Last updated on 2021-05-22 15:49:19 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.6.0 | 39.01 | 164.38 | 203.39 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.6.0 | 33.87 | 125.30 | 159.17 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.6.0 | 274.00 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.6.0 | 260.42 | ERROR | |||
| r-devel-windows-x86_64 | 1.6.0 | 50.00 | 201.00 | 251.00 | ERROR | |
| r-devel-windows-x86_64-gcc10-UCRT | 1.6.0 | ERROR | ||||
| r-patched-linux-x86_64 | 1.6.0 | 40.55 | 195.53 | 236.08 | ERROR | |
| r-patched-solaris-x86 | 1.6.0 | 426.40 | ERROR | |||
| r-release-linux-x86_64 | 1.6.0 | 37.17 | 194.32 | 231.49 | ERROR | |
| r-release-macos-x86_64 | 1.6.0 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 1.6.0 | 50.00 | 201.00 | 251.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.6.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.6.0 | 48.00 | 154.00 | 202.00 | ERROR |
Version: 1.6.0
Check: examples
Result: ERROR
Running examples in 'AMR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.rsi
> ### Title: Interpret MIC and Disk Values, or Clean Raw R/SI Data
> ### Aliases: as.rsi rsi is.rsi is.rsi.eligible as.rsi.mic as.rsi.disk
> ### as.rsi.data.frame
>
> ### ** Examples
>
> summary(example_isolates) # see all R/SI results at a glance
date hospital_id ward_icu ward_clinical
Min. :2002-01-02 A:321 Mode :logical Mode :logical
1st Qu.:2005-07-31 B:663 FALSE:1354 FALSE:536
Median :2009-07-31 C:254 TRUE :646 TRUE :1464
Mean :2009-11-20 D:762
3rd Qu.:2014-05-30
Max. :2017-12-28
ward_outpatient age gender patient_id
Mode :logical Min. :14.00 Length:2000 Length:2000
FALSE:1880 1st Qu.:63.00 Class :character Class :character
TRUE :120 Median :74.00 Mode :character Mode :character
Mean :71.06
3rd Qu.:82.00
Max. :97.00
mo PEN OXA
Class :mo Class:rsi Class:rsi
<NA> :0 %R :73.7% (n=1201) %R :31.2% (n=114)
Unique:90 %SI :26.3% (n=428) %SI :68.8% (n=251)
#1 :B_ESCHR_COLI - %S :25.6% (n=417) - %S :68.8% (n=251)
#2 :B_STPHY_CONS - %I : 0.7% (n=11) - %I : 0.0% (n=0)
#3 :B_STPHY_AURS
FLC AMX AMC
Class:rsi Class:rsi Class:rsi
%R :29.5% (n=278) %R :59.6% (n=804) %R :23.7% (n=446)
%SI :70.5% (n=665) %SI :40.4% (n=546) %SI :76.3% (n=1433)
- %S :70.5% (n=665) - %S :40.2% (n=543) - %S :71.4% (n=1342)
- %I : 0.0% (n=0) - %I : 0.2% (n=3) - %I : 4.8% (n=91)
AMP TZP CZO
Class:rsi Class:rsi Class:rsi
%R :59.6% (n=804) %R :12.6% (n=126) %R :44.6% (n=199)
%SI :40.4% (n=546) %SI :87.4% (n=875) %SI :55.4% (n=247)
- %S :40.2% (n=543) - %S :86.1% (n=862) - %S :54.9% (n=245)
- %I : 0.2% (n=3) - %I : 1.3% (n=13) - %I : 0.4% (n=2)
FEP CXM FOX
Class:rsi Class:rsi Class:rsi
%R :14.2% (n=103) %R :26.3% (n=470) %R :27.4% (n=224)
%SI :85.8% (n=621) %SI :73.7% (n=1319) %SI :72.6% (n=594)
- %S :85.6% (n=620) - %S :72.5% (n=1297) - %S :71.6% (n=586)
- %I : 0.1% (n=1) - %I : 1.2% (n=22) - %I : 1.0% (n=8)
CTX CAZ CRO
Class:rsi Class:rsi Class:rsi
%R :15.5% (n=146) %R :66.5% (n=1204) %R :15.5% (n=146)
%SI :84.5% (n=797) %SI :33.5% (n=607) %SI :84.5% (n=797)
- %S :84.4% (n=796) - %S :33.5% (n=607) - %S :84.4% (n=796)
- %I : 0.1% (n=1) - %I : 0.0% (n=0) - %I : 0.1% (n=1)
GEN TOB AMK
Class:rsi Class:rsi Class:rsi
%R :24.6% (n=456) %R :34.4% (n=465) %R :63.7% (n=441)
