From 373bd250a837a3723aa220d9429e0dad95ceaf12 Mon Sep 17 00:00:00 2001 From: Edoardo Mancini Date: Fri, 17 Nov 2023 15:23:46 +0000 Subject: [PATCH 1/4] #76 TERMNAME -> TERMCHAR in get_terms --- DESCRIPTION | 2 +- NEWS.md | 4 +++- R/get_terms.R | 4 ++-- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ff0b66c..15730f3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: pharmaversesdtm Type: Package Title: Test Data for the Pharmaverse Family of Packages -Version: 0.1.1.9000 +Version: 0.1.1.9001 Authors@R: c( person("Edoardo", "Mancini", email = "edoardo.mancini@roche.com", role = c("aut", "cre")), person("Gayatri", "G", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 734c36b..c70cde6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,7 @@ ## New Features -Following Vaccine Specific SDTM datasets have been added. (#4) +The following Vaccine Specific SDTM datasets have been added. (#4) - `ce_vaccine` - `dm_vaccine` @@ -15,6 +15,8 @@ Following Vaccine Specific SDTM datasets have been added. (#4) - `suppex_vaccine` - `suppface_vaccine` +- `get_terms()` now expects `TERMCHAR` instead of `TERMNAME` in alignment with [this](https://github.com/pharmaverse/admiral/issues/2186) `{admiral}` issue. (#76) + # pharmaversesdtm 0.1.1 ## Documentation diff --git a/R/get_terms.R b/R/get_terms.R index 71337da..b63c22a 100644 --- a/R/get_terms.R +++ b/R/get_terms.R @@ -32,7 +32,7 @@ get_terms <- function(basket_select, select_id <- NULL } keep_cols <- c( - TERMNAME = "termname", + TERMCHAR = "termchar", SRCVAR = "termvar", GRPNAME = "smq_name", select_id @@ -57,7 +57,7 @@ get_terms <- function(basket_select, select_id <- NULL } keep_cols <- c( - TERMNAME = "termname", + TERMCHAR = "termchar", SRCVAR = "termvar", GRPNAME = "sdg_name", select_id From a6d5f66b6cfbf4098a2c058a4fe47bc826801f6a Mon Sep 17 00:00:00 2001 From: Edoardo Mancini Date: Fri, 17 Nov 2023 18:54:26 +0000 Subject: [PATCH 2/4] #76 update to query databases --- data-raw/query_databases.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/data-raw/query_databases.R b/data-raw/query_databases.R index 2f61e61..761e732 100644 --- a/data-raw/query_databases.R +++ b/data-raw/query_databases.R @@ -6,7 +6,7 @@ library(dplyr) # Create smq dataset ---- pregsmq <- tribble( - ~termname, ~scope, + ~termchar, ~scope, "Achromotrichia congenital", "narrow", "Craniosynostosis", "narrow", "Hypophosphatasia", "narrow", @@ -36,7 +36,7 @@ pregsmq <- tribble( ) bilismq <- tribble( - ~termname, ~scope, + ~termchar, ~scope, "Bile duct cancer recurrent", "narrow", "Bile duct cancer recurrent", "broad", "Bile duct squamous cell carcinoma", "narrow", @@ -78,7 +78,7 @@ usethis::use_data(smq_db, overwrite = TRUE) # Create sdg dataset ---- sdg_db <- tribble( - ~termname, + ~termchar, "AMINOSALICYLIC ACID", "AMINOSALICYLATE