR 2 R 4.77
9 9 TR 1 T 3.16
18 9 TR 2 R 1.88
19 10 RT 1 R 4.98
28 10 RT 2 T 3.19
20 11 RT 1 R 7.14
29 11 RT 2 T 9.83
21 12 RT 1 R 1.81
30 12 RT 2 T 2.91
22 13 RT 1 R 7.34
31 13 RT 2 T 4.58
23 14 RT 1 R 4250000
32 14 RT 2 T 7050000
24 15 RT 1 R 6.66
33 15 RT 2 T 3.41
25 16 RT 1 R 4.76
34 16 RT 2 T 2.49
26 17 RT 1 R 7.16
35 17 RT 2 T 6.18
27 18 RT 1 R 5520000
36 18 RT 2 T 2850000
37 changes: 37 additions & 0 deletions test/csv/2x2rds5.csv
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@@ -0,0 +1,37 @@
ObsNumber Subj Seq Per Trt Var
1 1 TR 1 T 2.52
2 2 TR 1 T 8.87
3 3 TR 1 T 79.0
4 4 TR 1 T 1.68
5 5 TR 1 T 6.95
6 6 TR 1 T 1.05
7 7 TR 1 T 0.99
8 8 TR 1 T 5.6
9 9 TR 1 T 3.16
10 1 TR 2 R 5.47
11 2 TR 2 R 4.84
12 3 TR 2 R 2.25
13 4 TR 2 R 1.82
14 5 TR 2 R 7.87
15 6 TR 2 R 3.25
16 7 TR 2 R 12.39
17 8 TR 2 R 4.77
18 9 TR 2 R 1.88
19 10 RT 1 R 4.98
20 11 RT 1 R 7.14
21 12 RT 1 R 1.81
22 13 RT 1 R 7.34
23 14 RT 1 R 4.25
24 15 RT 1 R 6.66
25 16 RT 1 R 4.76
26 17 RT 1 R 7.16
27 18 RT 1 R 5.52
28 10 RT 2 T 3.19
29 11 RT 2 T 9.83
30 12 RT 2 T 2.91
31 13 RT 2 T 4.58
32 14 RT 2 T 7.05
33 15 RT 2 T 3.41
34 16 RT 2 T 2.49
35 17 RT 2 T 6.18
36 18 RT 2 T 2.85
201 changes: 201 additions & 0 deletions test/csv/2x2rds6.csv
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ObsNumber Subj Seq Per Trt Var
1 1 TR 1 T 4.34635
2 1 TR 2 R 4.45488
3 2 TR 1 T 3.22579
4 2 TR 2 R 1.78912
5 3 TR 1 T 1.46572
6 3 TR 2 R 2.55294
7 4 TR 1 T 4.05118
8 4 TR 2 R 4.58297
9 5 TR 1 T 3.65939
10 5 TR 2 R 2.12957
11 6 TR 1 T 1.40002
12 6 TR 2 R 2.14148
13 7 TR 1 T 3.67227
14 7 TR 2 R 4.58497
15 8 TR 1 T 4.04046
16 8 TR 2 R 2.53935
17 9 TR 1 T 1.46176
18 9 TR 2 R 1.79842
19 10 TR 1 T 3.2398
20 10 TR 2 R 4.46071
21 11 TR 1 T 4.33865
22 11 TR 2 R 2.98584
23 12 TR 1 T 1.64605
24 12 TR 2 R 1.55107
25 13 TR 1 T 2.78824
26 13 TR 2 R 4.22009
27 14 TR 1 T 4.5302
28 14 TR 2 R 3.43345
29 15 TR 1 T 1.93819
30 15 TR 2 R 1.41915
31 16 TR 1 T 2.35354
32 16 TR 2 R 3.88228
33 17 TR 1 T 4.59986
34 17 TR 2 R 3.84653
35 18 TR 1 T 2.31491
36 18 TR 2 R 1.41315
37 19 TR 1 T 1.97034
38 19 TR 2 R 3.47419
39 20 TR 1 T 4.54207
40 20 TR 2 R 4.19218
41 21 TR 1 T 2.7462
42 21 TR 2 R 1.53357
43 22 TR 1 T 1.66916
44 22 TR 2 R 3.02832
45 23 TR 1 T 4.36145
46 23 TR 2 R 4.44286
47 24 TR 1 T 3.19772
48 24 TR 2 R 1.77079
49 25 TR 1 T 1.474
50 25 TR 2 R 2.5802
51 26 TR 1 T 4.07237
52 26 TR 2 R 4.5786
53 27 TR 1 T 3.63348
54 27 TR 2 R 2.10594
55 28 TR 1 T 1.40039
56 28 TR 2 R 2.16552
57 29 TR 1 T 3.69786
58 29 TR 2 R 4.5886
59 30 TR 1 T 4.01878
60 30 TR 2 R 2.5123
61 31 TR 1 T 1.45421
62 31 TR 2 R 1.81731
63 32 TR 1 T 3.26777
64 32 TR 2 R 4.47204
65 33 TR 1 T 4.32293
66 33 TR 2 R 2.95752
67 34 TR 1 T 1.63117
68 34 TR 2 R 1.56332
69 35 TR 1 T 2.81634
70 35 TR 2 R 4.23823
71 36 TR 1 T 4.52169
72 36 TR 2 R 3.40612
73 37 TR 1 T 1.91716
74 37 TR 2 R 1.42377
75 38 TR 1 T 2.37955
76 38 TR 2 R 3.90577
77 39 TR 1 T 4.59923
78 39 TR 2 R 3.82237
79 40 TR 1 T 2.28942
80 40 TR 2 R 1.40978
81 41 TR 1 T 1.99218
82 41 TR 2 R 3.50117