%SI :75.4% (n=1399) %SI :65.6% (n=886) %SI :36.3% (n=251)
- %S :74.0% (n=1372) - %S :65.1% (n=879) - %S :36.3% (n=251)
- %I : 1.5% (n=27) - %I : 0.5% (n=7) - %I : 0.0% (n=0)
KAN TMP SXT
Class:rsi Class:rsi Class:rsi
%R :100.0% (n=471) %R :38.1% (n=571) %R :20.5% (n=361)
%SI : 0.0% (n=0) %SI :61.9% (n=928) %SI :79.5% (n=1398)
- %S : 0.0% (n=0) - %S :61.2% (n=918) - %S :79.1% (n=1392)
- %I : 0.0% (n=0) - %I : 0.7% (n=10) - %I : 0.3% (n=6)
NIT FOS LNZ
Class:rsi Class:rsi Class:rsi
%R :17.1% (n=127) %R :42.2% (n=148) %R :69.3% (n=709)
%SI :82.9% (n=616) %SI :57.8% (n=203) %SI :30.7% (n=314)
- %S :76.0% (n=565) - %S :57.8% (n=203) - %S :30.7% (n=314)
- %I : 6.9% (n=51) - %I : 0.0% (n=0) - %I : 0.0% (n=0)
CIP MFX VAN
Class:rsi Class:rsi Class:rsi
%R :16.2% (n=228) %R :33.6% (n=71) %R :38.3% (n=712)
%SI :83.8% (n=1181) %SI :66.4% (n=140) %SI :61.7% (n=1149)
- %S :78.9% (n=1112) - %S :64.5% (n=136) - %S :61.7% (n=1149)
- %I : 4.9% (n=69) - %I : 1.9% (n=4) - %I : 0.0% (n=0)
TEC TCY TGC
Class:rsi Class:rsi Class:rsi
%R :75.7% (n=739) %R :29.8% (n=357) %R :12.7% (n=101)
%SI :24.3% (n=237) %SI :70.3% (n=843) %SI :87.3% (n=697)
- %S :24.3% (n=237) - %S :68.3% (n=820) - %S :87.3% (n=697)
- %I : 0.0% (n=0) - %I : 1.9% (n=23) - %I : 0.0% (n=0)
DOX ERY CLI
Class:rsi Class:rsi Class:rsi
%R :27.7% (n=315) %R :57.2% (n=1084) %R :61.2% (n=930)
%SI :72.3% (n=821) %SI :42.8% (n=810) %SI :38.8% (n=590)
- %S :71.7% (n=814) - %S :42.3% (n=801) - %S :38.6% (n=586)
- %I : 0.6% (n=7) - %I : 0.5% (n=9) - %I : 0.3% (n=4)
AZM IPM MEM
Class:rsi Class:rsi Class:rsi
%R :57.2% (n=1084) %R : 6.2% (n=55) %R : 5.9% (n=49)
%SI :42.8% (n=810) %SI :93.8% (n=834) %SI :94.1% (n=780)
- %S :42.3% (n=801) - %S :92.7% (n=824) - %S :94.1% (n=780)
- %I : 0.5% (n=9) - %I : 1.1% (n=10) - %I : 0.0% (n=0)
MTR CHL COL
Class:rsi Class:rsi Class:rsi
%R :14.7% (n=5) %R :21.4% (n=33) %R :81.2% (n=1331)
%SI :85.3% (n=29) %SI :78.6% (n=121) %SI :18.8% (n=309)
- %S :85.3% (n=29) - %S :78.6% (n=121) - %S :18.8% (n=309)
- %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0)
MUP RIF
Class:rsi Class:rsi
%R : 5.9% (n=16) %R :69.6% (n=698)
%SI :94.1% (n=254) %SI :30.4% (n=305)
- %S :93.0% (n=251) - %S :30.2% (n=303)
- %I : 1.1% (n=3) - %I : 0.2% (n=2)
>
> if (require("skimr")) {
+ # class <rsi> supported in skim() too:
+ skim(example_isolates)
+ }
Loading required package: skimr
Error: Problem with `summarise()` column `skimmed`.
i `skimmed = purrr::map2(...)`.
x Problem with `summarise()` input `..1`.
i `..1 = dplyr::across(variable_names, mangled_skimmers$funs)`.
x could not find function "pm_n_distinct"
Backtrace:
x
1. +-skimr::skim(example_isolates)
2. | +-dplyr::summarize(...)
3. | \-dplyr:::summarise.grouped_df(...)
4. | \-dplyr:::summarise_cols(.data, ..., caller_env = caller_env())
5. | +-base::withCallingHandlers(...)
6. | \-mask$eval_all_summarise(quo)
7. +-purrr::map2(...)
8. | +-skimr:::.f(.x[[1L]], .y[[1L]], ...)
9. | \-skimr:::skim_by_type.data.frame(.x[[1L]], .y[[1L]], ...)
10. | +-dplyr::summarize(data, dplyr::across(variable_names, mangled_skimmers$funs))
11. | \-dplyr:::summarise.data.frame(...)
12. | \-dplyr:::summarise_cols(.data, ..., caller_env = caller_env())
13. | +-base::withCallingHandlers(...)
14. | \-mask$eval_all_summarise(quo)
15. +-base::.handleSimpleError(...)