CALCIUM", "AMINOSALICYLATE CALCIUM ALUMINIUM", From 2dee0e4b38b83a740c2a4ba899b0f7b8189373ff Mon Sep 17 00:00:00 2001 From: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> Date: Mon, 20 Nov 2023 17:29:53 +0000 Subject: [PATCH 3/4] Closes #76 TERMNAME -> TERMCHAR in get_terms (#77) * #76 TERMNAME -> TERMCHAR in get_terms * #76 update to query databases --- DESCRIPTION | 2 +- NEWS.md | 4 +++- R/get_terms.R | 4 ++-- data-raw/query_databases.R | 6 +++--- 4 files changed, 9 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ff0b66c..15730f3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: pharmaversesdtm Type: Package Title: Test Data for the Pharmaverse Family of Packages -Version: 0.1.1.9000 +Version: 0.1.1.9001 Authors@R: c( person("Edoardo", "Mancini", email = "edoardo.mancini@roche.com", role = c("aut", "cre")), person("Gayatri", "G", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 734c36b..c70cde6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,7 @@ ## New Features -Following Vaccine Specific SDTM datasets have been added. (#4) +The following Vaccine Specific SDTM datasets have been added. (#4) - `ce_vaccine` - `dm_vaccine` @@ -15,6 +15,8 @@ Following Vaccine Specific SDTM datasets have been added. (#4) - `suppex_vaccine` - `suppface_vaccine` +- `get_terms()` now expects `TERMCHAR` instead of `TERMNAME` in alignment with [this](https://github.com/pharmaverse/admiral/issues/2186) `{admiral}` issue. (#76) + # pharmaversesdtm 0.1.1 ## Documentation diff --git a/R/get_terms.R b/R/get_terms.R index 71337da..b63c22a 100644 --- a/R/get_terms.R +++ b/R/get_terms.R @@ -32,7 +32,7 @@ get_terms <- function(basket_select, select_id <- NULL } keep_cols <- c( - TERMNAME = "termname", + TERMCHAR = "termchar", SRCVAR = "termvar", GRPNAME = "smq_name", select_id @@ -57,7 +57,7 @@ get_terms <- function(basket_select, select_id <- NULL } keep_cols <- c( - TERMNAME = "termname", + TERMCHAR = "termchar", SRCVAR = "termvar", GRPNAME = "sdg_name", select_id diff --git a/data-raw/query_databases.R b/data-raw/query_databases.R index 2f61e61..761e732 100644 --- a/data-raw/query_databases.R +++ b/data-raw/query_databases.R @@ -6,7 +6,7 @@ library(dplyr) # Create smq dataset ---- pregsmq <- tribble( - ~termname, ~scope, + ~termchar, ~scope, "Achromotrichia congenital", "narrow", "Craniosynostosis", "narrow", "Hypophosphatasia", "narrow", @@ -36,7 +36,7 @@ pregsmq <- tribble( ) bilismq <- tribble( - ~termname, ~scope, + ~termchar, ~scope, "Bile duct cancer recurrent", "narrow", "Bile duct cancer recurrent", "broad", "Bile duct squamous cell carcinoma", "narrow", @@ -78,7 +78,7 @@ usethis::use_data(smq_db, overwrite = TRUE) # Create sdg dataset ---- sdg_db <- tribble( - ~termname, + ~termchar, "AMINOSALICYLIC ACID", "AMINOSALICYLATE CALCIUM", "AMINOSALICYLATE