643c5ed807
(v0.7.1.9022) CI fix for codecov
2019-08-04 11:33:56 +02:00
d6ab3896a1
(v0.7.1.9021) CI fix for resistance_predict
2019-08-04 10:48:41 +02:00
4f3ef53c78
(v0.7.1.9020) CI fix 2
2019-08-03 21:51:08 +02:00
a6606d334c
(v0.7.1.9019) CI fix
2019-07-30 19:20:13 +02:00
2a62c3d62a
(v0.7.1.9018) deps
2019-07-30 13:12:40 +02:00
ec0ca20dee
(v0.7.1.9017) deps
2019-07-29 21:20:26 +02:00
b7e2d7b9b8
(v0.7.1.9016) deps
2019-07-29 17:34:57 +02:00
240f03a672
(v0.7.1.9015) Remove freq()
2019-07-29 13:33:48 +02:00
9ac5a34b36
(v0.7.1.9014) MO codes update
2019-07-16 16:14:11 +02:00
c652c6913f
(v0.7.1.9013) guess_mo_ab speed improvement
2019-07-11 13:39:18 +02:00
68230d0712
(v0.7.1.90012) mo_shortname fix
2019-07-10 21:36:51 +02:00
b452de2fe4
(v0.7.1.9010) eucast informative text in verbose mode
2019-07-09 13:36:03 +02:00
b15d59cf03
(v0.7.1.9009) note for WHOCC
2019-07-09 11:22:46 +02:00
d9e257f8db
(v0.7.1.9008) ab update
2019-07-04 19:08:18 +02:00
c57ad26c5b
(v0.7.1.9007) mdro update
2019-07-04 15:26:07 +02:00
4ff20af123
(v0.7.1.9006) new rsi calculations, atc class removal
2019-07-02 16:48:52 +02:00
156d550895
(v0.7.1.9005) new rsi calculations, atc class removal
2019-07-01 14:03:15 +02:00
65c6702b21
(v0.7.1.9004) atc class removal
2019-06-27 11:57:45 +02:00
6013fbefae
(v0.7.1.9003) website update
2019-06-23 21:35:17 +02:00
f2d7a19118
(v0.7.1.9002) website update
2019-06-23 17:44:36 +02:00
78ec32b990
v0.7.1
2019-06-23 17:41:31 +02:00
278244140c
(v0.7.0.9015) vignette fix
2019-06-22 21:33:13 +02:00
b94638d53e
(v0.7.0.9014) unit tests
2019-06-22 20:14:06 +02:00
c9156c004a
(v0.7.0.9013) mo_synonym fix
2019-06-22 14:49:12 +02:00
409397a337
(v0.7.0.9012) unit test
2019-06-18 19:28:26 +02:00
9c39c35f86
(v0.7.0.9010) mo_synonyms, plot/barplot fixes
2019-06-16 21:42:40 +02:00
980be2b22d
(v0.7.0.9009) global note
2019-06-13 16:40:35 +02:00
254745061c
(v0.7.0.9008) T. vaginalis, rsi_df
2019-06-13 14:28:46 +02:00
699e87ab4a
(v0.7.0.9007) renamed notes fix
2019-06-12 16:08:20 +02:00
44ab53128e
(v0.7.0.9006) ab algorithm fix for ATC codes
2019-06-11 15:31:32 +02:00
8f674e19bb
(v0.7.0.9005) ab algorithm update
2019-06-11 14:18:25 +02:00
f6c47c8c88
(v0.7.0.9004) pkgdown update
2019-06-09 08:57:54 +02:00
ec48f1d83b
(v0.7.0.9003) scale fix
2019-06-08 23:50:06 +02:00
f50d3a5ba1
(v0.7.0.9002) scale fix
2019-06-08 15:00:28 +02:00
f02679fb63
(v0.7.0.9001) new pathovars, small fixes
2019-06-07 22:47:37 +02:00
04c75e8e36
(v0.7.0.9000) new dev version
2019-06-03 20:52:24 +02:00
270aa0dd33
v0.7.0
2019-06-03 17:45:22 +02:00
bd73988f15
(v0.6.1.9053) prerelease fixes
2019-06-02 19:23:19 +02:00
8de0495008
(v0.6.1.9052) website update
2019-06-01 21:28:18 +02:00
5608b27c7c
(v0.6.1.9051) support staged install
2019-06-01 20:54:56 +02:00
2667fff8a7
(v0.6.1.9050) support staged install
2019-06-01 20:40:49 +02:00
a665612cb8
(v0.6.1.9049) data creation fix
2019-05-31 21:20:16 +02:00
4bac768557
(v0.6.1.9048) data creation fox
2019-05-31 21:01:14 +02:00
0a6580b4eb
(v0.6.1.9047) ggplot fix
2019-05-31 20:48:22 +02:00
4ed27c7e7a
(v0.6.1.9046) ggplot fix
2019-05-31 20:25:57 +02:00
f03f71eced
(v0.6.1.9045) age test fix
2019-05-31 14:40:15 +02:00
493ae2ba0c
(v0.6.1.9044) first_isolate fix for species
2019-05-31 14:25:11 +02:00
1f8ee3ec3e
(v0.6.1.9043) age doc fix
2019-05-30 08:51:38 +02:00
8b5e2b030b
added boxplot for (grouped) freq()
2019-05-29 19:56:17 +02:00
