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updated tests and snaps and added test for equality between database …
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…and sysdata
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@joshwlambert
joshwlambert committed Nov 17, 2023
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8 changes: 4 additions & 4 deletions tests/testthat/_snaps/epidist_db.md
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Code
epidist_db()
Message
Returning 118 results that match the criteria (95 are parameterised).
Returning 122 results that match the criteria (99 are parameterised).
Use subset to filter by entry variables or single_epidist to return a single entry.
To retrieve the short citation for each use the 'get_citation' function
Output
List of <epidist> objects
Number of entries in library: 118
Number of studies in library: 45
Number of entries in library: 122
Number of studies in library: 47
Number of diseases: 23
Number of delay distributions: 108
Number of delay distributions: 112
Number of offspring distributions: 10

# epidist_db print method works as expected for <= 5 <epidist>
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219 changes: 120 additions & 99 deletions tests/testthat/_snaps/list_distributions.md
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88 COVID-19 incubation period
89 COVID-19 incubation period
90 COVID-19 serial interval
91 COVID-19 incubation period
92 COVID-19 incubation period
91 COVID-19 serial interval
92 COVID-19 serial interval
93 COVID-19 incubation period
94 COVID-19 incubation period
94 COVID-19 serial interval
95 COVID-19 incubation period
96 COVID-19 incubation period
97 COVID-19 onset to hospitalisation
98 COVID-19 onset to hospitalisation
99 COVID-19 onset to death
100 COVID-19 hospitalisation to death
101 COVID-19 incubation period
97 COVID-19 incubation period
98 COVID-19 incubation period
99 COVID-19 incubation period
100 COVID-19 incubation period
101 COVID-19 onset to hospitalisation
102 COVID-19 onset to hospitalisation
103 COVID-19 onset to hospitalisation
104 COVID-19 onset to death
105 COVID-19 hospitalisation to death
106 COVID-19 incubation period
107 COVID-19 incubation period
108 COVID-19 incubation period
109 COVID-19 incubation period
110 Mpox serial interval
111 Mpox serial interval
112 Mpox serial interval
113 Mpox incubation period
114 Mpox incubation period
115 Mpox incubation period
116 Mpox incubation period
103 COVID-19 onset to death
104 COVID-19 hospitalisation to death
105 COVID-19 incubation period
106 COVID-19 onset to hospitalisation
107 COVID-19 onset to hospitalisation
108 COVID-19 onset to death
109 COVID-19 hospitalisation to death
110 COVID-19 incubation period
111 COVID-19 incubation period
112 COVID-19 incubation period
113 COVID-19 incubation period
114 Mpox serial interval
115 Mpox serial interval
116 Mpox serial interval
117 Mpox incubation period
118 Mpox incubation period
119 Mpox incubation period
120 Mpox incubation period
121 Mpox incubation period
122 Mpox incubation period
prob_distribution author year
1 lnorm Justin L.... 2009
2 lnorm Justin L.... 2009
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88 <NA> Balram R.... 2022
89 <NA> Muluneh .... 2021
90 <NA> Muluneh .... 2021
91 <NA> Christel.... 2021
92 weibull Long V. .... 2020
93 lnorm Conor Mc.... 2020
94 lnorm Conor Mc.... 2020
95 lnorm Natalie .... 2020
96 lnorm Natalie .... 2020
97 gamma Natalie .... 2020
98 gamma Natalie .... 2020
91 lnorm Hiroshi .... 2020
92 weibull Hiroshi .... 2020
93 weibull Lin Yang.... 2020
94 norm Lin Yang.... 2020
95 <NA> Christel.... 2021
96 weibull Long V. .... 2020
97 lnorm Conor Mc.... 2020
98 lnorm Conor Mc.... 2020
99 lnorm Natalie .... 2020
100 weibull Natalie .... 2020
101 lnorm Natalie .... 2020
102 lnorm Natalie .... 2020
100 lnorm Natalie .... 2020
101 gamma Natalie .... 2020
102 gamma Natalie .... 2020
103 lnorm Natalie .... 2020
104 lnorm Natalie .... 2020
104 weibull Natalie .... 2020
105 lnorm Natalie .... 2020
106 lnorm Stephen .... 2020
107 lnorm Stephen .... 2020
108 lnorm Stephen .... 2020
109 lnorm Stephen .... 2020
110 gamma Zihao Gu.... 2022
111 <NA> Shuqi Wa.... 2022
112 <NA> Shuqi Wa.... 2022
113 <NA> Shuqi Wa.... 2022
114 <NA> Shuqi Wa.... 2022
106 lnorm Natalie .... 2020
107 lnorm Natalie .... 2020
108 lnorm Natalie .... 2020
109 lnorm Natalie .... 2020
110 lnorm Stephen .... 2020
111 lnorm Stephen .... 2020
112 lnorm Stephen .... 2020
113 lnorm Stephen .... 2020
114 gamma Zihao Gu.... 2022
115 <NA> Shuqi Wa.... 2022
116 <NA> Fengying.... 2022
117 <NA> Fengying.... 2022
118 <NA> Fengying.... 2022
116 <NA> Shuqi Wa.... 2022
117 <NA> Shuqi Wa.... 2022
118 <NA> Shuqi Wa.... 2022
119 <NA> Shuqi Wa.... 2022
120 <NA> Fengying.... 2022
121 <NA> Fengying.... 2022
122 <NA> Fengying.... 2022