CALCIUM ALUMINIUM", From 267a7a4aaa9585082de8657218af9ee27a79d2cf Mon Sep 17 00:00:00 2001 From: Stefan Bundfuss Date: Tue, 21 Nov 2023 14:07:36 +0000 Subject: [PATCH 4/4] #76 termname_termchar: update db datasets --- data/sdg_db.rda | Bin 487 -> 477 bytes data/smq_db.rda | Bin 968 -> 964 bytes 2 files changed, 0 insertions(+), 0 deletions(-) diff --git a/data/sdg_db.rda b/data/sdg_db.rda index 996eeb9b586fd335b5512351d75e04cb4ada6bd5..2fc5505d8d7064e41c02066915b5deae059e4432 100644 GIT binary patch literal 477 zcmV<30V4iFT4*^jL0KkKS$#3A@&E$3|HA+Jd5K^%awtFNo^ZeCpP)bh00ck*zybK? zngEp~(?9?NKmY*KMiWMj000~`(<2dt(*XynGG^DGy*A2L8-J%n2iHK02%-Q zX`ll@RT7#R4K$h~)HDFl0qS``2dLVHhpFWjB$QZ{a;>RI0revc#@FUf3e$w@G}W7b zAMK<&;Kzr0UhpWlAu};RRHac`_SKAECE4!tUV?aMr729_R+O{spgIDf2q6Ou*%K%u z;|CPN8Kxe#II%K|)0{E}V5tUh^#qqX~jE(W4MF$&r8nhcw8@WWfy> zOcADy7=flti~s}*qC}X{i8PHgX`lcaH1z;_k5T0wq3Uf!?un;;5<4#73)F0|9ABDO z<&Y#uP^6&e&--NsOlQr^{_G?rOCr^55n7EUJqaeS<|<^Ty4w~RSkS7fMLXUbH~=CaV3>7-C7gL9f+K@s?Rw^U+U zzL=ClmCG0~D2fV3DOQ=4h|WgJDG;1zNQ46;yCpD{5P)hW7HMWljB%Q2n^tCm(dp_! z>D7c?Ttf}nb~6j{LATv4)X*9NNS9Gaey|c*(d-2 diff --git a/data/smq_db.rda b/data/smq_db.rda index 1a7fc4c554a12eb388e2c3e1cd9b5b820499eae2..587a0cf0a41158b00e95a1d868d1b94d4ac7fb77 100644 GIT binary patch delta 949 zcmV;m14{hJ2gC;sLRx4!F+o`-Q(4G@{pOJlAAcSJ)dYYjjxuD?pfqWS$k4C0H6c#3l*eQh4 zjdjRDQ1yNiMdE-%5L0oUqt`M*lrl4ji+_odI5u5Ll_4Z?l%$0uUO=VC5r0W)SimC3 z8ECqKn4lMV0Z#BKHJ(^{`+%pI6vvy06!QX`flb@NPY5JjwM7Nu*|<<7Uj&VK2*xh) z$1UgK1c?DB^Z59IPJmM^Psr#cqMJQPr<=}n9)ME}MKAavBc8?F0Fi*SNgrhYR)5%_ z4n`UQx7<~h+42g3GDK89k_3O-&ro}6V0m7%0>dyF3UullvWlMUDp+}H0AO_NCjdBR zSx2IxnmUZ!tK}?MIzi&dVjzehhe*M1K2<65PgwrAU3?^JE)?SnrbK9h|hGAJ>S54DP$0KHPZh|UfK!29psvU%inNSDL!Z5=OPNjqg21~+V1(Zmk9u5aZ zfx^wLDILo4<^^ac>#Bfo3b5*Uqf>KEQh?4GhGD8b%@kK@yNeMWyf_MPr@NmSo5gHp z26Y+k9F1`@*O&AAZe|CfH~0-(w)cZk0J4$a-7xKsIk-m)!w%S7z>bDfFMlQyB2g=; z-n_116cXcxWX1}zkW~hgVl&^(p5Y(x0J&2E%T$F(#WlPD3>N`am1O{9DH9?HhU&DU zK_Z~k*8!t(PC_&XFdfai_K9+F#+)GJ%u>&FD9E&1zmTQkIG9e;wsUKy4M+w0_Glx9 zT$2!Rr9#9I)Y@JI5H>u#{C_j0M^9+b94A<$YYSMofWFsT$;U^v9TQYO(6;_pKcN$z?UH~nnq=VA_zC%un1J2k4`i=eZ0MGgbEa&Oq^Y@xYU9To;%G;(AH%*)#*QGxYLc;~peUM8!7A2P`!W XJQp6z3V+_h2LBgwML1B9$b$XmzpAKx delta 953 zcmV;q14jJB2gnBwLRx4!F+o`-Q(4ha~GaXHQG+snf+LM%nzpYK-$IwY5Zetat1vfsMOuBj1n^>dH){yBcPGJt>knoqT78DBg^_a9VCqPq;z@WN0WDpq<@jp z@3YJGU0pk;Y+iwKO7N zu`ja89j>d)FUI41zPR5s;dEk~CV${o|+^Q~3w>k0jCk2S4@boqr&OU*$$ zEajJ#D~C-}x3@zt4+f6Ww(dXEehP`TU3(PP<7u;|W-9B?TD9u|G^yFlQqcJ>PB;;nPlD^H%O2;i*DO)$Z=N?Wc9Q6Ff}&W`7chnk8;x zxT=+08B^-r3k@* zq7W(!!!ndpx)`eRUfDxN<-00qImb5_FA^}0N@>oHJ&74jgjA$MM$H6?h*y?8JYwp* zSh)aC47!76mV1zy+Vdq8mw&i%6j3sG`@M^;dTHcnI}W6ZZ<%DlLmat@#^8=D!R*Y$ z96A-6X%L}HMkX6zi4%zq6hwyP^w^%X(2OUlIxHV>5+1@?#|J}VKu}?g6UqZ5hw@u} zMs9J+aaq!wvf4R_k%f2|VqG}#8N+j4`w1w!p)$aBdq?HlbPm0b&mzN|*I129k~nJ# by`H4Edk3#1kNezVzs1~