From b67613ce0826cfcccbab12f4e4ae4189b7d8b6e6 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Fri, 7 Mar 2025 22:27:21 +0100 Subject: [PATCH] (v2.1.1.9187) WISCA fix --- DESCRIPTION | 2 +- NEWS.md | 2 +- PythonPackage/AMR/AMR.egg-info/PKG-INFO | 2 +- PythonPackage/AMR/dist/amr-2.1.1.9186.tar.gz | Bin 10092 -> 0 bytes ...ny.whl => amr-2.1.1.9187-py3-none-any.whl} | Bin 10282 -> 10282 bytes PythonPackage/AMR/dist/amr-2.1.1.9187.tar.gz | Bin 0 -> 10098 bytes PythonPackage/AMR/setup.py | 2 +- R/antibiogram.R | 6 ++---- R/data.R | 1 - R/temp_file | 1 - R/zz_deprecated.R | 1 + R/zzz.R | 4 +++- ....txt => gpt_training_text_v2.1.1.9187.txt} | 5 +---- man/AMR-deprecated.Rd | 2 -- man/antimicrobials.Rd | 1 - 15 files changed, 11 insertions(+), 18 deletions(-) delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9186.tar.gz rename PythonPackage/AMR/dist/{amr-2.1.1.9186-py3-none-any.whl => amr-2.1.1.9187-py3-none-any.whl} (86%) create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9187.tar.gz delete mode 100644 R/temp_file rename data-raw/{gpt_training_text_v2.1.1.9186.txt => gpt_training_text_v2.1.1.9187.txt} (99%) diff --git a/DESCRIPTION b/DESCRIPTION index ac7a6527b..5c98dfcad 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9186 +Version: 2.1.1.9187 Date: 2025-03-07 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 22993b25c..46a72496a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9186 +# AMR 2.1.1.9187 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)* diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index fe244a9f4..6ffb36834 100644 --- a/PythonPackage/AMR/AMR.egg-info/PKG-INFO +++ b/PythonPackage/AMR/AMR.egg-info/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 2.2 Name: AMR -Version: 2.1.1.9186 +Version: 2.1.1.9187 Summary: A Python wrapper for the AMR R package Home-page: https://github.com/msberends/AMR Author: Matthijs Berends diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9186.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9186.tar.gz deleted file mode 100644 index 5ddbf31b9159ba6a4addce58b3246124affda572..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 10092 zcmch7RZtv2*Cj5&J-Azd;O-CtBxp!*cXtamxVyUrOK_K%;x** zuiAaux83Tx)u&ILs_v(I`<`z41T3s?YEyP72n!ca9)Y*~|Asifn8;gi3s0o;;6Sgv zj+P@>z2?x~8P7+Zj=E0g<)_7>Y397Z!=09lLN7r{pd1Se5=5I+*(X#oEKa8y>N&tz!1l1W6-s?rh8qd`WU=p9;M~dc`J^4-o zMB%+AJ9|kzLUU{nddUJ`qfU$u?gt?-_vZKGL_((FZkU39b;fW%9EUo~AZ}I%jBuW1 zS33}>HVAqkyyT(qGy(d{BOXr5yIyMAV8J1f`GS)QaaxuuA4*y%J1n~5rE1Ez{SrFu&}BM z3Ka%btMoE~aDcM&T)6~}aYCe!{W)7}-pmLo8Ho0(obi5&t1WNuZC(2g#&m_JKuS2aIk`RxXNZdN_$rdotG@+A zsG$>vPVW^hk;$4NjL6x;tTo5PXdKPl7}s`aVrA*?t2fj2U6Ev2>d3#}g%Dn-in~us zbH>2?GrzfavmbO7db%n#T*4*8t2&IUjVZf&{1~Xdh?V!C*Q^)UTzXrPk>v zJcr$ZOU@+6RoR)pe7c@gNpZN#E@zobG9!{7t=M8eGSx|UL9$i$vi;BqM(i6eS(HAD z=Fc6X^%PYkGTh0xtUsvKC^Yen=CL?*pP*bR# zJ4l8~H-USo&PROW+Cmyh?Ugq7q`~euZ)3h{Ggq>5sO(AI(?8N_7?IjYogxa-$hFtjNsBm zYb3nb=qEZgDJIh|SCAwZX>=lxI z$hWsnMS4eNaNrn3Kt*yGcR)wpH!Ry@HJyte@_A5C^~2H6=@=9s@dxoV^au5=1Ycx~ zZ|itS1%E+CMFCpz2BxFGTFni2vY!3J6@ClgyzZdOQoEb>8jJ+nMe3nzjgirFAX-5bm4?2UIAXfi+t3d zQor?2Kk=Kr?