16. | \-dplyr:::h(simpleError(msg, call))
17. | \-rlang::abort(bullets, class = "dplyr_error")
18. | \-rlang:::signal_abort(cnd)
19. | \-base::signalCondition(cnd)
20. \-(function (e) ...
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.6.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'AMR.Rmd' using rmarkdown
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Joining, by = "patient_id"
Quitting from lines 161-162 (AMR.Rmd)
Error: processing vignette 'AMR.Rmd' failed with diagnostics:
invalid value 0 for 'digits' argument
--- failed re-building 'AMR.Rmd'
--- re-building 'MDR.Rmd' using rmarkdown
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 99-102 (MDR.Rmd)
Error: processing vignette 'MDR.Rmd' failed with diagnostics:
invalid value 0 for 'digits' argument
--- failed re-building 'MDR.Rmd'
--- re-building 'datasets.Rmd' using rmarkdown
--- finished re-building 'datasets.Rmd'
--- re-building 'welcome_to_AMR.Rmd' using rmarkdown
--- finished re-building 'welcome_to_AMR.Rmd'
SUMMARY: processing the following files failed:
'AMR.Rmd' 'MDR.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.6.0
Check: examples
Result: ERROR
Running examples in ‘AMR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.rsi
> ### Title: Interpret MIC and Disk Values, or Clean Raw R/SI Data
> ### Aliases: as.rsi rsi is.rsi is.rsi.eligible as.rsi.mic as.rsi.disk
> ### as.rsi.data.frame
>
> ### ** Examples
>
> summary(example_isolates) # see all R/SI results at a glance
date hospital_id ward_icu ward_clinical
Min. :2002-01-02 A:321 Mode :logical Mode :logical
1st Qu.:2005-07-31 B:663 FALSE:1354 FALSE:536
Median :2009-07-31 C:254 TRUE :646 TRUE :1464
Mean :2009-11-20 D:762
3rd Qu.:2014-05-30
Max. :2017-12-28
ward_outpatient age gender patient_id
Mode :logical Min. :14.00 Length:2000 Length:2000
FALSE:1880 1st Qu.:63.00 Class :character Class :character
TRUE :120 Median :74.00 Mode :character Mode :character
Mean :71.06
3rd Qu.:82.00
Max. :97.00
mo PEN OXA
Class :mo Class:rsi Class:rsi
<NA> :0 %R :73.7% (n=1201) %R :31.2% (n=114)
Unique:90 %SI :26.3% (n=428) %SI :68.8% (n=251)
#1 :B_ESCHR_COLI - %S :25.6% (n=417) - %S :68.8% (n=251)
#2 :B_STPHY_CONS - %I : 0.7% (n=11) - %I : 0.0% (n=0)
#3 :B_STPHY_AURS
FLC AMX AMC
Class:rsi Class:rsi Class:rsi
%R :29.5% (n=278) %R :59.6% (n=804) %R :23.7% (n=446)
%SI :70.5% (n=665) %SI :40.4% (n=546) %SI :76.3% (n=1433)
- %S :70.5% (n=665) - %S :40.2% (n=543) - %S :71.4% (n=1342)
- %I : 0.0% (n=0) - %I : 0.2% (n=3) - %I : 4.8% (n=91)
AMP TZP CZO
Class:rsi Class:rsi Class:rsi
%R :59.6% (n=804) %R :12.6% (n=126) %R :44.6% (n=199)
%SI :40.4% (n=546) %SI :87.4% (n=875) %SI :55.4% (n=247)
- %S :40.2% (n=543) - %S :86.1% (n=862) - %S :54.9% (n=245)
- %I : 0.2% (n=3) - %I : 1.3% (n=13) - %I : 0.4% (n=2)
FEP CXM FOX
Class:rsi Class:rsi Class:rsi
%R :14.2% (n=103) %R :26.3% (n=470) %R :27.4% (n=224)
%SI :85.8% (n=621) %SI :73.7% (n=1319) %SI :72.6% (n=594)
- %S :85.6% (n=620) - %S :72.5% (n=1297) - %S :71.6% (n=586)
- %I : 0.1% (n=1) - %I : 1.2% (n=22) - %I : 1.0% (n=8)
CTX CAZ CRO
Class:rsi Class:rsi Class:rsi
%R :15.5% (n=146) %R :66.5% (n=1204) %R :15.5% (n=146)
%SI :84.5% (n=797) %SI :33.5% (n=607) %SI :84.5% (n=797)
- %S :84.4% (n=796) - %S :33.5% (n=607) - %S :84.4% (n=796)
- %I : 0.1% (n=1) - %I : 0.0% (n=0) - %I : 0.1% (n=1)
GEN TOB AMK
Class:rsi Class:rsi Class:rsi
