74 lines
1.7 KiB
R
74 lines
1.7 KiB
R
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rm(list = ls(all.names = TRUE)) # Clear the memory of variables from previous run.
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cat("\014") # Clear the console
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# load packages -----------------------------------------------------------
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box::use(
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magrittr[`%>%`]
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,here[here]
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,dplyr
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,readr
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,tidyr
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,ggplot2
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)
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# globals -----------------------------------------------------------------
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test_list_names <- c(
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"BUN" = "51006"
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,"CA" = "50893"
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,"CO2" = "50882"
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,"CL" = "50902"
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,"CREA" = "50912"
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,"GLU" = "50931"
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,"K" = "50971"
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,"NA" = "50983"
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,"TSH" = "50993"
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,"FT4" = "50995"
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,"RBC" = "51279"
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,"WBC" = "51300"
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,"HCT" = "51221"
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,"HGB" = "51222"
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,"PLT" = "51265"
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)
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# load data ---------------------------------------------------------------
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ds_high_tsh_raw <- readr$read_rds(
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here("ML","data-unshared","ds_high_tsh.RDS")
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)
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# data manipulation -------------------------------------------------------
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#here I am adding a column to determine if the Free T4 Value is diagnostic or not
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# using the FT4 Referance range low as the cut off (0.93)
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ds_high_tsh <- ds_high_tsh_raw %>%
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dplyr$mutate(ft4_dia = dplyr$if_else(`50995` < 0.93, 1, 0)) %>%
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#can rename with a vector using either of these
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# dplyr$rename_with(~names(test_list_names), dplyr$all_of(test_list_names))
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dplyr$rename(!!!test_list_names)
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# basic visualization -----------------------------------------------------
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test <- dplyr$as_tibble(colSums(is.na(ds_high_tsh)), rownames = NA ) %>%
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tibble::rownames_to_column()
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g1 <- ds_high_tsh %>%
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dplyr$select(-subject_id, - charttime) %>%
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dplyr$mutate(dplyr$across(gender, ~dplyr$recode(.,M = 1, F = 2))) %>%
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tidyr$pivot_longer(cols = dplyr$everything())
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