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Attempt to solve issue #59 #70

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Attempt to solve issue #59 #70

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b5b937f
Attempt solve issue #59
stefan-mueller Jun 27, 2017
7c2cdf9
Merge pull request #1 from stefan-mueller/issue-59
stefan-mueller Jun 27, 2017
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34 changes: 32 additions & 2 deletions R/dwplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@
#'
#' @export

dwplot <- function(x, alpha = .05, dodge_size = .15, order_vars = NULL,
dwplot <- function(x, alpha = .05, alpha2 = NULL, dodge_size = .15, order_vars = NULL,
show_intercept = FALSE, model_name = "model",
dot_args = NULL, whisker_args = NULL, ...) {
# If x is model object(s), convert to a tidy data.frame
Expand All @@ -85,7 +85,7 @@ dwplot <- function(x, alpha = .05, dodge_size = .15, order_vars = NULL,
if (!show_intercept) df <- df %>% filter(!grepl("^\\(Intercept\\)$|^\\w+\\|\\w+$", term)) # enable detecting intercept in polr objects

# Set variables that will appear in pipelines to NULL to make R CMD check happy
estimate <- model <- lb <- ub <- term <- std.error <- NULL
estimate <- model <- lb <- ub <- lb_alpha2 <- ub_alpha2 <- term <- std.error <- NULL

n_vars <- length(unique(df$term))
dodge_size <- dodge_size
Expand Down Expand Up @@ -140,7 +140,24 @@ dwplot <- function(x, alpha = .05, dodge_size = .15, order_vars = NULL,
df <- transform(df, lb=NA, ub=NA)
}
}

# Confirm alpha within bounds (for second alpha)
if (alpha2 < 0 | alpha2 > 1) {
stop("Value of alpha for the confidence intervals should be between 0 and 1.")
}

# Generate lower and upper bound if not included in results
if ((!"lb_alpha2" %in% names(df)) || (!"ub_alpha2" %in% names(df))) {
if ("std.error_alpha2" %in% names(df)) {
ci2 <- 1 - alpha2/2
df <- transform(df,
lb_alpha2 = estimate - stats::qnorm(ci2) * std.error,
ub_alpha2 = estimate + stats::qnorm(ci2) * df$std.error)
} else {
df <- transform(df, lb_alpha2=NA, ub_alpha2=NA)
}
}

# Calculate y-axis shift for plotting multiple models
if (n_models == 1) {
shift <- 0
Expand All @@ -160,6 +177,12 @@ dwplot <- function(x, alpha = .05, dodge_size = .15, order_vars = NULL,
y = y_ind + shift, yend = y_ind + shift),
na.rm = TRUE)
segment_args <- c(seg_args0, whisker_args)

# Generate argument to geom_segment for second alpha
seg_args0_alpha2 <- list(aes(x = lb_alpha2, xend = ub_alpha2,
y = y_ind + shift, yend = y_ind + shift), size = 3, alpha = 0.8,
na.rm = TRUE)
segment_args_alpha2 <- c(seg_args0_alpha2, whisker_args)

point_args0 <- list(na.rm = TRUE)
point_args <- c(point_args0, dot_args)
Expand All @@ -170,6 +193,7 @@ dwplot <- function(x, alpha = .05, dodge_size = .15, order_vars = NULL,
aes(x = estimate, y = y_ind + shift, colour = model)) +
do.call(geom_segment, segment_args) + # Draw segments first ...
do.call(geom_point, point_args) +
do.call(geom_segment, segment_args_alpha2) +
scale_y_continuous(breaks = y_ind, labels = var_names) +
coord_cartesian(ylim = c(.5, n_vars+.5)) +
ylab("") + xlab("")
Expand Down Expand Up @@ -273,5 +297,11 @@ add_NAs <- function(df = df, n_models = n_models, mod_names = mod_names,
df$lb <- as.numeric(df$lb)
}

if ("ub_alpha2" %in% names(df)) {
df$ub_alpha2 <- as.numeric(df$ub_alpha2)
}
if ("lb_alpha2" %in% names(df)) {
df$lb_alpha2 <- as.numeric(df$lb_alpha2)
}
return(df)
}