27380fa021
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
3688fcaabf
doc fix
2019-05-23 17:59:43 +02:00
bbf8b611e3
doc fix
2019-05-23 17:35:58 +02:00
60983a1640
added mdr_tb()
2019-05-23 16:58:59 +02:00
07d26cd485
faster determination of abx
2019-05-20 19:12:41 +02:00
6eb08a2ea3
new git flow to repository
2019-05-20 14:16:53 +02:00
4ca00e1868
speed improvement eucast_rules(), support more old MO codes
2019-05-20 12:00:18 +02:00
c3ae6b7699
freq fix
2019-05-17 09:09:18 +02:00
4c3cf85a65
ab_info, other bug fixes
2019-05-16 21:20:00 +02:00
38a4421450
CI tests
2019-05-13 10:10:16 +02:00
fcc77164e9
mdro fix
2019-05-11 23:30:10 +02:00
68cc7ef0d0
new antibiotics
2019-05-10 16:44:59 +02:00
73f1ee1159
freq/age fix
2019-04-11 00:54:48 +02:00
cffb7787d8
cfta streptococci
2019-04-09 10:34:40 +02:00
9e20ade0a7
ci update
2019-04-06 20:03:46 +02:00
c6bf982ba6
ci update
2019-04-06 16:50:59 +02:00
0ff299394a
an another go
2019-04-06 16:23:43 +02:00
501f5db020
prevent staged install
2019-04-06 11:09:06 +02:00
fbc9191b13
new EUCAST rules algorithm
2019-04-05 18:47:39 +02:00
248e508e9b
CI - test also on r-devel
2019-03-29 14:34:39 +01:00
b25f2d6213
v0.6.1
2019-03-28 21:33:28 +01:00
429814c29b
v0.6.0
2019-03-27 11:22:36 +01:00
29f444543d
added Becker 2019
2019-03-26 14:24:03 +01:00
c6a12266e7
DSMZ data
2019-03-18 14:29:41 +01:00
fdffc2791b
memory for as.mo()
2019-03-15 13:57:25 +01:00
504a042fba
uncertainty levels, new WHONET codes
2019-03-12 12:19:27 +01:00
b319b89750
WHONET fix
2019-03-09 08:21:00 +01:00
5c7a061a5d
filter_ab_class fix
2019-03-06 09:32:48 +01:00
74e0ae21fd
con WHONET, filter ab class
2019-03-05 22:47:42 +01:00
e835525cf6
unknown codes, rsi fix
2019-03-02 22:47:04 +01:00
c5efb272fd
mo_source improvement
2019-03-01 09:34:04 +01:00
2565b60024
rlang dependency, new fungi
2019-02-28 13:56:28 +01:00
54162522bd
age_groups fix
2019-02-27 11:36:12 +01:00
f9ded23023
as.mo improvement
2019-02-26 12:33:26 +01:00
0ec76cfa98
as.mo improvement
2019-02-25 10:42:57 +01:00
1a6314769b
as.mo improvement
2019-02-23 16:02:31 +01:00
41ad7a22c8
mo_rank mo_url, added Tremellales
2019-02-22 22:12:10 +01:00
68a9a35ed6
algorithm update
2019-02-21 18:55:52 +01:00
13120f465f
website update
2019-02-20 13:57:23 +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
9209787a53
SPSS tutorial
2019-02-14 15:18:17 +01:00
efb2af9e3a
benchmarks plots
2019-02-14 10:23:51 +01:00
ae44b185e6
fix freq length calculation
2019-02-13 17:14:59 +01:00
30ff770c93
freq update
2019-02-12 15:38:31 +01:00
76ed26d27e
resistance predict update
2019-02-11 10:27:10 +01:00
70105086c8
as.rsi warning, site update
2019-02-10 08:42:28 +01:00
c56b179857
as.rsi warning, site update
2019-02-09 22:16:24 +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
cd07d65734
freq and website update
2019-02-01 16:55:55 +01:00
0b3dc0231f
freq fix
2019-01-30 16:00:55 +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
f6336fdd89
quasiquotation for freq()
2019-01-28 11:20:32 +01:00
e76961a66b
less deps
2019-01-27 19:30:40 +01:00
b39055c018
deprecated fix
2019-01-27 00:33:58 +01:00
f836722269
atc_ functions
2019-01-26 23:22:56 +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
c6c3088e9f
select() fix for freq
2019-01-17 12:08:04 +01:00
046d195064
resistance predict
2019-01-15 12:45:24 +01:00
5aad26035c
edited g.test
2019-01-12 11:06:58 +01:00
641d866db2
