Closed andreranza closed 1 year ago
If I understand the question correctly, most of the items you have listed below are substrates used in testing such as "MycoPrep Specimen Digestion/Decontamination kit [240863], 10x 150 mL NALC-NaOH sol, 10 x phosphate buffer." They are not the actual diagnostic test.
For filtering the products list, I would use the string "TB molecular diagnostics."
From: Andrea Ranzato @.> Sent: Monday, September 4, 2023 6:50 AM To: cynkra/findtb @.> Cc: Mariame Diabate @.>; Mention @.> Subject: [cynkra/findtb] Divide tests from instruments in Global Fund data (Issue #82)
@diabatem-findhttps://github.com/diabatem-find could you please help?
Instruments should be those from Cepheid with "instruments" and Cepheid GeneXpert IV system with desktop computer (two sites) [GXIV-2-D]. All others are tests.
Anything else?
Cepheid Xpert MTB/RIF kit (10s, 50s) [CGXMTBRIF] Cepheid Xpert MTB/RIF Ultra (50s) [GXMTB/RIF-ULTRA-50] XPERTCHECK 1 kit [XPERTCHECK-CE-5] BACTEC MGIT 960 PZA Drug Kit 50s [245128] BACTEC MGIT 960 PZA Medium 25s [245115] BACTEC MGIT 960 SIRE Kit 40s [245123] BACTEC MGIT 960 Supplement Kit 100s [245124] BBL MGIT 7 ml Tube (100 tests) [245122] MycoPrep Specimen Digestion/Decontamination kit [240863], 10x 150 mL NALC-NaOH sol, 10 x phosphate buffer Cepheid GeneXpert Model GX-IV- 4 module Instrument with laptop [GXIV-4-L] GenoLyse V1 [51610] Cepheid GeneXpert Model GX-IV- 4 module Instrument with desktop [GXIV-4D] Consumables kit for 1000 sputum smears GenoType Mycobacterium CM 12s, 96s [299, 29996] GenoTypeMTBDR plus tests 12s, 96s [304A, 30496A] , Hot start DNA polymerase (with MgCl2&PCR buffer) [70060030] GenoType MTBC 12s, 96s [301, 30196] GenoType MTBDRsl Version 2.0 [31796A] GenoType Mycobacterium AS 12s, 96s [298, 29896] GenoType Mycobacterium CM Version 2.0, 96s [29996A] BACTEC MGIT 960 EMB 7.5 Kit 50s [245127] BD MGIT™ - OADC Enrichment (for 625 tubes = 150s) [245116] Cepheid GeneXpert Model GX-XVI-16 module instrument with desktop[GXXVI-16-D] Cepheid GeneXpert Model GX-XVI-16 module instrument with laptop [GXXVI-16-L] BACTEC MGIT 960 mycobacterial detection system [445870] GenoType MTBDRsl 12s, 96s [317, 31796] GenoType MTBDRplus tests and GenoLyse 12s, 96s [304AM, 30496AM] SD BIOLINE TB Ag MPT64 Rapid [08FK50] Cepheid GeneXpert IV system with desktop computer (two sites) [GXIV-2-D] BD MGIT™ - PANTA™ Antibiotic Mixture (for 625 tubes = 150s) [245114] BD Middlebrook OADC enrichment 20mL/tube, 10 tubes [211886] BD MGIT™ TBc Identification Test/Card [245159] MycoPrep™ Specimen Digestion/Decontamination Kit [240862], 10x 75 mL NALC-NaOH sol, 5 x phosphate buffer BACTEC MGIT 320 mycobacterial detection system [441743]
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Thanks @diabatem-find.
So, the ones with TB molecular diagnostics
are not tests, and we should not consider them. Is that correct?