%R :24.6% (n=456) %R :34.4% (n=465) %R :63.7% (n=441)
%SI :75.4% (n=1399) %SI :65.6% (n=886) %SI :36.3% (n=251)
- %S :74.0% (n=1372) - %S :65.1% (n=879) - %S :36.3% (n=251)
- %I : 1.5% (n=27) - %I : 0.5% (n=7) - %I : 0.0% (n=0)
KAN TMP SXT
Class:rsi Class:rsi Class:rsi
%R :100.0% (n=471) %R :38.1% (n=571) %R :20.5% (n=361)
%SI : 0.0% (n=0) %SI :61.9% (n=928) %SI :79.5% (n=1398)
- %S : 0.0% (n=0) - %S :61.2% (n=918) - %S :79.1% (n=1392)
- %I : 0.0% (n=0) - %I : 0.7% (n=10) - %I : 0.3% (n=6)
NIT FOS LNZ
Class:rsi Class:rsi Class:rsi
%R :17.1% (n=127) %R :42.2% (n=148) %R :69.3% (n=709)
%SI :82.9% (n=616) %SI :57.8% (n=203) %SI :30.7% (n=314)
- %S :76.0% (n=565) - %S :57.8% (n=203) - %S :30.7% (n=314)
- %I : 6.9% (n=51) - %I : 0.0% (n=0) - %I : 0.0% (n=0)
CIP MFX VAN
Class:rsi Class:rsi Class:rsi
%R :16.2% (n=228) %R :33.6% (n=71) %R :38.3% (n=712)
%SI :83.8% (n=1181) %SI :66.4% (n=140) %SI :61.7% (n=1149)
- %S :78.9% (n=1112) - %S :64.5% (n=136) - %S :61.7% (n=1149)
- %I : 4.9% (n=69) - %I : 1.9% (n=4) - %I : 0.0% (n=0)
TEC TCY TGC
Class:rsi Class:rsi Class:rsi
%R :75.7% (n=739) %R :29.8% (n=357) %R :12.7% (n=101)
%SI :24.3% (n=237) %SI :70.3% (n=843) %SI :87.3% (n=697)
- %S :24.3% (n=237) - %S :68.3% (n=820) - %S :87.3% (n=697)
- %I : 0.0% (n=0) - %I : 1.9% (n=23) - %I : 0.0% (n=0)
DOX ERY CLI
Class:rsi Class:rsi Class:rsi
%R :27.7% (n=315) %R :57.2% (n=1084) %R :61.2% (n=930)
%SI :72.3% (n=821) %SI :42.8% (n=810) %SI :38.8% (n=590)
- %S :71.7% (n=814) - %S :42.3% (n=801) - %S :38.6% (n=586)
- %I : 0.6% (n=7) - %I : 0.5% (n=9) - %I : 0.3% (n=4)
AZM IPM MEM
Class:rsi Class:rsi Class:rsi
%R :57.2% (n=1084) %R : 6.2% (n=55) %R : 5.9% (n=49)
%SI :42.8% (n=810) %SI :93.8% (n=834) %SI :94.1% (n=780)
- %S :42.3% (n=801) - %S :92.7% (n=824) - %S :94.1% (n=780)
- %I : 0.5% (n=9) - %I : 1.1% (n=10) - %I : 0.0% (n=0)
MTR CHL COL
Class:rsi Class:rsi Class:rsi
%R :14.7% (n=5) %R :21.4% (n=33) %R :81.2% (n=1331)
%SI :85.3% (n=29) %SI :78.6% (n=121) %SI :18.8% (n=309)
- %S :85.3% (n=29) - %S :78.6% (n=121) - %S :18.8% (n=309)
- %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0)
MUP RIF
Class:rsi Class:rsi
%R : 5.9% (n=16) %R :69.6% (n=698)
%SI :94.1% (n=254) %SI :30.4% (n=305)
- %S :93.0% (n=251) - %S :30.2% (n=303)
- %I : 1.1% (n=3) - %I : 0.2% (n=2)
>
> if (require("skimr")) {
+ # class <rsi> supported in skim() too:
+ skim(example_isolates)
+ }
Loading required package: skimr
Error: Problem with `summarise()` column `skimmed`.
ℹ `skimmed = purrr::map2(...)`.
✖ Problem with `summarise()` input `..1`.
ℹ `..1 = dplyr::across(variable_names, mangled_skimmers$funs)`.
✖ could not find function "pm_n_distinct"
Backtrace:
█
1. ├─skimr::skim(example_isolates)
2. │ ├─dplyr::summarize(...)
3. │ └─dplyr:::summarise.grouped_df(...)
4. │ └─dplyr:::summarise_cols(.data, ..., caller_env = caller_env())
5. │ ├─base::withCallingHandlers(...)
6. │ └─mask$eval_all_summarise(quo)
7. ├─purrr::map2(...)
8. │ ├─skimr:::.f(.x[[1L]], .y[[1L]], ...)
9. │ └─skimr:::skim_by_type.data.frame(.x[[1L]], .y[[1L]], ...)
10. │ ├─dplyr::summarize(data, dplyr::across(variable_names, mangled_skimmers$funs))
11. │ └─dplyr:::summarise.data.frame(...)
12. │ └─dplyr:::summarise_cols(.data, ..., caller_env = caller_env())
13. │ ├─base::withCallingHandlers(...)
14. │ └─mask$eval_all_summarise(quo)
15. ├─base::.handleSimpleError(...)