# list_distributions works for incubation period with db

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53 COVID-19 incubation period <NA> Ke Men, .... 2020
54 COVID-19 incubation period <NA> Balram R.... 2022
55 COVID-19 incubation period <NA> Muluneh .... 2021
56 COVID-19 incubation period <NA> Christel.... 2021
57 COVID-19 incubation period weibull Long V. .... 2020
58 COVID-19 incubation period lnorm Conor Mc.... 2020
56 COVID-19 incubation period weibull Lin Yang.... 2020
57 COVID-19 incubation period <NA> Christel.... 2021
58 COVID-19 incubation period weibull Long V. .... 2020
59 COVID-19 incubation period lnorm Conor Mc.... 2020
60 COVID-19 incubation period lnorm Natalie .... 2020
60 COVID-19 incubation period lnorm Conor Mc.... 2020
61 COVID-19 incubation period lnorm Natalie .... 2020
62 COVID-19 incubation period lnorm Natalie .... 2020
63 COVID-19 incubation period lnorm Stephen .... 2020
63 COVID-19 incubation period lnorm Natalie .... 2020
64 COVID-19 incubation period lnorm Stephen .... 2020
65 COVID-19 incubation period lnorm Stephen .... 2020
66 COVID-19 incubation period lnorm Stephen .... 2020
67 Mpox incubation period <NA> Shuqi Wa.... 2022
67 COVID-19 incubation period lnorm Stephen .... 2020
68 Mpox incubation period <NA> Shuqi Wa.... 2022
69 Mpox incubation period <NA> Shuqi Wa.... 2022
70 Mpox incubation period <NA> Fengying.... 2022
70 Mpox incubation period <NA> Shuqi Wa.... 2022
71 Mpox incubation period <NA> Fengying.... 2022
72 Mpox incubation period <NA> Fengying.... 2022
73 Mpox incubation period <NA> Fengying.... 2022

# list_distributions works for different distribution with db

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10 MERS serial interval lnorm Abdullah.... 2013
11 MERS serial interval gamma B J Cowl.... 2015
12 COVID-19 serial interval <NA> Muluneh .... 2021
13 Mpox serial interval gamma Zihao Gu.... 2022
14 Mpox serial interval <NA> Shuqi Wa.... 2022
15 Mpox serial interval <NA> Shuqi Wa.... 2022
13 COVID-19 serial interval lnorm Hiroshi .... 2020
14 COVID-19 serial interval weibull Hiroshi .... 2020
15 COVID-19 serial interval norm Lin Yang.... 2020
16 Mpox serial interval gamma Zihao Gu.... 2022
17 Mpox serial interval <NA> Shuqi Wa.... 2022
18 Mpox serial interval <NA> Shuqi Wa.... 2022