Those marked with TRUE below are those we will keep.
library(tidyverse)
pkgload::load_all()
#> ℹ Loading findtb
df <-
read_gf_procurement("gf_2023-07-26_procurement.csv") |>
tidy_gf_procurement(year = 2019) |>
distinct(product, description)
df |>
mutate(
is_test = if_else(str_detect(product, "diagno"), FALSE, TRUE),
.after = product
) |>
print(n = Inf)
#> # A tibble: 34 × 3
#> product is_test description
#> <chr> <lgl> <chr>
#> 1 TB molecular diagnostics FALSE Cepheid Xpert MTB/RIF kit (10s,…
#> 2 TB molecular diagnostics FALSE Cepheid Xpert MTB/RIF Ultra (50…
#> 3 TB testing consumables/test kits TRUE XPERTCHECK 1 kit [XPERTCHECK-CE…
#> 4 TB testing consumables/test kits TRUE BACTEC MGIT 960 PZA Drug Kit 5…
#> 5 TB testing consumables/test kits TRUE BACTEC MGIT 960 PZA Medium 25s …
#> 6 TB testing consumables/test kits TRUE BACTEC MGIT 960 SIRE Kit 40s […
#> 7 TB testing consumables/test kits TRUE BACTEC MGIT 960 Supplement Kit…
#> 8 TB testing consumables/test kits TRUE BBL MGIT 7 ml Tube (100 tests) …
#> 9 TB testing consumables/test kits TRUE MycoPrep Specimen Digestion/Dec…
#> 10 TB molecular diagnostics FALSE Cepheid GeneXpert Model GX-IV- …
#> 11 TB molecular diagnostics FALSE GenoLyse V1 [51610]
#> 12 TB molecular diagnostics FALSE Cepheid GeneXpert Model GX-IV- …
#> 13 TB testing consumables/test kits TRUE Consumables kit for 1000 sputum…
#> 14 TB molecular diagnostics FALSE GenoType Mycobacterium CM 12s, …
#> 15 TB molecular diagnostics FALSE GenoTypeMTBDR plus tests 12s, 9…
#> 16 TB molecular diagnostics FALSE Hot start DNA polymerase (with …
#> 17 TB molecular diagnostics FALSE GenoType MTBC 12s, 96s [301, 30…
#> 18 TB molecular diagnostics FALSE GenoType MTBDRsl Version 2.0 [3…
#> 19 TB molecular diagnostics FALSE GenoType Mycobacterium AS 12s, …
#> 20 TB molecular diagnostics FALSE GenoType Mycobacterium CM Versi…
#> 21 TB testing consumables/test kits TRUE BACTEC MGIT 960 EMB 7.5 Kit 50s…
#> 22 TB testing consumables/test kits TRUE BD MGIT™ - OADC Enrichment (for…
#> 23 TB molecular diagnostics FALSE Cepheid GeneXpert Model GX-XVI-…
#> 24 TB molecular diagnostics FALSE Cepheid GeneXpert Model GX-XVI-…
#> 25 TB testing equipment (non-molecular) TRUE BACTEC MGIT 960 mycobacterial d…
#> 26 TB molecular diagnostics FALSE GenoType MTBDRsl 12s, 96s [317,…
#> 27 TB testing consumables/test kits TRUE GenoType MTBDRplus tests and Ge…
#> 28 TB testing consumables/test kits TRUE SD BIOLINE TB Ag MPT64 Rapid [0…
#> 29 TB molecular diagnostics FALSE Cepheid GeneXpert IV system wit…
#> 30 TB testing consumables/test kits TRUE BD MGIT™ - PANTA™ Antibiotic Mi…
#> 31 TB testing consumables/test kits TRUE BD Middlebrook OADC enrichment …
#> 32 TB testing consumables/test kits TRUE BD MGIT™ TBc Identification Tes…
#> 33 TB testing consumables/test kits TRUE MycoPrep™ Specimen Digestion/De…
#> 34 TB testing equipment (non-molecular) TRUE BACTEC MGIT 320 mycobacterial d…
Created on 2023-09-04 with reprex v2.0.2
No, the opposite. They are the ones that should be considered. The previous list you sent, is what should be filtered out.