guess_ab_col, benchmarks
2019-01-11 20:37:23 +01:00
193a2d2863
EUCAST update, as.mo bugfix for empty vlaues
2019-01-08 16:23:45 +01:00
bc15f660d6
guess_ab()
2019-01-06 20:23:49 +01:00
0205b6178d
guess_mo deprecation
2019-01-06 16:40:55 +01:00
f01d62ee5d
language
2019-01-05 21:51:48 +01:00
6b2d464f8c
big website update, licence txt update
2019-01-02 23:24:07 +01:00
2e4d703338
eucast rules fix, 1st isolate fix, website update
2018-12-31 01:48:53 +01:00
469b145d8c
bye bye packrat
2018-12-30 12:00:53 +01:00
92a32b62a7
new website, freq updates
2018-12-29 22:24:19 +01:00
92d2553dfe
gitlab pages
2018-12-23 21:26:21 +01:00
0b8084871d
dplyr 0.8.0 support, fixes #7
2018-12-22 22:39:34 +01:00
2018d5b477
age and age_groups
2018-12-15 22:40:07 +01:00
81af7be36e
note about portions
2018-12-14 07:23:25 +01:00
9478ab71be
freq - decimals
2018-12-10 10:13:40 +01:00
8e8a9cd190
AI improvements
2018-12-07 12:04:55 +01:00
60fe98bbbd
better as.mo handling
2018-12-06 14:36:39 +01:00
5cfa5bbfe3
v0.5.0
2018-11-30 16:16:04 +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
a8132922af
unit test read.4d, unselecting freq cols
2018-11-19 13:00:22 +01:00
4fcc2b409a
MDRO update
2018-11-16 20:50:50 +01:00
fab64e6728
read.4D improvements
2018-11-15 12:42:35 +01:00
6b0f4ffbd4
new kingdom
2018-11-09 13:11:54 +01:00
d07e9b904e
new function get_locale
2018-11-05 13:20:32 +01:00
5476fecc73
eucast update
2018-11-01 20:23:33 +01:00
9cd4ab928a
speed improvement as.mo, freq title
2018-10-31 12:10:49 +01:00
1bf8dc2983
as.mo speedup: assigned to namespace
2018-10-29 17:26:17 +01:00
87757748bd
switch to gitlab
2018-10-23 16:49:40 +02:00
299c5bea43
na freq, removed factors
2018-10-23 09:42:26 +02:00
c2a93b46db
breaks param, tidyr dep change, freq markdown
2018-10-22 12:32:59 +02:00
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
d5a41de711
parameter combine_IR
2018-10-16 09:59:31 +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
c7c57f4042
0.4.0, just published on CRAN
2018-10-01 19:36:42 +02:00
3119a221e5
authors from ITIS, diff for freq
2018-10-01 11:39:43 +02:00
768fe17324
removed clipboard functions as it violated CRAN policies
2018-09-28 16:05:18 +02:00
2b0080995e
speed improvement for as.mo, more old taxonomic names
2018-09-27 23:23:48 +02:00
9c566585b0
first inclusion of ITIS data
2018-09-24 23:33:29 +02:00
db14781593
add labels_rsi_count
2018-09-16 22:11:17 +02:00
26f5be0033
support for portuguese, language determination based on system
2018-09-08 16:06:47 +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
a100d07da6
removed ratio, better rsi_calc, update for freq
2018-08-24 11:08:20 +02:00
0c0e538ef4
dependencies
2018-08-23 22:05:17 +02:00
8ab93b6688
unit tests
2018-08-23 01:01:50 +02:00
da5379c881
quasiquotation, alpha for geom_rsi
2018-08-23 00:40:36 +02:00
3e87c8f409
count_* functions
2018-08-22 00:02:26 +02:00
6bab01948e
v0.3.0
2018-08-14 13:25:24 +02:00
e5193c7749
AppVeyor
2018-08-13 23:05:53 +02:00
dba06c3295
abname improvement, small fixes
2018-08-13 11:00:53 +02:00
e5d32cafe0
new unit tests for ggplot, small fixes
2018-08-12 17:44:06 +02:00
1ba7d883fe
new ggplot enhancement
2018-08-11 21:30:00 +02:00
53fa198e35
new portion functions
2018-08-10 15:01:05 +02:00
ae2433a020
rsi family for resistance analysis
2018-08-03 14:49:29 +02:00
bd9bcfef78
thesis advisors
2018-08-03 09:59:39 +02:00
6262315527
Becker classification
...
