e2aa4f996b
(v0.7.1.9075) new microorganism codes
2019-09-18 15:46:09 +02:00
93be16484b
(v0.7.1.9063) septic_patients -> example_isolates
2019-08-27 16:45:42 +02:00
7108454ba5
(v0.7.1.9055) algorithm improvements
2019-08-13 16:15:08 +02:00
1d423cca89
(v0.7.1.9035) cephalosporins and unit tests
2019-08-11 19:07:26 +02:00
3f5828e74a
(v0.7.1.9034) mo.codes fix for Dracunculus spp.
2019-08-09 23:45:26 +02:00
6598c5615d
(v0.7.1.9033) 5000 new fungi
2019-08-09 23:22:10 +02:00
3a1f960f89
(v0.7.1.9024) eucast_rules() fix, new MOs
2019-08-06 14:39:22 +02:00
9ac5a34b36
(v0.7.1.9014) MO codes update
2019-07-16 16:14:11 +02:00
d9e257f8db
(v0.7.1.9008) ab update
2019-07-04 19:08:18 +02:00
65c6702b21
(v0.7.1.9004) atc class removal
2019-06-27 11:57:45 +02:00
c9156c004a
(v0.7.0.9013) mo_synonym fix
2019-06-22 14:49:12 +02:00
254745061c
(v0.7.0.9008) T. vaginalis, rsi_df
2019-06-13 14:28:46 +02:00
8f674e19bb
(v0.7.0.9005) ab algorithm update
2019-06-11 14:18:25 +02:00
0a6580b4eb
(v0.6.1.9047) ggplot fix
2019-05-31 20:48:22 +02:00
27380fa021
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
60983a1640
added mdr_tb()
2019-05-23 16:58:59 +02:00
4c3cf85a65
ab_info, other bug fixes
2019-05-16 21:20:00 +02:00
fcc77164e9
mdro fix
2019-05-11 23:30:10 +02:00
68cc7ef0d0
new antibiotics
2019-05-10 16:44:59 +02:00
fbc9191b13
new EUCAST rules algorithm
2019-04-05 18:47:39 +02:00
29f444543d
added Becker 2019
2019-03-26 14:24:03 +01:00
c6a12266e7
DSMZ data
2019-03-18 14:29:41 +01:00
504a042fba
uncertainty levels, new WHONET codes
2019-03-12 12:19:27 +01:00
e835525cf6
unknown codes, rsi fix
2019-03-02 22:47:04 +01:00
2565b60024
rlang dependency, new fungi
2019-02-28 13:56:28 +01:00
f9ded23023
as.mo improvement
2019-02-26 12:33:26 +01:00
41ad7a22c8
mo_rank mo_url, added Tremellales
2019-02-22 22:12:10 +01:00
fb1fc3686c
Catalogue of life
2019-02-20 00:04:48 +01:00
54f8258f8c
Catalogue of Life, replaces ITIS
2019-02-18 02:33:37 +01:00
efb2af9e3a
benchmarks plots
2019-02-14 10:23:51 +01:00
ed30312048
mo codes for WHONET
2019-02-08 16:06:54 +01:00
587e00b7be
is.rsi.eligible update
2019-02-04 12:24:07 +01:00
3efb54d016
freq update
2019-01-29 20:20:09 +01:00
6aae206320
WHONET/EARS-Net support
2019-01-29 00:06:50 +01:00
f4ff98b470
WHO update, antibiotics update
2019-01-25 13:18:41 +01:00
46dcc7e2e8
set_mo_source
2019-01-21 15:53:01 +01:00
31e977937d
fix for as.mo and freq
2018-11-30 12:05:59 +01:00
9ddf6dc530
support A. species for as.mo, cleanup
2018-11-24 20:25:09 +01:00
6b0f4ffbd4
new kingdom
2018-11-09 13:11:54 +01:00
9cd4ab928a
speed improvement as.mo, freq title
2018-10-31 12:10:49 +01:00
86b03577a7
fix for as.mo, added also_single_tested
2018-10-19 13:53:31 +02:00
693f64bdbf
new EUCAST rules: clinical breakpoints
2018-10-17 17:32:34 +02:00
5b5b95a47b
count_all and some fixes
2018-10-12 16:35:18 +02:00
95c9fdc552
CRAN fixes for release 0.4.0
...