16. │ └─dplyr:::h(simpleError(msg, call))
17. │ └─rlang::abort(bullets, class = "dplyr_error")
18. │ └─rlang:::signal_abort(cnd)
19. │ └─base::signalCondition(cnd)
20. └─(function (e) ...
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.6.0
Check: installed package size
Result: NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
R 4.2Mb
data 3.5Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.6.0
Check: examples
Result: ERROR
Running examples in ‘AMR-Ex.R’ failed
The error most likely occurred in:
> ### Name: as.rsi
> ### Title: Interpret MIC and Disk Values, or Clean Raw R/SI Data
> ### Aliases: as.rsi rsi is.rsi is.rsi.eligible as.rsi.mic as.rsi.disk
> ### as.rsi.data.frame
>
> ### ** Examples
>
> summary(example_isolates) # see all R/SI results at a glance
date hospital_id ward_icu ward_clinical
Min. :2002-01-02 A:321 Mode :logical Mode :logical
1st Qu.:2005-07-31 B:663 FALSE:1354 FALSE:536
Median :2009-07-31 C:254 TRUE :646 TRUE :1464
Mean :2009-11-20 D:762
3rd Qu.:2014-05-30
Max. :2017-12-28
ward_outpatient age gender patient_id
Mode :logical Min. :14.00 Length:2000 Length:2000
FALSE:1880 1st Qu.:63.00 Class :character Class :character
TRUE :120 Median :74.00 Mode :character Mode :character
Mean :71.06
3rd Qu.:82.00
Max. :97.00
mo PEN OXA
Class :mo Class:rsi Class:rsi
<NA> :0 %R :73.7% (n=1201) %R :31.2% (n=114)
Unique:90 %SI :26.3% (n=428) %SI :68.8% (n=251)
#1 :B_ESCHR_COLI - %S :25.6% (n=417) - %S :68.8% (n=251)
#2 :B_STPHY_CONS - %I : 0.7% (n=11) - %I : 0.0% (n=0)
#3 :B_STPHY_AURS
FLC AMX AMC
Class:rsi Class:rsi Class:rsi
%R :29.5% (n=278) %R :59.6% (n=804) %R :23.7% (n=446)
%SI :70.5% (n=665) %SI :40.4% (n=546) %SI :76.3% (n=1433)
- %S :70.5% (n=665) - %S :40.2% (n=543) - %S :71.4% (n=1342)
- %I : 0.0% (n=0) - %I : 0.2% (n=3) - %I : 4.8% (n=91)
AMP TZP CZO
Class:rsi Class:rsi Class:rsi
%R :59.6% (n=804) %R :12.6% (n=126) %R :44.6% (n=199)
%SI :40.4% (n=546) %SI :87.4% (n=875) %SI :55.4% (n=247)
- %S :40.2% (n=543) - %S :86.1% (n=862) - %S :54.9% (n=245)
- %I : 0.2% (n=3) - %I : 1.3% (n=13) - %I : 0.4% (n=2)
FEP CXM FOX
Class:rsi Class:rsi Class:rsi
%R :14.2% (n=103) %R :26.3% (n=470) %R :27.4% (n=224)
%SI :85.8% (n=621) %SI :73.7% (n=1319) %SI :72.6% (n=594)
- %S :85.6% (n=620) - %S :72.5% (n=1297) - %S :71.6% (n=586)
- %I : 0.1% (n=1) - %I : 1.2% (n=22) - %I : 1.0% (n=8)
CTX CAZ CRO
Class:rsi Class:rsi Class:rsi
%R :15.5% (n=146) %R :66.5% (n=1204) %R :15.5% (n=146)
%SI :84.5% (n=797) %SI :33.5% (n=607) %SI :84.5% (n=797)
- %S :84.4% (n=796) - %S :33.5% (n=607) - %S :84.4% (n=796)
- %I : 0.1% (n=1) - %I : 0.0% (n=0) - %I : 0.1% (n=1)
GEN TOB AMK
Class:rsi Class:rsi Class:rsi
%R :24.6% (n=456) %R :34.4% (n=465) %R :63.7% (n=441)
%SI :75.4% (n=1399) %SI :65.6% (n=886) %SI :36.3% (n=251)
- %S :74.0% (n=1372) - %S :65.1% (n=879) - %S :36.3% (n=251)
- %I : 1.5% (n=27) - %I : 0.5% (n=7) - %I : 0.0% (n=0)
KAN TMP SXT
Class:rsi Class:rsi Class:rsi
%R :100.0% (n=471) %R :38.1% (n=571) %R :20.5% (n=361)
%SI : 0.0% (n=0) %SI :61.9% (n=928) %SI :79.5% (n=1398)
- %S : 0.0% (n=0) - %S :61.2% (n=918) - %S :79.1% (n=1392)