>g7r&s7gC`38Q^*YZ8`nQP@8rGZ9tFt+-#rq`WcC*_EF;ovS;6D#~# zL}AY;?IdFvB6j^@Uv99ittiu8U!||b{;ER9tiZqtJM6SzF-OCnb(4NSaH^f`4{W9CaFn`Fu(N`C%+(pSB>0oc(mH{Gl9S(s8+} zglvlOd^XcnZ&zy`DJy}d@j>neir?wN&C1pmi?zRZS>FbFmrfl) zRyf}rLed?yx++AnW;_RZOLfo2ZodDpMlSy~S$!Myy@W__f7*g&WIps6$n|Mbx&a~E)ZmVsnmw4{y0s~s$Gopfh9KYw@2c(DkjnSDQzvYyC)0SgYAmmz z&Y0@U%%gY)Am_?t#C3`gd1xaA@f1o~=U-pUP)@*2mdfMfWP=d2$uKWi{#qT)1I@&AUBXwwi^p1RXIOQ`%`D zI2-{Eed95UIjcaT5XZ?eF%EO8W~Fz))Kej&@h)A-(I9-xq-fF>>Wjd(28Am)d!lB@ z$lBXg(gXkW1bSUZ(9h#D1@VA;O8p!eSa@FLk+nhR65dsuE5d?T9ImH>Bs4>D;d09d zwO{0)v!VD}w2-fOmwJnkp`n#fDtjE9UX3Y3C$HtBUKTf^1-6H^+u@4>XqoGv!jG3Z ztMhG0;x}1*e98QWBwr=zgx6XqAeviXiMU|;UrTrBG%L7(1PdSnTvq3lsKM@BY`HO% zJMuyT>b4DH2+_T*IiPa?)-fBismy)&m`){1RdCxf$l|B~kT+@nY__BE(-ApsFZ!#r zEB!B$7-fCI*;?NCEZVgh3HA#djBen~|}&?enrXj%@JAfRoV>db36J&7#UL z=hXc~f|I5qvTAu9gnuIMyz zU65;s{?#72=}e%-1twO7uYXFVmrf=6p)5~PB;CI2<$#gRm49v10!u1N%XYtBPvXvi zWMe&+9j#v8rQr3}{~}oy+ILo_ixsy6c8_b5pM17S@USnlvqvta+e}a;?GeG62jMQO zQdzwpHu^w2A8on)71^f$=F#ZdTkVusTel#mw_Q3w5Sf%ckUU1gZDaOio3W-*Tp2aa zx!8@&ZdNvE#5lpfxZSnDYg=9H;QVLugJceGjc$SX$G@$7_FJ?L@1K!MbyA0i4xUe! 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  • 5{zi>zt_4scv1uZZvEwog{m{-X!os(lB}_GC(H=Gb3J+@jEQ|V(u(FPHu#o= z$dJZ^ z0fC%l;CxhJHO3qG%Bmj|s2VtNVekZd?1FAZx>EyRj+oWmTykc}aaOmX77LQkb5)0Fz-i-}&;2%n1 zm$2p)&>mZq!i(g6f+fuO8OILbO}Qem8CW>}`k+HI znBNf;`lVs?NRW{DMU+_x8qH-@wGBMVo_HC_LWcYl?}Pv0R00gF6Z4ObZ{zwlF7kFP zme;n1@txm2xjsvNlj_evg<-tI&`g^MHYT>A!#2*Q?R^>UNlScOYYg~nk87-VvViL5 z?HAy-PJLUqTDsVSoW)&zE3ou*9NS*BtIoQ^mKg)<#rcc0WRWtNw$-=C8YTn-MYLLvx{JSomTtj7dQCSkpu>+$*bYsfW2YT_!sA@OxC<)D0#}8IokRu}jfKOhmf`J-vCgXbZ7sSC+v8X8 zfu%l6=ejW?&MB+yM_oaTstl`3s7vdDM%PozU4*dlNjX`(JRWE!vukE(={YhEZ`1Lb z^}C#Owp^Fa$|pA74IN1cxhncYkiREITNDCMkflUeMOHw+^zW~TS+lm+2Wsh#ealCo zkEY)v$HD>hz=D?0Jj&6Jh28aGS<7E3#7@qJ*?WA3T?OS!EkK zy#>&_QJRlZ^+0+u-5W{?aJv`n-EJy)a{_$L;U&;4!>y+WcJ~gEd+@hoWM&q z)doSn$x4n1U-iuw7InbywEiE#d(L&LN(d0B^K!Uz0Nd(Xg+J3jgOZwuKy=^nG~q93 zQ20<30(IkK{~%~+7qAG0Cq)i(z;40}E{+0fc5ML{`V2WIbJ4nGUNu($)<433z(z_r zNdGqG0yGZ=9zO{Uft>GFp1UnxF7V|}4uOeiX% - # also for WISCA, refrain from anything below 15 isolates: - subset(n_tested > 15) mins <- sum(out$n_tested < minimum, na.rm = TRUE) if (wisca == FALSE) { out <- out %pm>% @@ -620,7 +617,6 @@ antibiogram.default <- function(x, warning_("Number of tested isolates per regimen should exceed ", minimum, " for each species. Coverage estimates might be inaccurate.", call = FALSE) } } - if (NROW(out) == 0) { return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram")) } @@ -671,6 +667,7 @@ antibiogram.default <- function(x, out_wisca <- out %pm>% pm_group_by(ab) } + out_wisca <- out_wisca %pm>% pm_summarise( coverage = NA_real_, @@ -680,6 +677,7 @@ antibiogram.default <- function(x, n_tested = sum(n_tested, na.rm = TRUE), n_susceptible = sum(n_susceptible, na.rm = TRUE) ) + out_wisca$p_susceptible <- out_wisca$n_susceptible / out_wisca$n_tested if (isTRUE(has_syndromic_group)) { diff --git a/R/data.R b/R/data.R index 869ff3936..960973d0e 100755 --- a/R/data.R +++ b/R/data.R @@ -74,7 +74,6 @@ #' * European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: #' @inheritSection WHOCC WHOCC #' @seealso [microorganisms], [intrinsic_resistant] -#' @aliases antibiotics #' @examples #' antimicrobials #' antivirals diff --git a/R/temp_file b/R/temp_file deleted file mode 100644 index 2cec545fc..000000000 --- a/R/temp_file +++ /dev/null @@ -1 +0,0 @@ -test_that("key_antimicrobials works", { diff --git a/R/zz_deprecated.R b/R/zz_deprecated.R index 06ec4ad20..e03ef4c2b 100755 --- a/R/zz_deprecated.R +++ b/R/zz_deprecated.R @@ -36,6 +36,7 @@ NULL #' @rdname AMR-deprecated +#' @usage NULL #' @export "antibiotics" diff --git a/R/zzz.R b/R/zzz.R index d89f1e869..9ee8a7e1f 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -210,7 +210,9 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x" # deprecated antibiotics data set makeActiveBinding("antibiotics", function() { - deprecation_warning(old = "antibiotics", new = "antimicrobials", is_function = FALSE, is_dataset = TRUE) + if (interactive()) { + deprecation_warning(old = "antibiotics", new = "antimicrobials", is_function = FALSE, is_dataset = TRUE) + } AMR::antimicrobials }, env = asNamespace(pkgname)) diff --git a/data-raw/gpt_training_text_v2.1.1.9186.txt b/data-raw/gpt_training_text_v2.1.1.9187.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9186.txt rename to data-raw/gpt_training_text_v2.1.1.9187.txt index 396aa19d7..e7b496041 100644 --- a/data-raw/gpt_training_text_v2.1.1.9186.txt +++ b/data-raw/gpt_training_text_v2.1.1.9187.txt @@ -1,6 +1,6 @@ This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse. -First and foremost, you are trained on version 2.1.1.9186. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9187. Remember this whenever someone asks which AMR package version you’re at. Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens. ---------------------------------------------------------------------------------------------------- @@ -735,8 +735,6 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/AMR-deprecated.Rd': An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 487 rows and 14 columns. } \usage{ -antibiotics - ab_class(...) ab_selector(...) @@ -2498,7 +2496,6 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/antimicrobials.Rd': \docType{data} \name{antimicrobials} \alias{antimicrobials} -\alias{antibiotics} \alias{antivirals} \title{Data Sets with 607 Antimicrobial Drugs} \format{ diff --git a/man/AMR-deprecated.Rd b/man/AMR-deprecated.Rd index 173621038..b5ba9f605 100644 --- a/man/AMR-deprecated.Rd +++ b/man/AMR-deprecated.Rd @@ -11,8 +11,6 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 487 rows and 14 columns. } \usage{ -antibiotics - ab_class(...) ab_selector(...) diff --git a/man/antimicrobials.Rd b/man/antimicrobials.Rd index 5d8ac88d4..9de86e7f9 100644 --- a/man/antimicrobials.Rd +++ b/man/antimicrobials.Rd @@ -3,7 +3,6 @@ \docType{data} \name{antimicrobials} \alias{antimicrobials} -\alias{antibiotics} \alias{antivirals} \title{Data Sets with 607 Antimicrobial Drugs} \format{