# list_distributions works for COVID-19 db

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2 COVID-19 incubation period <NA> Balram R.... 2022
3 COVID-19 incubation period <NA> Muluneh .... 2021
4 COVID-19 serial interval <NA> Muluneh .... 2021
5 COVID-19 incubation period <NA> Christel.... 2021
6 COVID-19 incubation period weibull Long V. .... 2020
7 COVID-19 incubation period lnorm Conor Mc.... 2020
8 COVID-19 incubation period lnorm Conor Mc.... 2020
9 COVID-19 incubation period lnorm Natalie .... 2020
10 COVID-19 incubation period lnorm Natalie .... 2020
11 COVID-19 onset to hospitalisation gamma Natalie .... 2020
12 COVID-19 onset to hospitalisation gamma Natalie .... 2020
13 COVID-19 onset to death lnorm Natalie .... 2020
14 COVID-19 hospitalisation to death weibull Natalie .... 2020
15 COVID-19 incubation period lnorm Natalie .... 2020
16 COVID-19 onset to hospitalisation lnorm Natalie .... 2020
17 COVID-19 onset to hospitalisation lnorm Natalie .... 2020
18 COVID-19 onset to death lnorm Natalie .... 2020
19 COVID-19 hospitalisation to death lnorm Natalie .... 2020
20 COVID-19 incubation period lnorm Stephen .... 2020
21 COVID-19 incubation period lnorm Stephen .... 2020
22 COVID-19 incubation period lnorm Stephen .... 2020
23 COVID-19 incubation period lnorm Stephen .... 2020
5 COVID-19 serial interval lnorm Hiroshi .... 2020
6 COVID-19 serial interval weibull Hiroshi .... 2020
7 COVID-19 incubation period weibull Lin Yang.... 2020
8 COVID-19 serial interval norm Lin Yang.... 2020
9 COVID-19 incubation period <NA> Christel.... 2021
10 COVID-19 incubation period weibull Long V. .... 2020
11 COVID-19 incubation period lnorm Conor Mc.... 2020
12 COVID-19 incubation period lnorm Conor Mc.... 2020
13 COVID-19 incubation period lnorm Natalie .... 2020
14 COVID-19 incubation period lnorm Natalie .... 2020
15 COVID-19 onset to hospitalisation gamma Natalie .... 2020
16 COVID-19 onset to hospitalisation gamma Natalie .... 2020
17 COVID-19 onset to death lnorm Natalie .... 2020
18 COVID-19 hospitalisation to death weibull Natalie .... 2020
19 COVID-19 incubation period lnorm Natalie .... 2020
20 COVID-19 onset to hospitalisation lnorm Natalie .... 2020
21 COVID-19 onset to hospitalisation lnorm Natalie .... 2020
22 COVID-19 onset to death lnorm Natalie .... 2020
23 COVID-19 hospitalisation to death lnorm Natalie .... 2020
24 COVID-19 incubation period lnorm Stephen .... 2020
25 COVID-19 incubation period lnorm Stephen .... 2020
26 COVID-19 incubation period lnorm Stephen .... 2020
27 COVID-19 incubation period lnorm Stephen .... 2020