- %I : 0.0% (n=0) - %I : 0.7% (n=10) - %I : 0.3% (n=6)
NIT FOS LNZ
Class:rsi Class:rsi Class:rsi
%R :17.1% (n=127) %R :42.2% (n=148) %R :69.3% (n=709)
%SI :82.9% (n=616) %SI :57.8% (n=203) %SI :30.7% (n=314)
- %S :76.0% (n=565) - %S :57.8% (n=203) - %S :30.7% (n=314)
- %I : 6.9% (n=51) - %I : 0.0% (n=0) - %I : 0.0% (n=0)
CIP MFX VAN
Class:rsi Class:rsi Class:rsi
%R :16.2% (n=228) %R :33.6% (n=71) %R :38.3% (n=712)
%SI :83.8% (n=1181) %SI :66.4% (n=140) %SI :61.7% (n=1149)
- %S :78.9% (n=1112) - %S :64.5% (n=136) - %S :61.7% (n=1149)
- %I : 4.9% (n=69) - %I : 1.9% (n=4) - %I : 0.0% (n=0)
TEC TCY TGC
Class:rsi Class:rsi Class:rsi
%R :75.7% (n=739) %R :29.8% (n=357) %R :12.7% (n=101)
%SI :24.3% (n=237) %SI :70.3% (n=843) %SI :87.3% (n=697)
- %S :24.3% (n=237) - %S :68.3% (n=820) - %S :87.3% (n=697)
- %I : 0.0% (n=0) - %I : 1.9% (n=23) - %I : 0.0% (n=0)
DOX ERY CLI
Class:rsi Class:rsi Class:rsi
%R :27.7% (n=315) %R :57.2% (n=1084) %R :61.2% (n=930)
%SI :72.3% (n=821) %SI :42.8% (n=810) %SI :38.8% (n=590)
- %S :71.7% (n=814) - %S :42.3% (n=801) - %S :38.6% (n=586)
- %I : 0.6% (n=7) - %I : 0.5% (n=9) - %I : 0.3% (n=4)
AZM IPM MEM
Class:rsi Class:rsi Class:rsi
%R :57.2% (n=1084) %R : 6.2% (n=55) %R : 5.9% (n=49)
%SI :42.8% (n=810) %SI :93.8% (n=834) %SI :94.1% (n=780)
- %S :42.3% (n=801) - %S :92.7% (n=824) - %S :94.1% (n=780)
- %I : 0.5% (n=9) - %I : 1.1% (n=10) - %I : 0.0% (n=0)
MTR CHL COL
Class:rsi Class:rsi Class:rsi
%R :14.7% (n=5) %R :21.4% (n=33) %R :81.2% (n=1331)
%SI :85.3% (n=29) %SI :78.6% (n=121) %SI :18.8% (n=309)
- %S :85.3% (n=29) - %S :78.6% (n=121) - %S :18.8% (n=309)
- %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0)
MUP RIF
Class:rsi Class:rsi
%R : 5.9% (n=16) %R :69.6% (n=698)
%SI :94.1% (n=254) %SI :30.4% (n=305)
- %S :93.0% (n=251) - %S :30.2% (n=303)
- %I : 1.1% (n=3) - %I : 0.2% (n=2)
>
> if (require("skimr")) {
+ # class <rsi> supported in skim() too:
+ skim(example_isolates)
+ }
Loading required package: skimr
Error: Problem with `summarise()` column `skimmed`.
ℹ `skimmed = purrr::map2(...)`.
✖ Problem with `summarise()` input `..1`.
ℹ `..1 = dplyr::across(variable_names, mangled_skimmers$funs)`.
✖ could not find function "pm_n_distinct"
Backtrace:
█
1. ├─skimr::skim(example_isolates)
2. │ ├─dplyr::summarize(...)
3. │ └─dplyr:::summarise.grouped_df(...)
4. │ └─dplyr:::summarise_cols(.data, ..., caller_env = caller_env())
5. │ ├─base::withCallingHandlers(...)
6. │ └─mask$eval_all_summarise(quo)
7. ├─purrr::map2(...)
8. │ ├─skimr:::.f(.x[[1L]], .y[[1L]], ...)
9. │ └─skimr:::skim_by_type.data.frame(.x[[1L]], .y[[1L]], ...)
10. │ ├─dplyr::summarize(data, dplyr::across(variable_names, mangled_skimmers$funs))
11. │ └─dplyr:::summarise.data.frame(...)
12. │ └─dplyr:::summarise_cols(.data, ..., caller_env = caller_env())
13. │ ├─base::withCallingHandlers(...)
14. │ └─mask$eval_all_summarise(quo)
15. ├─base::.handleSimpleError(...)
16. │ └─dplyr:::h(simpleError(msg, call))
17. │ └─rlang::abort(bullets, class = "dplyr_error")
18. │ └─rlang:::signal_abort(cnd)
19. │ └─base::signalCondition(cnd)
20. └─(function (e) ...