From: Andrea Ranzato @.> Sent: Monday, September 4, 2023 8:39 AM To: cynkra/findtb @.> Cc: Mariame Diabate @.>; Mention @.> Subject: Re: [cynkra/findtb] Divide tests from instruments in Global Fund data (Issue #82)
Thanks @diabatem-findhttps://github.com/diabatem-find.
So, the ones with TB molecular diagnostics are not tests, and we should not consider them. Is that correct?
Those marked with TRUE below are those we will keep.
library(tidyverse) pkgload::load_all()
df <- read_gf_procurement("gf_2023-07-26_procurement.csv") |> tidy_gf_procurement(year = 2019) |> distinct(product, description)
df |> mutate( is_test = if_else(str_detect(product, "diagno"), FALSE, TRUE), .after = product ) |> print(n = Inf)
Created on 2023-09-04 with reprex v2.0.2https://reprex.tidyverse.org/
— Reply to this email directly, view it on GitHubhttps://github.com/cynkra/findtb/issues/82#issuecomment-1705201908, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BBQUZVEJVJBKA6CUJE2HVVDXYXDYRANCNFSM6AAAAAA4KHKEKY. You are receiving this because you were mentioned.Message ID: @.***>
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Thanks a lot for clarifying @diabatem-find. Just one more question. I realised that disregarding the year, productsTuberculin test
and TB IGRA
appear too. Are those to be considered as well?
library(tidyverse)
pkgload::load_all()
#> ℹ Loading findtb
df <-
read_gf_procurement("gf_2023-07-26_procurement.csv") |>
tidy_gf_procurement() |>
distinct(product, description) |>
arrange(product)
df |>
filter(product %in% c("Tuberculin test", "TB IGRA"))
#> # A tibble: 3 × 2
#> product description
#> <chr> <chr>
#> 1 TB IGRA QFT-Plus Blood Collection Tubes [622526] PQR
#> 2 TB IGRA QuantiFERON-TB Gold Plus 2 Plate Kit ELISA [622120] PQR
#> 3 Tuberculin test Tuberculine PPD, 5TU /0.1 mL
Created on 2023-09-04 with reprex v2.0.2
Of the three items that you have listed below, only option 3, "Tuberculin test Tuberculine PPD, 5TU /0.1 mL" should be included. The other two items are used for test prep.
From: Andrea Ranzato @.> Sent: Monday, September 4, 2023 9:09 AM To: cynkra/findtb @.> Cc: Mariame Diabate @.>; Mention @.> Subject: Re: [cynkra/findtb] Divide tests from instruments in Global Fund data (Issue #82)
Thanks a lot for clarifying @diabatem-findhttps://github.com/diabatem-find. Just one more question. I realised that disregarding the year, productsTuberculin test and TB IGRA appear too. Are those to be considered as well?
library(tidyverse) pkgload::load_all()
df <- read_gf_procurement("gf_2023-07-26_procurement.csv") |> tidy_gf_procurement() |> distinct(product, description) |> arrange(product)
df |> filter(product %in% c("Tuberculin test", "TB IGRA"))
Created on 2023-09-04 with reprex v2.0.2https://reprex.tidyverse.org/
— Reply to this email directly, view it on GitHubhttps://github.com/cynkra/findtb/issues/82#issuecomment-1705248147, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BBQUZVG7SXSU5SWMMZ3Y3QDXYXHIZANCNFSM6AAAAAA4KHKEKY. You are receiving this because you were mentioned.Message ID: @.***>
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This e-mail message may contain confidential and/or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you.
@diabatem-find could you please help?
Instruments should be those from Cepheid with "instruments" and
Cepheid GeneXpert IV system with desktop computer (two sites) [GXIV-2-D]
. All others should be tests.Anything else?