Lancefield classification
Added Lancefield groups to `microorganisms` data set
2018-08-02 13:15:45 +02:00
edd2dd09dc
rsi for freq
2018-08-01 22:37:28 +02:00
211e3bae14
remove reshape2 dependency
2018-07-30 01:18:40 +02:00
feab1cad6b
small fixes
2018-07-28 09:34:03 +02:00
498e88b5cf
improvement for forecasting resistance
2018-07-26 16:30:42 +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
9920ac8a5c
fix for keyab, more examples
2018-07-23 10:35:39 +02:00
ad662d7bab
new col names for key_antibiotics
2018-07-19 15:11:23 +02:00
5cb9c541f8
new algorithm key abs
2018-07-17 13:02:05 +02:00
a5a4354651
speed improvements
2018-07-17 10:32:26 +02:00
715a7630ca
support format.freq
2018-07-16 16:41:48 +02:00
6eaf33baf3
speed improvements
2018-07-15 22:56:41 +02:00
8240959f38
support older mac release
2018-07-13 19:40:50 +02:00
b6655f6454
Welcome C++!
2018-07-13 17:23:46 +02:00
a28289562a
remove print function, out of scope
2018-07-11 20:12:19 +02:00
e3e10c2e88
fix for macOS and older tidyr versions
2018-07-11 12:34:02 +02:00
eca406b18b
travis build fails for macos
2018-07-11 11:46:06 +02:00
f63414d519
new g.test, extra unit tests
2018-07-10 12:27:07 +02:00
fc30d3fb13
freq: support for table
2018-07-09 14:02:58 +02:00
14b990d769
kurtosis, skewness, start with ML
2018-07-08 22:14:55 +02:00
34ee0247ac
addins and small improvements to microorganisms dataset
2018-07-04 17:20:03 +02:00
2ca01e2d8d
remove rlang dependency
2018-07-01 22:23:34 +02:00
965fe8681b
rlang dep for Travis/macOS
2018-07-01 21:50:34 +02:00
3527894b49
new g.test() and edited freq()
2018-07-01 21:40:37 +02:00
6ee713cec1
move tbl_parse_guess
2018-06-29 08:56:03 +02:00
649a8025aa
add clipboard functions again
2018-06-27 15:54:56 +02:00
a9bd5472d0
top_freq
2018-06-20 14:47:37 +02:00
bdc860e29c
atc_groups
2018-06-19 10:05:38 +02:00
0a5898b17d
fix for printing tibbles, improve guess_bactid
2018-06-08 12:06:54 +02:00
efdf5a3dc5
prevent dplyr:row_number warning
2018-05-31 14:19:25 +02:00
5593aee19e
edit as.rsi algor.
2018-05-30 23:02:16 +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
c0fc82c794
Added function n_rsi
2018-05-02 14:56:25 +02:00
8fe70d5652
Fix Latex PDF error
2018-04-30 16:24:11 +02:00
970e3ed7f1
EUCAST rules for MDRO
2018-04-25 15:33:58 +02:00
82fec5cc51
Try to support older R versions
2018-04-19 14:10:57 +02:00
e7396b8f39
Try to support older R versions
2018-04-19 12:50:23 +02:00
a814d82b4b
try to support older R versions
2018-04-18 14:50:16 +02:00
2509e2413d
MDRO, freq tables, new print format for tibbles
2018-04-18 12:24:54 +02:00
972e923484
testthat for macOS
2018-04-02 16:21:03 +02:00
07bdd61241
update dependencies
2018-04-02 16:05:09 +02:00
c182a9673d
fix clipboard on linux
2018-04-02 11:11:21 +02:00
1b3cc41c08
fix tests
2018-03-27 17:58:46 +02:00
6f7730dcaa
add tests using testthat
2018-03-27 17:43:42 +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
0fec64a240
Add ORCID identifier
2018-03-19 10:28:35 +01:00
04fc3573ec
add barplots
2018-03-13 14:34:10 +01:00
be51a95448
rename columns
2018-02-26 10:53:54 +01:00
3f859210d5
new date for push test
2018-02-22 22:04:22 +01:00
d8da8daf9a
First CRAN submission edits
2018-02-22 20:48:48 +01:00
62304dc23f
first commit
2018-02-21 11:52:31 +01:00
