I get the warning “Removed 1 rows containing missing values (geom_point).” when plotting using density_plot_type scatter.
This happens because when using scatter, some points are jittered and may end up visually outside of the plotting range, so they can’t be displayed. That warning informs you (in a cryptic way) of this fact. Given that the jittering is randomised, sometimes you might get that warning, sometimes you won’t, even for the same input.
If you want to silence the warning, use suppressWarning() when you print the plot for displaying.
For my continuous outcome, lower values are better
In some cases, for the continuous outcome, lower values might be considered better than higher values. By default, the win odds are calculated assuming that higher values are better. In order to calculate the correct win odds, the user can set the lowerBetter parameter in the maraca() or plot.hce() function to TRUE.
Additionally, it is possible to display the continuous outcome on a reverse scale using the parameter trans = "reverse" in the plotting functions.
Rates_A <- c(10, 15)
Rates_P <- c(12, 15)
dat <- simHCE(n = 2500, TTE_A = Rates_A, TTE_P = Rates_P,
CM_A = 6, CM_P = 10, CSD_A = 16, CSD_P = 15, fixedfy = 3, seed = 1)
plot(dat, lowerBetter = TRUE, trans = "reverse")
Outcome axis labels are overlapping
Sometimes for some of the outcomes, only very few patients had an event. Since the x-axis range for each endpoint is based on the proportion of patients that had the event, this can lead to close x-axis ticks and overlapping labels.
data(hce_scenario_a, package = "maraca")
data <- hce_scenario_a
column_names <- c(
outcome = "GROUP",
arm = "TRTP",
value = "AVAL0"
)
step_outcomes <- c(
"Outcome I", "Outcome II", "Outcome III", "Outcome IV"
)
last_outcome <- "Continuous outcome"
arm_levels = c(active = "Active", control = "Control")
# We will only include a few patients with outcome III
data2 <- data[data$GROUP == "Outcome II",]
data3 <- data[data$GROUP == "Outcome III",]
data <- rbind(data2[sample(1:nrow(data2),5),],
data3[sample(1:nrow(data3),5),],
data[!(data$GROUP %in% c("Outcome II","Outcome III")),])
mar <- maraca(
data, step_outcomes, last_outcome, arm_levels, column_names,
fixed_followup_days = 3*365,
compute_win_odds = TRUE
)
# Now the x-axis labels are overlapping
plot(mar)
One potential workaround in this situation is to add a line break after or before one of the outcomes in order to space them further apart.
data[data$GROUP == "Outcome II","GROUP"] <- "Outcome II\n"
step_outcomes <- c(
"Outcome I", "Outcome II\n", "Outcome III", "Outcome IV"
)
mar <- maraca(
data, step_outcomes, last_outcome, arm_levels, column_names,
fixed_followup_days = 3*365,
compute_win_odds = TRUE
)
plot(mar)
I get the error “outcome [XY] is not present in column”
The maraca package expects that for every outcome specified in the step_outcomes parameter, at least one patient has had that event.
data(hce_scenario_a, package = "maraca")
data <- hce_scenario_a
column_names <- c(
outcome = "GROUP",
arm = "TRTP",
value = "AVAL0"
)
step_outcomes <- c(
"Outcome I", "Outcome II", "Outcome III", "Outcome IV"
)
last_outcome <- "Continuous outcome"
arm_levels = c(active = "Active", control = "Control")
# Let's pretend no one in the study had outcome II
data <- data[data$GROUP != "Outcome II", ]
# Now we will get an error
mar <- maraca(
data, step_outcomes, last_outcome, arm_levels, column_names,
fixed_followup_days = 3*365,
compute_win_odds = TRUE
)
## Error in .reformat_and_check_data(data, step_outcomes, last_outcome, arm_levels, : Outcome Outcome II is not present in column GROUP
If the outcome is not part of the data at all, it cannot be displayed as part of the plot. The outcome has to be removed from the step_outcomes parameter. Additionally, the user can for example add a footnote explaining why the outcome is not included in the plot.