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86
Version: 1.6.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘AMR.Rmd’ using rmarkdown
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Joining, by = "patient_id"
Quitting from lines 161-162 (AMR.Rmd)
Error: processing vignette 'AMR.Rmd' failed with diagnostics:
invalid value 0 for 'digits' argument
--- failed re-building ‘AMR.Rmd’
--- re-building ‘MDR.Rmd’ using rmarkdown
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 99-102 (MDR.Rmd)
Error: processing vignette 'MDR.Rmd' failed with diagnostics:
invalid value 0 for 'digits' argument
--- failed re-building ‘MDR.Rmd’
--- re-building ‘datasets.Rmd’ using rmarkdown
--- finished re-building ‘datasets.Rmd’
--- re-building ‘welcome_to_AMR.Rmd’ using rmarkdown
--- finished re-building ‘welcome_to_AMR.Rmd’
SUMMARY: processing the following files failed:
‘AMR.Rmd’ ‘MDR.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.6.0
Check: examples
Result: ERROR
Running examples in 'AMR-Ex.R' failed
The error most likely occurred in:
> ### Name: as.rsi
> ### Title: Interpret MIC and Disk Values, or Clean Raw R/SI Data
> ### Aliases: as.rsi rsi is.rsi is.rsi.eligible as.rsi.mic as.rsi.disk
> ### as.rsi.data.frame
>
> ### ** Examples
>
> summary(example_isolates) # see all R/SI results at a glance
date hospital_id ward_icu ward_clinical
Min. :2002-01-02 A:321 Mode :logical Mode :logical
1st Qu.:2005-07-31 B:663 FALSE:1354 FALSE:536
Median :2009-07-31 C:254 TRUE :646 TRUE :1464
Mean :2009-11-20 D:762
3rd Qu.:2014-05-30
Max. :2017-12-28
ward_outpatient age gender patient_id
Mode :logical Min. :14.00 Length:2000 Length:2000
FALSE:1880 1st Qu.:63.00 Class :character Class :character
TRUE :120 Median :74.00 Mode :character Mode :character
Mean :71.06
3rd Qu.:82.00
Max. :97.00
mo PEN OXA
Class :mo Class:rsi Class:rsi
<NA> :0 %R :73.7% (n=1201) %R :31.2% (n=114)
Unique:90 %SI :26.3% (n=428) %SI :68.8% (n=251)
#1 :B_ESCHR_COLI - %S :25.6% (n=417) - %S :68.8% (n=251)
#2 :B_STPHY_CONS - %I : 0.7% (n=11) - %I : 0.0% (n=0)
#3 :B_STPHY_AURS
FLC AMX AMC
Class:rsi Class:rsi Class:rsi
%R :29.5% (n=278) %R :59.6% (n=804) %R :23.7% (n=446)
%SI :70.5% (n=665) %SI :40.4% (n=546) %SI :76.3% (n=1433)
- %S :70.5% (n=665) - %S :40.2% (n=543) - %S :71.4% (n=1342)
- %I : 0.0% (n=0) - %I : 0.2% (n=3) - %I : 4.8% (n=91)
AMP TZP CZO
Class:rsi Class:rsi Class:rsi
%R :59.6% (n=804) %R :12.6% (n=126) %R :44.6% (n=199)
%SI :40.4% (n=546) %SI :87.4% (n=875) %SI :55.4% (n=247)
- %S :40.2% (n=543) - %S :86.1% (n=862) - %S :54.9% (n=245)
- %I : 0.2% (n=3) - %I : 1.3% (n=13) - %I : 0.4% (n=2)
FEP CXM FOX
Class:rsi Class:rsi Class:rsi
%R :14.2% (n=103) %R :26.3% (n=470) %R :27.4% (n=224)
%SI :85.8% (n=621) %SI :73.7% (n=1319) %SI :72.6% (n=594)
- %S :85.6% (n=620) - %S :72.5% (n=1297) - %S :71.6% (n=586)
- %I : 0.1% (n=1) - %I : 1.2% (n=22) - %I : 1.0% (n=8)
CTX CAZ CRO
Class:rsi Class:rsi Class:rsi
%R :15.5% (n=146) %R :66.5% (n=1204) %R :15.5% (n=146)
%SI :84.5% (n=797) %SI :33.5% (n=607) %SI :84.5% (n=797)
- %S :84.4% (n=796) - %S :33.5% (n=607) - %S :84.4% (n=796)
- %I : 0.1% (n=1) - %I : 0.0% (n=0) - %I : 0.1% (n=1)
GEN TOB AMK
Class:rsi Class:rsi Class:rsi
%R :24.6% (n=456) %R :34.4% (n=465) %R :63.7% (n=441)
%SI :75.4% (n=1399) %SI :65.6% (n=886) %SI :36.3% (n=251)
- %S :74.0% (n=1372) - %S :65.1% (n=879) - %S :36.3% (n=251)
- %I : 1.5% (n=27) - %I : 0.5% (n=7) - %I : 0.0% (n=0)
KAN TMP SXT
