18b75356a9
re-add atc_ddd and atc_groups
2019-01-27 13:33:43 +01:00
6ec940bc75
atc_ functions
2019-01-27 10:53:59 +01:00
b39055c018
deprecated fix
2019-01-27 00:33:58 +01:00
f836722269
atc_ functions
2019-01-26 23:22:56 +01:00
5493e1f05d
website update
2019-01-25 20:47:57 +01:00
f4ff98b470
WHO update, antibiotics update
2019-01-25 13:18:41 +01:00
9529d097b6
as.mo
2019-01-21 21:24:40 +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
1ee710c861
resistance predict
2019-01-15 16:51:49 +01:00
8db87a15e9
fixes
2019-01-15 16:38:54 +01:00
046d195064
resistance predict
2019-01-15 12:45:24 +01:00
cda7087722
website update
2019-01-12 19:31:30 +01:00
3661df7365
direct warning if failing as.mo
2019-01-12 16:45:20 +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
2c798547bf
language
2019-01-05 21:40:04 +01:00
6652f7d82b
fix warnings
2019-01-04 09:49:42 +01:00
80ea555663
guess_ab
2019-01-03 23:56:19 +01:00
6b2d464f8c
big website update, licence txt update
2019-01-02 23:24:07 +01:00
68baf058cd
website update
2018-12-31 10:35:26 +01:00
2e4d703338
eucast rules fix, 1st isolate fix, website update
2018-12-31 01:48:53 +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
b937662a97
limits for scale_y_percent - Licence update
2018-12-16 22:45:12 +01:00
bd5f46d734
age_groups fix
2018-12-16 09:50:14 +01:00
2018d5b477
age and age_groups
2018-12-15 22:40:07 +01:00
ecebc60bfd
C stack error fix
2018-12-14 11:44:15 +01:00
857f565db0
reorganised notes and warnings
2018-12-14 10:52:20 +01:00
dec4947103
freq header fix for NAs
2018-12-14 10:08:51 +01:00
e4737d3add
date transformation fix for tibbles
2018-12-14 09:31:53 +01:00
7e5fe75a17
small text fixes
2018-12-14 07:48:12 +01:00
81af7be36e
note about portions
2018-12-14 07:23:25 +01:00
01a6d56334
add kingdom to mo_taxonomy
2018-12-10 21:47:25 +01:00
5ab7eb07bc
keyab automatic
2018-12-10 15:14:29 +01:00
9478ab71be
freq - decimals
2018-12-10 10:13:40 +01:00
8e8a9cd190
AI improvements
2018-12-07 12:04:55 +01:00
74a7f4453b
small CI fix
2018-12-06 16:07:06 +01:00
60fe98bbbd
better as.mo handling
2018-12-06 14:36:39 +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
63ba4b2980
small error in freq
2018-11-19 13:06:07 +01:00
a8132922af
unit test read.4d, unselecting freq cols
2018-11-19 13:00:22 +01:00
83c7da85ab
unit tests
2018-11-16 22:28:55 +01:00
d22b7f00da
unit tests
2018-11-16 22:22:42 +01:00
373e0cb32f
unit test fail
2018-11-16 21:57:55 +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
5cb8f3cf72
get_locale improvement
2018-11-12 15:07:43 +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
ee664f2a4c
small fix
2018-11-05 15:36:07 +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
d0bc05e5b1
speed improvement is.rsi.eligible
2018-11-02 14:55:29 +01:00
40a159e78d
more unit tests
2018-11-02 10:27:57 +01:00
e601fd259a
test syntax fix
2018-11-01 20:50:10 +01:00
5476fecc73
eucast update
2018-11-01 20:23:33 +01:00
f7687557c9
eucast updates
2018-11-01 17:06:08 +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
707aa20a37
fixes
2018-10-23 14:59:36 +02:00
7997de6a6d
mdro and 1st isolate improvements
2018-10-23 11:15:05 +02:00
299c5bea43
na freq, removed factors
2018-10-23 09:42:26 +02:00
9c56257da1
freq - print title bold in markdown
2018-10-22 13:06:54 +02:00
c2a93b46db
breaks param, tidyr dep change, freq markdown
2018-10-22 12:32:59 +02:00
ec15b82fd6
param header for freq
2018-10-19 21:52:08 +02:00
86b03577a7
fix for as.mo, added also_single_tested
2018-10-19 13:53:31 +02:00
032c0d51ef
better verbose in EUCAST
2018-10-19 00:57:10 +02:00
b464dd524a
new verbose
2018-10-19 00:17:03 +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
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
e7d937d36e
update NEWS
2018-10-10 10:50:19 +02:00
67521394f6
more unit tests
2018-10-09 15:41:44 +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
6d761436f7
benchmarks on readme and speed improvement for direct mo codes
2018-10-01 16:26:02 +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
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
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
7680e4edd8
add shortest and longest to freq for characters
2018-09-17 09:42:09 +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
b0ca49d68d
small improvement for is.rsi.eligible, more unit tests
2018-09-14 11:54:01 +02:00
cf5711fb0b
algorithm improvement
2018-09-14 10:31:21 +02:00
d049ec9e69
ggplot2_rsi fix
2018-09-13 14:48:34 +02:00
cb0d74a4f0
support for French and Italian, added quote to freq
2018-09-10 15:45:25 +02:00
b83e6a9380
algoritm improvement, removed all Catabacter except for C. hongkongensis
2018-09-10 11:40:54 +02:00
4816419f0c
AI improvements for microorganisms
2018-09-09 12:11:44 +02:00
936198372e
translate CoNS
2018-09-08 16:24:12 +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
de36b0be23
fix for empty values in mo_property
2018-09-05 12:21:27 +02:00
e39a9a8b05
added mo_shortname
