# Generate testdata for dst_baseliner()
## EpiInfo admission and lab
### Admission data
epi_adm <-
data.frame(APID = paste0("XYZ", 1:8), stringsAsFactors = F) %>%
dplyr::mutate(
STARTTRE = lubridate::dmy(c(rep("1/1/10", 8))),
indictor_dst = factor(c(
"DSTB",
"Inh-mono",
"Inh-mono",
"pre-XDRTB (SLI)",
NA_character_,
"RRTB",
"XDRTB",
"DSTB"
))
)
class(epi_adm) <- c(class(epi_adm), "epiinfo")
saveRDS(epi_adm, "inst/testdata/dst_baseliner_epi_adm.rds", version = 2)
### Laboratory data
epi_lab <-
structure(
list(
APID = c(
"XYZ1",
"XYZ2",
"XYZ3",
"XYZ4",
"XYZ4",
"XYZ5",
"XYZ6",
"XYZ6",
"XYZ7",
"XYZ8"
),
samp_date = structure(
c(14608,
14608, 14608, 14608, NA, 14608, 14558, 14608, 14608, 14608),
class = "Date"
),
hain_inh = structure(
c(1L, 2L, 1L, NA, 1L, NA, NA, NA, 2L, NA),
.Label = c("Sensitive",
"Resistant"),
class = "factor"
),
hain_rif = structure(
c(1L,
1L, 1L, 2L, 1L, NA, NA, NA, 2L, NA),
.Label = c("Sensitive", "Resistant"),
class = "factor"
),
xpert_res = structure(
c(2L, 2L, 1L,
1L, 1L, NA, 2L, 2L, NA, 2L),
.Label = c("Negative", "Positive"),
class = "factor"
),
xpert_rif = structure(
c(NA, 1L, 1L, 1L, 1L, NA, 1L, 2L, NA, 1L),
.Label = c("Not detected",
"Detected"),
class = "factor"
),
dst_p_rif = structure(
c(1L,
1L, 1L, 1L, 1L, NA, NA, NA, 1L, NA),
.Label = c("Sensitive", "Resistant"),
class = "factor"
),
dst_p_inh = structure(
c(1L, 1L, 2L,
1L, 1L, NA, NA, NA, 2L, NA),
.Label = c("Sensitive", "Resistant"),
class = "factor"
),
dst_p_pza = structure(
c(1L, 1L, 1L, 1L, 1L, NA, NA, NA, 2L, NA),
.Label = c("Sensitive",
"Resistant"),
class = "factor"
),
dst_p_eth = structure(
c(1L,
1L, 1L, 1L, 1L, NA, NA, NA, NA, NA),
.Label = c("Sensitive", "Resistant"),
class = "factor"
),
dst_p_cm = structure(
c(1L, 1L, 1L,
2L, 1L, NA, NA, NA, 1L, NA),
.Label = c("Sensitive", "Resistant"),
class = "factor"
),
dst_p_mfx = structure(
c(NA, 1L, 1L, 1L, 2L, NA, NA, NA, NA, NA),
.Label = c("Sensitive",
"Resistant"),
class = "factor"
),
dst_p_km = structure(
c(1L,
2L, 1L, 1L, 1L, NA, NA, NA, 2L, NA),
.Label = c("Sensitive", "Resistant"),
class = "factor"
),
dst_p_ofx = structure(
c(1L, 1L, 2L,
1L, 1L, NA, NA, NA, 2L, NA),
.Label = c("Sensitive", "Resistant"),
class = "factor"
)
),
row.names = c(NA,-10L),
class = c("tbl_df", "tbl", "data.frame")
) %>%
dplyr::mutate(MICRLABN = paste0("09-000", 1:nrow(.))) %>%
dplyr::select(APID, MICRLABN, samp_date, dplyr::everything())
class(epi_lab) <- c(class(epi_lab), "epiinfo")
saveRDS(epi_lab, "inst/testdata/dst_baseliner_epi_lab.rds", version = 2)
# ================================================
# Koch 6 with Grozny lab
### Admission data
k6_groz_adm <- epi_adm %>%
rename(registrationnb = APID,
Starttre = STARTTRE) %>%
mutate(dstnumber = as.character(1:length(unique(.$registrationnb)))) %>%
select(registrationnb, dstnumber, dplyr::everything())
class(k6_groz_adm) <- c(class(k6_groz_adm), "koch6")
saveRDS(k6_groz_adm, "inst/testdata/dst_baseliner_k6_groz_adm.rds", version = 2)
### Laboratory data
k6_groz_lab <- epi_lab %>%
rename(registrationnb = APID,
dst_p_am = dst_p_km,
dst_p_lfx = dst_p_ofx) %>%
mutate(dst_p_mfxhigh = dst_p_mfx) %>%
left_join(k6_groz_adm, by = "registrationnb") %>%
select(-registrationnb, -MICRLABN, -Starttre) %>%
select(dstnumber, dplyr::everything())
class(k6_groz_lab) <- c(class(k6_groz_lab), "grozny")
saveRDS(k6_groz_lab, "inst/testdata/dst_baseliner_k6_groz_lab.rds", version = 2)
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