Class:rsi Class:rsi Class:rsi
%R :100.0% (n=471) %R :38.1% (n=571) %R :20.5% (n=361)
%SI : 0.0% (n=0) %SI :61.9% (n=928) %SI :79.5% (n=1398)
- %S : 0.0% (n=0) - %S :61.2% (n=918) - %S :79.1% (n=1392)
- %I : 0.0% (n=0) - %I : 0.7% (n=10) - %I : 0.3% (n=6)
NIT FOS LNZ
Class:rsi Class:rsi Class:rsi
%R :17.1% (n=127) %R :42.2% (n=148) %R :69.3% (n=709)
%SI :82.9% (n=616) %SI :57.8% (n=203) %SI :30.7% (n=314)
- %S :76.0% (n=565) - %S :57.8% (n=203) - %S :30.7% (n=314)
- %I : 6.9% (n=51) - %I : 0.0% (n=0) - %I : 0.0% (n=0)
CIP MFX VAN
Class:rsi Class:rsi Class:rsi
%R :16.2% (n=228) %R :33.6% (n=71) %R :38.3% (n=712)
%SI :83.8% (n=1181) %SI :66.4% (n=140) %SI :61.7% (n=1149)
- %S :78.9% (n=1112) - %S :64.5% (n=136) - %S :61.7% (n=1149)
- %I : 4.9% (n=69) - %I : 1.9% (n=4) - %I : 0.0% (n=0)
TEC TCY TGC
Class:rsi Class:rsi Class:rsi
%R :75.7% (n=739) %R :29.8% (n=357) %R :12.7% (n=101)
%SI :24.3% (n=237) %SI :70.3% (n=843) %SI :87.3% (n=697)
- %S :24.3% (n=237) - %S :68.3% (n=820) - %S :87.3% (n=697)
- %I : 0.0% (n=0) - %I : 1.9% (n=23) - %I : 0.0% (n=0)
DOX ERY CLI
Class:rsi Class:rsi Class:rsi
%R :27.7% (n=315) %R :57.2% (n=1084) %R :61.2% (n=930)
%SI :72.3% (n=821) %SI :42.8% (n=810) %SI :38.8% (n=590)
- %S :71.7% (n=814) - %S :42.3% (n=801) - %S :38.6% (n=586)
- %I : 0.6% (n=7) - %I : 0.5% (n=9) - %I : 0.3% (n=4)
AZM IPM MEM
Class:rsi Class:rsi Class:rsi
%R :57.2% (n=1084) %R : 6.2% (n=55) %R : 5.9% (n=49)
%SI :42.8% (n=810) %SI :93.8% (n=834) %SI :94.1% (n=780)
- %S :42.3% (n=801) - %S :92.7% (n=824) - %S :94.1% (n=780)
- %I : 0.5% (n=9) - %I : 1.1% (n=10) - %I : 0.0% (n=0)
MTR CHL COL
Class:rsi Class:rsi Class:rsi
%R :14.7% (n=5) %R :21.4% (n=33) %R :81.2% (n=1331)
%SI :85.3% (n=29) %SI :78.6% (n=121) %SI :18.8% (n=309)
- %S :85.3% (n=29) - %S :78.6% (n=121) - %S :18.8% (n=309)
- %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0)
MUP RIF
Class:rsi Class:rsi
%R : 5.9% (n=16) %R :69.6% (n=698)
%SI :94.1% (n=254) %SI :30.4% (n=305)
- %S :93.0% (n=251) - %S :30.2% (n=303)
- %I : 1.1% (n=3) - %I : 0.2% (n=2)
>
> if (require("skimr")) {
+ # class <rsi> supported in skim() too:
+ skim(example_isolates)
+ }
Loading required package: skimr
Error: Problem with `summarise()` column `skimmed`.
i `skimmed = purrr::map2(...)`.
x Problem with `summarise()` input `..1`.
i `..1 = dplyr::across(variable_names, mangled_skimmers$funs)`.
x could not find function "pm_n_distinct"
Backtrace:
x
1. +-skimr::skim(example_isolates)
2. | +-dplyr::summarize(...)
3. | \-dplyr:::summarise.grouped_df(...)
4. | \-dplyr:::summarise_cols(.data, ..., caller_env = caller_env())
5. | +-base::withCallingHandlers(...)
6. | \-mask$eval_all_summarise(quo)
7. +-purrr::map2(...)
8. | +-skimr:::.f(.x[[1L]], .y[[1L]], ...)
9. | \-skimr:::skim_by_type.data.frame(.x[[1L]], .y[[1L]], ...)
10. | +-dplyr::summarize(data, dplyr::across(variable_names, mangled_skimmers$funs))
11. | \-dplyr:::summarise.data.frame(...)
12. | \-dplyr:::summarise_cols(.data, ..., caller_env = caller_env())
13. | +-base::withCallingHandlers(...)
14. | \-mask$eval_all_summarise(quo)
15. +-base::.handleSimpleError(...)
16. | \-dplyr:::h(simpleError(msg, call))
17. | \-rlang::abort(bullets, class = "dplyr_error")
18. | \-rlang:::signal_abort(cnd)
19. | \-base::signalCondition(cnd)
20. \-(function (e) ...
Execution halted
Flavors: r-devel-windows-x86_64, r-devel-windows-x86_64-gcc10-UCRT, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64