2018-09-05 10:51:46 +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
e25dd0e282
fix for joins
2018-09-03 10:04:49 +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
98ff131680
support for older versions of ggplot2
2018-08-29 16:39:28 +02:00
d654444c8e
re added nrow
2018-08-29 16:35:32 +02:00
d9e68e0a50
ggplot_rsi example update, more unit tests
2018-08-29 16:25:57 +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
baaf4cc3e1
few extra tests
2018-08-24 14:18:38 +02:00
a100d07da6
removed ratio, better rsi_calc, update for freq
2018-08-24 11:08:20 +02:00
febd0ca885
geom_rsi - any parameter
2018-08-23 21:27:15 +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
59ce1eb1b1
ggplot_rsi improvements
2018-08-13 16:42:37 +02:00
dba06c3295
abname improvement, small fixes
2018-08-13 11:00:53 +02:00
ce2cdb9309
support groups for portion_df, update README
2018-08-12 22:34:03 +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
227121af3d
add Dialister to microorganisms
2018-08-03 11:46:06 +02:00
db5a0d32a5
typos of Becker algorithm
2018-08-03 10:58:48 +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
d8f70a74de
clipboard error
2018-08-01 10:32:24 +02:00
a59d0661f7
check CMD error
2018-08-01 09:45:11 +02:00
7c667eb732
emph guess_bactid
2018-08-01 08:03:31 +02:00
211e3bae14
remove reshape2 dependency
2018-07-30 01:18:40 +02:00
510e8f22aa
more unit tests
2018-07-30 00:57:49 +02:00
d0a115d995
bactid speed improvement
2018-07-30 00:14:06 +02:00
826694323b
new functions R, RI, SI, S
2018-07-29 22:14:51 +02:00
8421e3f005
more mic classes
2018-07-28 10:48:27 +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
03a3cb397b
clipboard update
2018-07-23 15:09:19 +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
0d64c166f0
keyab fixes
2018-07-17 19:51:09 +02:00
2a4d759fbc
check fails
2018-07-17 14:48:11 +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
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
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
2ca01e2d8d
remove rlang dependency
2018-07-01 22:23:34 +02:00
3527894b49
new g.test() and edited freq()
2018-07-01 21:40:37 +02:00
f7af8a81da
update man page
2018-06-29 09:06:47 +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
4a027f3c34
extra unit tests, add row.names to freq
2018-06-19 15:20:14 +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
MS Berends
7a6d5fb6b7
rsi/mic fix
2018-05-31 09:02:49 +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
MS Berends
0d80647d41
fix SI and IR
2018-05-16 11:19:45 +02:00
f05e7178cb
added vignette of freq
2018-05-09 11:44:46 +02:00
25b3346d9a
edit methodology of rsi
2018-05-03 10:19:02 +02:00
c0fc82c794
Added function n_rsi
2018-05-02 14:56:25 +02:00
6eaf594cb7
update data info
2018-05-01 09:57:50 +02:00
19ccc51f40
remove clipboard functions
2018-05-01 09:36:45 +02:00
6fa93fc286
fix clipboard check
2018-04-30 16:54:37 +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
0b22ddef8e
more unit tests
2018-04-20 13:45:34 +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
d79132b29f
Try to support older R versions
2018-04-18 15:41:27 +02:00
4b5530ed64
Try to support older R versions
2018-04-18 15:19:00 +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
3165c50d06
more MOs
2018-04-03 16:07:32 +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
MS Berends
b7f29aa748
Update first_isolates.R
2018-03-29 15:15:31 +02:00
MS Berends
f1dbed6fcc
Update clipboard.R
2018-03-29 14:56:40 +02:00
MS Berends
136272cb71
Update clipboard.R
2018-03-29 14:16:42 +02:00
MS Berends
fd04df5f9d
Update clipboard.R
2018-03-29 13:23:02 +02:00
MS Berends
2f4823f7a7
Update clipboard.R
2018-03-29 13:10:55 +02:00
6f7730dcaa
add tests using testthat
2018-03-27 17:43:42 +02:00
MS Berends
9637b43357
Remove Windows only function
2018-03-23 14:59:02 +01:00
MS Berends
1b3daebc84
Remove Windows only function
2018-03-23 14:52:56 +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
fe803f7279
use guess_bactid for GLIMS codes
2018-03-19 21:23:21 +01:00
c765f424ab
typo
2018-03-19 21:03:23 +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
6c67c8f6c1
examples edit
2018-03-14 09:58:58 +01:00
46db3f7b13
import from graphics
2018-03-13 15:40:10 +01:00
53959d40c7
typo in examples
2018-03-13 14:40:52 +01:00
04fc3573ec
add barplots
2018-03-13 14:34:10 +01:00
e4b371d30a
add MIC values
...
add badges to readme
2018-03-13 11:57:30 +01:00
4ea0333349
Minor text changes for DDD definition
2018-03-13 11:48:30 +01:00
34e70a65ed
added septic_patients
2018-02-27 20:01:02 +01:00
8a603876d2
misc
2018-02-26 15:53:09 +01:00
915d4db23b
add rows to summary
2018-02-26 14:37:40 +01:00
6fa05fe33b
first isolates
2018-02-26 14:06:31 +01:00
d36a391747
export first_isolate
2018-02-26 12:15:52 +01:00
be51a95448
rename columns
2018-02-26 10:53:54 +01:00
11683b082e
EUCAST man pages
2018-02-22 21:42:01 +01:00
10380bcfae
add NEWS
2018-02-22 21:37:10 +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
