5eda991c47
ab_info fix
2019-05-16 22:07:31 +02:00
0dc0715dc6
CI tests
2019-05-13 12:21:57 +02:00
68cc7ef0d0
new antibiotics
2019-05-10 16:44:59 +02:00
cffb7787d8
cfta streptococci
2019-04-09 10:34:40 +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
fdffc2791b
memory for as.mo()
2019-03-15 13:57:25 +01:00
74e0ae21fd
con WHONET, filter ab class
2019-03-05 22:47:42 +01:00
2565b60024
rlang dependency, new fungi
2019-02-28 13:56:28 +01:00
642f6571fe
as.mo fix
2019-02-27 14:22:07 +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
76ed26d27e
resistance predict update
2019-02-11 10:27:10 +01:00
1a1e81c5d2
as.rsi warning, site update
2019-02-10 09:13:06 +01:00
cbad93d92b
wget dependency
2019-02-10 08:49:57 +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
f6336fdd89
quasiquotation for freq()
2019-01-28 11:20:32 +01:00
63e343d555
deps fix
2019-01-27 20:49:11 +01:00
18b75356a9
re-add atc_ddd and atc_groups
2019-01-27 13:33:43 +01:00
f836722269
atc_ functions
2019-01-26 23:22:56 +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
8db87a15e9
fixes
2019-01-15 16:38:54 +01:00
046d195064
resistance predict
2019-01-15 12:45:24 +01:00
641d866db2
guess_ab_col, benchmarks
2019-01-11 20:37:23 +01:00
80ea555663
guess_ab
2019-01-03 23:56:19 +01:00
92a32b62a7
new website, freq updates
2018-12-29 22:24:19 +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
8e8a9cd190
AI improvements
2018-12-07 12:04:55 +01:00
60fe98bbbd
better as.mo handling
2018-12-06 14:36:39 +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
9be5e0318b
freq: fix na.rm in groups
2018-11-08 16:10:03 +01:00
84e08f516a
grouping var for freq
2018-11-06 16:41:59 +01:00
d15bb2ab3f
read_4D
2018-11-05 15:30:49 +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
86b03577a7
fix for as.mo, added also_single_tested
2018-10-19 13:53:31 +02:00
0ef91be3ac
param rules for EUCAST
2018-10-18 12:10:10 +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
768fe17324
removed clipboard functions as it violated CRAN policies
2018-09-28 16:05:18 +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
db14781593
add labels_rsi_count
2018-09-16 22:11:17 +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
e39a9a8b05
added mo_shortname
2018-09-05 10:51:46 +02:00
b388e3fee7
Support for German and Spanish microorganism properties, cleanup
2018-09-04 11:33:30 +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
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
ce2cdb9309
support groups for portion_df, update README
2018-08-12 22:34:03 +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
826694323b
new functions R, RI, SI, S
2018-07-29 22:14:51 +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
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
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
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
10fce8382c
include IQR and MAD in freq
2018-07-03 11:30:40 +02:00
3d0d21f322
rename vector2ratio to ratio
2018-07-02 11:14:20 +02:00
2c8d4cb8bf
forgot namespace...
2018-07-01 22:37:47 +02:00
3527894b49
new g.test() and edited freq()
2018-07-01 21:40:37 +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
uscloud
dcc26dd942
Update freq function
2018-05-22 16:34:22 +02:00
c0fc82c794
Added function n_rsi
2018-05-02 14:56:25 +02:00
19ccc51f40
remove clipboard functions
2018-05-01 09:36:45 +02:00
970e3ed7f1
EUCAST rules for MDRO
2018-04-25 15:33:58 +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
MS Berends
39eb307968
Remove Windows only function
2018-03-23 14:58:46 +01:00
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
dd2517ecb7
- Added new algorithm to determine weighted isolates, can now be points or keyantibiotics, see ?first_isolate`
...
- Function `first_isolate` supports tidyverse-like evaluation of parameters (no need to quote them anymore)
- Functions `as.rsi` and `as.mic` now add the package name and version as attribute
2018-03-19 20:39:23 +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
46db3f7b13
import from graphics
2018-03-13 15:40:10 +01:00
04fc3573ec
add barplots
2018-03-13 14:34:10 +01:00
d36a391747
export first_isolate
2018-02-26 12:15:52 +01:00
d8da8daf9a
First CRAN submission edits
2018-02-22 20:48:48 +01:00
ab0503f8b8
abname, logo
2018-02-21 12:10:00 +01:00
62304dc23f
first commit
2018-02-21 11:52:31 +01:00
