Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup--------------------------------------------------------------------
library(metacore)
library(dplyr)
library(purrr)
library(stringr)
## ----error=TRUE---------------------------------------------------------------
spec_to_metacore(metacore_example("mock_spec.xlsx"))
## -----------------------------------------------------------------------------
metacore:::spec_type(metacore_example("mock_spec.xlsx"))
## -----------------------------------------------------------------------------
doc <- read_all_sheets(metacore_example("mock_spec.xlsx"))
doc %>% map(head)
## ----error=TRUE---------------------------------------------------------------
spec_type_to_ds_spec(doc)
## -----------------------------------------------------------------------------
doc$Domains %>% names()
## -----------------------------------------------------------------------------
ds_spec <- spec_type_to_ds_spec(doc,
cols = c("dataset" = "Name",
"structure" = "Data Structure",
"label" = "Label"))
head(ds_spec)
## ----error=TRUE---------------------------------------------------------------
spec_type_to_ds_vars(doc)
## -----------------------------------------------------------------------------
doc$Variables %>% head()
ds_vars<- spec_type_to_ds_vars(doc, cols = c("dataset" = "Domain",
"variable" = "[V|v]ariable [N|n]ame",
"order" = "[V|v]ariable [O|o]rder",
"keep" = "[M|m]andatory"),
key_seq_cols = c("dataset" = "Domain Name",
"key_seq" = "Key"),
sheet = "[V|v]ar|Domains")
head(ds_vars)
## -----------------------------------------------------------------------------
var_spec <- spec_type_to_var_spec(doc, cols = c("variable" = "Variable Name",
"length" = "[L|l]ength",
"label" = "[L|l]abel",
"type" = "[T|t]ype",
"dataset" = "[D|d]ataset|[D|d]omain",
"format" = "Format"))
head(var_spec)
## -----------------------------------------------------------------------------
var_spec <- var_spec %>%
mutate(format = if_else(str_detect(format, "\\."), format, ""))
## -----------------------------------------------------------------------------
value_spec <- spec_type_to_value_spec(doc, cols = c("dataset" = "VLM Name|Domain",
"variable" = "VLM Name|Variable Name",
"origin" = "[O|o]rigin",
"type" = "[T|t]ype",
"code_id" = "Controlled Term",
"where" = "Parameter Code",
"derivation_id" = "Method",
"predecessor" = "Method"),
where_sep_sheet = FALSE)
head(value_spec)
## -----------------------------------------------------------------------------
derivation <- spec_type_to_derivations(doc, cols = c("derivation_id" = "Name",
"derivation" = "[D|d]efinition|[D|d]escription"),
var_cols = c("dataset" = "Domain Name",
"variable" = "Variable Name|VLM",
"origin" = "[O|o]rigin",
"predecessor" = "Comment",
"comment" = "Comment"))
head(derivation)
## -----------------------------------------------------------------------------
codelist <- spec_type_to_codelist(doc, codelist_cols = c("code_id" = "Codelist Code",
"name" = "Codelist Name",
"code" = "Coded Value",
"decode" = "Decoded Value"),
simplify = TRUE,
dict_cols = NULL)
head(codelist)
## -----------------------------------------------------------------------------
metacore(ds_spec, ds_vars, var_spec, value_spec,
derivation, codelist)
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