Amended test scripts and documentation for release of v1_1_0. Still n…

…eed to update vignettes and sort qpdf issues.

R/Proportions.R

@@ -10,7 +10,6 @@
 #' @param n field name from data containing the number of cases in the sample (the denominator for the proportion);
 #'          unquoted string; no default
 #' @param multiplier the multiplier used to express the final values (eg 100 = percentage); numeric; default 1
-#' @param percentage this argument is deprecated, please use multiplier argument instead
 #'
 #' @inheritParams phe_dsr
 #'
@@ -21,7 +20,8 @@
 #' @importFrom rlang sym quo_name :=
 #'
 #' @section Notes: Wilson Score method [1,2] is applied using the \code{\link{wilson_lower}}
-#'  and \code{\link{wilson_upper}} functions.
+#'          and \code{\link{wilson_upper}} functions. \cr \cr
+#'          The percentage argument was deprecated in v1_1_0, please use multiplier argument instead
 #'
 #' @examples
 #'

R/Quantiles.R

@@ -82,13 +82,18 @@ phe_quantile <- function(data, values, highergeog = NULL, nquantiles=10L,
       data <- mutate(data,invert_calc = invert)
     } else if (inverttype == "field") {
       invert_q <- enquo(invert)
-      data <- rename(data,invert_calc = !!invert_q)
+      if (deparse(substitute(invert)) %in% colnames(data)) {
+
+          data <- mutate(data,invert_calc = !!invert_q)
+
+      } else stop("invert is not a field name from data")
+      #      data <- rename(data,invert_calc = !!invert_q)
     }
 
 
     # apply quotes to field names
     values_q     <- enquo(values)
-    highergeog_q = enquo(highergeog)
+    highergeog_q <- enquo(highergeog)
 
 
     # error handling for valid data types and values
@@ -118,13 +123,14 @@ phe_quantile <- function(data, values, highergeog = NULL, nquantiles=10L,
     phe_quantile <- data %>%
         add_count(naflag = is.na(!!values_q)) %>%
         mutate(adj_value = if_else(invert_calc == TRUE, max(!!values_q, na.rm=TRUE)-!!values_q,!!values_q),
-               rank = rank(adj_value, ties.method="min", na.last = "keep"),
-               quantile = floor((nquantiles+1)-ceiling(((n+1)-rank)/(n/nquantiles))),
-               quantile = if_else(quantile == 0,1,quantile)) %>%
+               rank      = rank(adj_value, ties.method="min", na.last = "keep"),
+               quantile  = floor((nquantiles+1)-ceiling(((n+1)-rank)/(n/nquantiles))),
+               quantile  = if_else(quantile == 0,1,quantile)) %>%
         select(-naflag,-n,-adj_value, -rank) %>%
-        mutate(nquantiles = nquantiles,
+        mutate(nquantiles        = nquantiles,
                highergeog_column = rlang::quo_name(highergeog_q),
-               invert = invert)
+               qinverted         = if_else(invert_calc == TRUE,"lowest quantile represents highest values",
+                                           "lowest quantile represents lowest values"))
 
 
     #rename quantile column in output - not implemented to ensure consistent output column names
@@ -135,9 +141,9 @@ phe_quantile <- function(data, values, highergeog = NULL, nquantiles=10L,
 
 
     # if invert provided as logical then delete invert_calc column created for calculation
-    if (inverttype == "logical") {
+#    if (inverttype == "logical") {
         phe_quantile <- phe_quantile %>% select(-invert_calc)
-    }
+ #   }
 
 
     # remove columns if not required based on value of type argument

R/utils.R

@@ -3,6 +3,8 @@
 #'
 #' converts NAs to zeros
 #'
+#' @param y input vector
+#'
 na.zero <- function (y) {
     y[is.na(y)] <- 0
     return(y)
@@ -17,6 +19,8 @@ na.zero <- function (y) {
 #'
 #' @param x the observed numbers of events; numeric vector; no default
 #'
+#' @inheritParams phe_dsr
+#'
 #' @return Returns lower confidence limits for observed numbers of events using Byar's method [1]
 #'
 #' @section Notes: \code{byars_lower} and \code{\link{byars_upper}} together return symmetric confidence
@@ -69,6 +73,8 @@ byars_lower <- function(x, confidence = 0.95) {
 #'
 #' @param x the observed numbers of events; numeric vector; no default
 #'
+#' @inheritParams phe_dsr
+#'
 #' @return Returns upper confidence limits for observed numbers of events using Byar's method [1]
 #'
 #' @section Notes: \code{\link{byars_lower}} and \code{byars_upper} together return symmetric confidence
@@ -111,6 +117,11 @@ byars_upper <- function(x, confidence = 0.95) {
 #'
 #' Calculates lower confidence limits for observed numbers of events using the Wilson Score method [1,2].
 #'
+#' @param x the observed numbers of cases in the samples meeting the required condition; numeric vector; no default
+#' @param n the numbers of cases in the samples; numeric vector; no default
+#'
+#' @inheritParams phe_dsr
+#'
 #' @return Returns lower confidence limits for observed numbers of events using the Wilson Score method [1,2]
 #'
 #' @section Notes: \code{wilson_lower} and \code{\link{wilson_upper}} together return symmetric confidence
@@ -164,6 +175,11 @@ wilson_lower <- function(x, n, confidence = 0.95) {
 #'
 #' Calculates upper confidence limits for observed numbers of events using the Wilson Score method [1,2].
 #'
+#' @param x the observed numbers of cases in the samples meeting the required condition; numeric vector; no default
+#' @param n the numbers of cases in the samples; numeric vector; no default
+#'
+#' @inheritParams phe_dsr
+#'
 #' @return Returns upper confidence limits for observed numbers of events using the Wilson Score method [1,2]
 #'
 #' @section Notes: \code{\link{wilson_lower}} and \code{wilson_upper} together return symmetric confidence