83 42 TR 1 T 4.54938
84 42 TR 2 R 4.1731
85 43 TR 1 T 2.71828
86 43 TR 2 R 1.52247
87 44 TR 1 T 1.68509
88 44 TR 2 R 3.05664
89 45 TR 1 T 4.37611
90 45 TR 2 R 4.43039
91 46 TR 1 T 3.16958
92 46 TR 2 R 1.75285
93 47 TR 1 T 1.48275
94 47 TR 2 R 2.6076
95 48 TR 1 T 4.09322
96 48 TR 2 R 4.57374
97 49 TR 1 T 3.60737
98 49 TR 2 R 2.08259
99 50 TR 1 T 1.40127
100 50 TR 2 R 2.18981
101 51 RT 1 R 3.72324
102 51 RT 2 T 4.59172
103 52 RT 1 R 3.99678
104 52 RT 2 T 2.4854
105 53 RT 1 R 1.44714
106 53 RT 2 T 1.83657
107 54 RT 1 R 3.29565
108 54 RT 2 T 4.48291
109 55 RT 1 R 4.30679
110 55 RT 2 T 2.92921
111 56 RT 1 R 1.61672
112 56 RT 2 T 1.57601
113 57 RT 1 R 2.84451
114 57 RT 2 T 4.25597
115 58 RT 1 R 4.5127
116 58 RT 2 T 3.37866
117 59 RT 1 R 1.89648
118 59 RT 2 T 1.42888
119 60 RT 1 R 2.40575
120 60 RT 2 T 3.92898
121 61 RT 1 R 4.5981
122 61 RT 2 T 3.79794
123 62 RT 1 R 2.26415
124 62 RT 2 T 1.4069
125 63 RT 1 R 2.01434
126 63 RT 2 T 3.52799
127 64 RT 1 R 4.55621
128 64 RT 2 T 4.15366
129 65 RT 1 R 2.69044
130 65 RT 2 T 1.51183
131 66 RT 1 R 1.70143
132 66 RT 2 T 3.08493
133 67 RT 1 R 4.39035
134 67 RT 2 T 4.41748
135 68 RT 1 R 3.14139
136 68 RT 2 T 1.73531
137 69 RT 1 R 1.49198
138 69 RT 2 T 2.63512
139 70 RT 1 R 4.11373
140 70 RT 2 T 4.56838
141 71 RT 1 R 3.58107
142 71 RT 2 T 2.05953
143 72 RT 1 R 1.40265
144 72 RT 2 T 2.21437
145 73 RT 1 R 3.74839
146 73 RT 2 T 4.59435
147 74 RT 1 R 3.97447
148 74 RT 2 T 2.45867
149 75 RT 1 R 1.44056
150 75 RT 2 T 1.8562
151 76 RT 1 R 3.32344
152 76 RT 2 T 4.49331
153 77 RT 1 R 4.29024
154 77 RT 2 T 2.90093
155 78 RT 1 R 1.6027
156 78 RT 2 T 1.58914
157 79 RT 1 R 2.87272
158 79 RT 2 T 4.27332
159 80 RT 1 R 4.50323
160 80 RT 2 T 3.35108
161 81 RT 1 R 1.87615
162 81 RT 2 T 1.43448
163 82 RT 1 R 2.43214
164 82 RT 2 T 3.95189
165 83 RT 1 R 4.59648
166 83 RT 2 T 3.77327
167 84 RT 1 R 2.23912
168 84 RT 2 T 1.40452
169 85 RT 1 R 2.0368
170 85 RT 2 T 3.55464
171 86 RT 1 R 4.56255
172 86 RT 2 T 4.13385
173 87 RT 1 R 2.6627
174 87 RT 2 T 1.50166
175 88 RT 1 R 1.71818
176 88 RT 2 T 3.1132
177 89 RT 1 R 4.40414
178 89 RT 2 T 4.40412
179 90 RT 1 R 3.11316
180 90 RT 2 T 1.71816
181 91 RT 1 R 1.50168
182 91 RT 2 T 2.66275
183 92 RT 1 R 4.13389
184 92 RT 2 T 4.56254
185 93 RT 1 R 3.55459
186 93 RT 2 T 2.03676
187 94 RT 1 R 1.40453
188 94 RT 2 T 2.23916
189 95 RT 1 R 3.77331
190 95 RT 2 T 4.59648
191 96 RT 1 R 3.95185
192 96 RT 2 T 2.4321
193 97 RT 1 R 1.43447
194 97 RT 2 T 1.87618
195 98 RT 1 R 3.35113
196 98 RT 2 T 4.50325
197 99 RT 1 R 4.27329
198 99 RT 2 T 2.87267
199 100 RT 1 R 1.58912
200 100 RT 2 T 1.60272
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2 comments on commit 9a9ef27

@PharmCat
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Registration pull request created: JuliaRegistries/General/90054

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.2.2 -m "<description of version>" 9a9ef279d3b66a8549980e10f062dc27a94e2f40
git push origin v0.2.2

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