# list_distributions works for disease & epi_dist subset with db

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1 COVID-19 incubation period <NA> Ke Men, .... 2020
2 COVID-19 incubation period <NA> Balram R.... 2022
3 COVID-19 incubation period <NA> Muluneh .... 2021
4 COVID-19 incubation period <NA> Christel.... 2021
5 COVID-19 incubation period weibull Long V. .... 2020
6 COVID-19 incubation period lnorm Conor Mc.... 2020
4 COVID-19 incubation period weibull Lin Yang.... 2020
5 COVID-19 incubation period <NA> Christel.... 2021
6 COVID-19 incubation period weibull Long V. .... 2020
7 COVID-19 incubation period lnorm Conor Mc.... 2020
8 COVID-19 incubation period lnorm Natalie .... 2020
8 COVID-19 incubation period lnorm Conor Mc.... 2020
9 COVID-19 incubation period lnorm Natalie .... 2020
10 COVID-19 incubation period lnorm Natalie .... 2020
11 COVID-19 incubation period lnorm Stephen .... 2020
11 COVID-19 incubation period lnorm Natalie .... 2020
12 COVID-19 incubation period lnorm Stephen .... 2020
13 COVID-19 incubation period lnorm Stephen .... 2020
14 COVID-19 incubation period lnorm Stephen .... 2020
15 COVID-19 incubation period lnorm Stephen .... 2020

# list_distribution works when supplied a subset db

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2 COVID-19 incubation period <NA> Balram R.... 2022
3 COVID-19 incubation period <NA> Muluneh .... 2021
4 COVID-19 serial interval <NA> Muluneh .... 2021
5 COVID-19 incubation period <NA> Christel.... 2021
6 COVID-19 incubation period weibull Long V. .... 2020
7 COVID-19 incubation period lnorm Conor Mc.... 2020
8 COVID-19 incubation period lnorm Conor Mc.... 2020
9 COVID-19 incubation period lnorm Natalie .... 2020
10 COVID-19 incubation period lnorm Natalie .... 2020
11 COVID-19 onset to hospitalisation gamma Natalie .... 2020
12 COVID-19 onset to hospitalisation gamma Natalie .... 2020
13 COVID-19 onset to death lnorm Natalie .... 2020
14 COVID-19 hospitalisation to death weibull Natalie .... 2020
15 COVID-19 incubation period lnorm Natalie .... 2020
16 COVID-19 onset to hospitalisation lnorm Natalie .... 2020
17 COVID-19 onset to hospitalisation lnorm Natalie .... 2020
18 COVID-19 onset to death lnorm Natalie .... 2020
19 COVID-19 hospitalisation to death lnorm Natalie .... 2020
20 COVID-19 incubation period lnorm Stephen .... 2020
21 COVID-19 incubation period lnorm Stephen .... 2020
22 COVID-19 incubation period lnorm Stephen .... 2020
23 COVID-19 incubation period lnorm Stephen .... 2020
5 COVID-19 serial interval lnorm Hiroshi .... 2020
6 COVID-19 serial interval weibull Hiroshi .... 2020
7 COVID-19 incubation period weibull Lin Yang.... 2020
8 COVID-19 serial interval norm Lin Yang.... 2020
9 COVID-19 incubation period <NA> Christel.... 2021
10 COVID-19 incubation period weibull Long V. .... 2020
11 COVID-19 incubation period lnorm Conor Mc.... 2020
12 COVID-19 incubation period lnorm Conor Mc.... 2020
13 COVID-19 incubation period lnorm Natalie .... 2020
14 COVID-19 incubation period lnorm Natalie .... 2020
15 COVID-19 onset to hospitalisation gamma Natalie .... 2020
16 COVID-19 onset to hospitalisation gamma Natalie .... 2020
17 COVID-19 onset to death lnorm Natalie .... 2020
18 COVID-19 hospitalisation to death weibull Natalie .... 2020
19 COVID-19 incubation period lnorm Natalie .... 2020
20 COVID-19 onset to hospitalisation lnorm Natalie .... 2020
21 COVID-19 onset to hospitalisation lnorm Natalie .... 2020
22 COVID-19 onset to death lnorm Natalie .... 2020
23 COVID-19 hospitalisation to death lnorm Natalie .... 2020
24 COVID-19 incubation period lnorm Stephen .... 2020
25 COVID-19 incubation period lnorm Stephen .... 2020
26 COVID-19 incubation period lnorm Stephen .... 2020
27 COVID-19 incubation period lnorm Stephen .... 2020

# list_distributions works as expected supplied with <epidist>

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