[Bug]: patient-profile app - Error: object 'ADCM' / 'ADMH' not found #218
Description
ADCM is missing in
- Vitals module
- Adverse Events
- Lab Values
ADMH is missing in
- Vitals
- Therapy
- Adverse Events
- Lab Values
- Patient Timeline
DOUBLE CHECK IF THIS DATA IS EVEN NEEDED in those modules. For example I don't think it's needed in Vitals.
Code from Vitals module
library(random.cdisc.data)
library(nestcolor)
ADSL <- radsl(seed = 1)
ADVS <- radvs(ADSL, seed = 1)
teal.data::col_labels(ADCM[c("CMINDC", "CMTRT", "ASTDY", "AENDY")]) <- c("Indication", "Reported Name of Drug, Med, or Therapy", "Study Day of Start of Medication", "Study Day of End of Medication")
teal.data::col_labels(ADMH[c("MHDISTAT")]) <- c("Status of Disease")
stopifnot(rlang::hash(ADSL) == "d6ae57c85cf4dbe4e4a953b09a99dad7") # @linksto ADSL
stopifnot(rlang::hash(ADVS) == "9c6d0e10a69fc8a7becbbbc4a6f23525") # @linksto ADVS
.raw_data <- list2env(list(ADSL = ADSL, ADVS = ADVS))
lockEnvironment(.raw_data) # @linksto .raw_data
ADVS <- dplyr::inner_join(x = ADVS, y = ADSL[, c("STUDYID", "USUBJID"), drop = FALSE], by = c("STUDYID", "USUBJID"))
ANL_1 <- ADVS %>% dplyr::select(STUDYID, USUBJID, PARAMCD, AVISIT, ADY, AVAL)
ANL <- ANL_1
ANL <- ANL %>% teal.data::col_relabel(PARAMCD = "Parameter Code", ADY = "Analysis Relative Day", AVAL = "Analysis Value")
ANL <- ANL[ANL[["USUBJID"]] == "AB12345-CHN-2-id-22", ]
vitals <- ANL %>% dplyr::group_by(PARAMCD, ADY) %>% dplyr::filter(PARAMCD %in% c("DIABP", "PULSE", "RESP", "SYSBP", "TEMP", "WEIGHT")) %>% dplyr::summarise(AVAL = max(AVAL, na.rm = TRUE)) %>% dplyr::mutate(AVAL = ifelse(is.infinite(AVAL), NA, AVAL), ADY = as.numeric(ADY))
max_day <- max(vitals[["ADY"]], na.rm = TRUE)
max_aval <- max(vitals[["AVAL"]], na.rm = TRUE)
max_aval_seq <- seq(0, max_aval, 10)
full_vita <- levels(ANL[["PARAMCD"]])
provided_vita <- c("DIABP", "PULSE", "RESP", "SYSBP", "TEMP", "WEIGHT")
known_vita <- c("SYSBP", "DIABP", "TEMP", "RESP", "OXYSAT", "PULSE")
paramcd_levels_e <- known_vita[stats::na.omit(match(provided_vita, known_vita))]
len_paramcd_levels_e <- length(paramcd_levels_e)
all_colors <- stats::setNames(nestcolor::color_palette(length(full_vita), "stream"), full_vita)
vars_colors <- all_colors[provided_vita]
names(vars_colors) <- provided_vita
base_stats <- stats::setNames(c(140, 90, 38, 20, 94, 100), known_vita)
paramcd_stats_e <- base_stats[paramcd_levels_e]
base_labels <- stats::setNames(c("140mmHg", "90mmHg", "38° C", "20/min", "94%", "100bpm"), known_vita)
paramcd_labels_e <- base_labels[paramcd_levels_e]
base_stats_df <- data.frame(x = rep(1, len_paramcd_levels_e), y = paramcd_stats_e, label = paramcd_labels_e, color = paramcd_levels_e)
plot <- ggplot2::ggplot(data = vitals, mapping = ggplot2::aes(x = ADY)) + ggplot2::geom_line(data = vitals, mapping = ggplot2::aes(y = AVAL, color = PARAMCD), size = 1.5, alpha = 0.5) + ggplot2::scale_color_manual(values = vars_colors) + ggplot2::geom_text(data = base_stats_df, ggplot2::aes(x = x, y = y, label = label, color = color), alpha = 1, nudge_y = 2.2, size = 12L/3.5, show.legend = FALSE) + ggplot2::geom_hline(data = base_stats_df, ggplot2::aes(yintercept = y, color = color), linetype = 2,
alpha = 0.5, size = 1, show.legend = FALSE) + ggplot2::scale_y_continuous(breaks = seq(0, max(vitals[["ADY"]], na.rm = TRUE), 50), minor_breaks = seq(0, max(vitals[["AVAL"]], na.rm = TRUE), 10)) + ggplot2::geom_text(data = data.frame(x = rep(max_day, length(max_aval_seq)), y = max_aval_seq, l = as.character(max_aval_seq)), ggplot2::aes(x = x, y = y, label = l), color = "black", alpha = 1, nudge_y = 2.2, size = 12L/3.5) + ggplot2::labs(title = "Patient ID: AB12345-CHN-2-id-22") + ggplot2::theme_minimal() +
ggplot2::theme(text = ggplot2::element_text(size = 12L), axis.text.y = ggplot2::element_blank(), axis.ticks.y = ggplot2::element_blank(), plot.title = ggplot2::element_text(size = 12L), legend.position = "top", panel.grid.minor = ggplot2::element_line(linewidth = 0.5, linetype = "dotted", colour = "grey"), panel.grid.major = ggplot2::element_line(linewidth = 0.5, linetype = "dotted", colour = "grey"))
ploterror
teal.data::col_labels(ADCM[c("CMINDC", "CMTRT", "ASTDY", "AENDY")]) <- c("In$
Error: object 'ADCM' not found
> teal.data::col_labels(ADMH[c("MHDISTAT")]) <- c("Status of Disease")
Error: object 'ADMH' not found