https://cran.r-project.org/web/checks/check_results_AMR.html
2018-10-09 13:53:33 +02:00
ed17db0263
renamed year columns to ref
2018-10-01 14:44:40 +02:00
3119a221e5
authors from ITIS, diff for freq
2018-10-01 11:39:43 +02:00
92c9cc2608
diff for freq, fix for mo_shortname
2018-09-29 21:54:32 +02:00
a6aa9e95fb
completed old taxonomic names
2018-09-28 20:13:13 +02:00
2b0080995e
speed improvement for as.mo, more old taxonomic names
2018-09-27 23:23:48 +02:00
450992baea
new: 1680 old taxonomic names
2018-09-25 16:44:40 +02:00
9c566585b0
first inclusion of ITIS data
2018-09-24 23:33:29 +02:00
5d80cef338
added taxonomic data from ITIS
2018-09-17 20:53:32 +02:00
b792a2754e
added prevalence column and alterted as.mo algorith to use it, added ab_name as alias
2018-09-16 16:43:29 +02:00
b0ca49d68d
small improvement for is.rsi.eligible, more unit tests
2018-09-14 11:54:01 +02:00
b83e6a9380
algoritm improvement, removed all Catabacter except for C. hongkongensis
2018-09-10 11:40:54 +02:00
26f5be0033
support for portuguese, language determination based on system
2018-09-08 16:06:47 +02:00
c5073f2fd1
small fix for microorganisms data set
2018-09-06 16:50:03 +02:00
790bd1622d
added vanA to vanE positive Enterococci
2018-09-05 09:49:19 +02:00
b388e3fee7
Support for German and Spanish microorganism properties, cleanup
2018-09-04 11:33:30 +02:00
75fe4d401f
new MOs, cleanup
2018-09-01 21:19:46 +02:00
5965d3c794
replaced bactid by mo
2018-08-31 13:36:19 +02:00
029157b3be
163 new trade names, added ab_tradenames
2018-08-29 12:27:37 +02:00
972fc4f6c7
ab_* functions, mo_* functions, 180 new microorganisms, speed improvement for bactid
2018-08-28 13:51:13 +02:00
2acdb1981c
atc and bactid functions, readme update
2018-08-25 22:01:14 +02:00
227121af3d
add Dialister to microorganisms
2018-08-03 11:46:06 +02:00
6262315527
Becker classification
...
Lancefield classification
Added Lancefield groups to `microorganisms` data set
2018-08-02 13:15:45 +02:00
d9e204031d
update to septic_patients, speed improvements
2018-07-25 14:17:04 +02:00
8421638b60
new class bactid
2018-07-23 14:14:03 +02:00
c768ba0d9c
A. lwoffi to A. lwoffii
2018-07-04 17:34:23 +02:00
34ee0247ac
addins and small improvements to microorganisms dataset
2018-07-04 17:20:03 +02:00
0a5898b17d
fix for printing tibbles, improve guess_bactid
2018-06-08 12:06:54 +02:00
uscloud
dcc26dd942
Update freq function
2018-05-22 16:34:22 +02:00
f05e7178cb
added vignette of freq
2018-05-09 11:44:46 +02:00
970e3ed7f1
EUCAST rules for MDRO
2018-04-25 15:33:58 +02:00
3165c50d06
more MOs
2018-04-03 16:07:32 +02:00
53464ff1c8
- For functions first_isolate, EUCAST_rules the antibiotic column names are case-insensitive
...
- Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore)
- Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
- Renamed dataset `bactlist` to `microorganisms`
2018-03-23 14:46:02 +01:00
502a44eb25
- Added new function guess_bactid to determine the ID of a microorganism based on genus/species
...
- Renamed `ablist` to `antibiotics`
- Added support for character vector in join functions
- Altered `%like%` to make it case insensitive
2018-03-19 12:43:22 +01:00
34e70a65ed
added septic_patients
2018-02-27 20:01:02 +01:00
98b2b99913
new atc codes
2018-02-26 16:06:49 +01:00
8a603876d2
misc
2018-02-26 15:53:09 +01:00
62304dc23f
first commit
2018-02-21 11:52:31 +01:00
