Fix \itemize formating issues

R/dgaps.R

@@ -238,18 +238,18 @@ dgaps <- function(data, u, D = 1, inc_cens = TRUE) {
 #'     2 N_1 log \theta - \theta q (I_0 T_0 + ... + I_N T_N),}
 #'    where
 #'     \itemize{
-#'       \item{\eqn{q} is the threshold exceedance probability, estimated by
-#'         the proportion of threshold exceedances,}
-#'       \item{\eqn{d = q D},}
-#'       \item{\eqn{I_j = 1} if \eqn{T_j > D} and \eqn{I_j = 0} otherwise,}
-#'       \item{\eqn{N_0} is the number of sample inter-exceedance times that
-#'         are left-censored, that is, are less than or equal to \eqn{D},}
-#'       \item{(apart from an adjustment for the contributions of \eqn{T_0} and
+#'       \item \eqn{q} is the threshold exceedance probability, estimated by
+#'         the proportion of threshold exceedances,
+#'       \item \eqn{d = q D},
+#'       \item \eqn{I_j = 1} if \eqn{T_j > D} and \eqn{I_j = 0} otherwise,
+#'       \item \eqn{N_0} is the number of sample inter-exceedance times that
+#'         are left-censored, that is, are less than or equal to \eqn{D},
+#'       \item (apart from an adjustment for the contributions of \eqn{T_0} and
 #'         \eqn{T_N}) \eqn{N_1} is the number of inter-exceedance times that
-#'         are uncensored, that is, are greater than \eqn{D},}
-#'       \item{specifically, if \code{inc_cens = TRUE} then \eqn{N_1} is equal
+#'         are uncensored, that is, are greater than \eqn{D},
+#'       \item specifically, if \code{inc_cens = TRUE} then \eqn{N_1} is equal
 #'         to the number of \eqn{T_1, ..., T_{N-1}}{T_1, ..., T_(N-1)} that are
-#'         uncensored plus \eqn{(I_0 + I_N) / 2}.}
+#'         uncensored plus \eqn{(I_0 + I_N) / 2}.
 #'     }
 #'    The differing treatment of uncensored and censored \eqn{K}-gaps reflects
 #'    differing contributions to the likelihood. Right-censored

R/exdex-package.R

@@ -9,14 +9,14 @@
 #' @details Functions to implement four estimators of the extremal index
 #'   are provided, namely
 #' \itemize{
-#'   \item{\code{\link{spm}}: semiparametric maxima estimator, using block
-#'     maxima: (Northrop, 2015; Berghaus and Bucher, 2018)}
-#'   \item{\code{\link{kgaps}}: \eqn{K}-gaps estimator, using threshold
-#'     inter-exceedance times (Suveges and Davison, 2010)}
-#'   \item{\code{\link{dgaps}}: \eqn{D}-gaps estimator, using threshold
-#'     inter-exceedance times (Holesovsky and Fusek, 2020))}
-#'   \item{\code{\link{iwls}}: iterated weighted least squares estimator,
-#'     using threshold inter-exceedance times: (Suveges, 2007)}
+#'   \item \code{\link{spm}}: semiparametric maxima estimator, using block
+#'     maxima: (Northrop, 2015; Berghaus and Bucher, 2018)
+#'   \item \code{\link{kgaps}}: \eqn{K}-gaps estimator, using threshold
+#'     inter-exceedance times (Suveges and Davison, 2010)
+#'   \item \code{\link{dgaps}}: \eqn{D}-gaps estimator, using threshold
+#'     inter-exceedance times (Holesovsky and Fusek, 2020))
+#'   \item \code{\link{iwls}}: iterated weighted least squares estimator,
+#'     using threshold inter-exceedance times: (Suveges, 2007)
 #' }
 #' The functions \code{\link{choose_b}}, \code{\link{choose_uk}} and
 #' \code{\link{choose_ud}} provide graphical diagnostics for choosing the
@@ -116,15 +116,14 @@
 #' The dataframe \code{uccle} contains daily maximum temperatures in degrees C
 #' recorded at the Uccle, Belgium from 1/1/1833 to 23/1/2011.  The Station
 #' identifier in the source file is 17 and the Source identifier is 117882.
-#' @format A data frame with 65036 observations on the following and 5
-#'   variables.
+#' @format A data frame with 65036 observations on the following and 5 variables.
 #' \itemize{
-#' \item{\code{temp:}}{ daily maximum temperature in degrees C.}
-#' \item{\code{year:}}{ the year.}
-#' \item{\code{month:}}{ the month of the year.}
-#' \item{\code{day:}}{ day of the month.}
-#' \item{\code{date:}}{ date with the \code{\link[base:Dates]{Date}} class,
-#'   in the format YYYY-MM-DD.}
+#' \item \code{temp:} daily maximum temperature in degrees C.
+#' \item \code{year:} the year.
+#' \item \code{month:} the month of the year.
+#' \item \code{day:} day of the month.
+#' \item \code{date:} date with the \code{\link[base:Dates]{Date}} class,
+#'   in the format YYYY-MM-DD.
 #' }
 #' @note There are 5336 missing values.
 #' @source Klein Tank, A.M.G. and Coauthors, 2002. Daily dataset of
@@ -143,15 +142,14 @@
 #' recorded at the Uccle, Belgium during July for the years 1901 to 1999.
 #' The Station identifier in the source file is 17 and the Source identifier is
 #' 117882.  These data are analysed in Holesovsky and Fusek (2020).
-#' @format A data frame with 3100 observations on the following and 5
-#'   variables.
+#' @format A data frame with 3100 observations on the following and 5 variables.
 #' \itemize{
-#' \item{\code{temp:}}{ daily maximum temperature in degrees C.}
-#' \item{\code{year:}}{ the year.}
-#' \item{\code{month:}}{ the month of the year.}
-#' \item{\code{day:}}{ day of the month.}
-#' \item{\code{date:}}{ date with the \code{\link[base:Dates]{Date}} class,
-#'   in the format YYYY-MM-DD.}
+#' \item \code{temp:} daily maximum temperature in degrees C.
+#' \item \code{year:} the year.
+#' \item \code{month:} the month of the year.
+#' \item \code{day:} day of the month.
+#' \item \code{date:} date with the \code{\link[base:Dates]{Date}} class,
+#'   in the format YYYY-MM-DD.
 #' }
 #' @note There are 6 missing values, one located in each of the years
 #'   1925, 1926, 1956, 1963, 1969 and 1976.

R/kgaps.R

@@ -208,18 +208,18 @@ kgaps <- function(data, u, k = 1, inc_cens = TRUE) {
 #'     \theta q (S_0 + ... + S_N),}
 #'    where
 #'     \itemize{
-#'       \item{\eqn{q} is the threshold exceedance probability, estimated by
-#'         the proportion of threshold exceedances,}
-#'       \item{\eqn{N_0} is the number of uncensored sample \eqn{K}-gaps that
-#'         are equal to zero,}
-#'       \item{(apart from an adjustment for the contributions of \eqn{S_0}
+#'       \item \eqn{q} is the threshold exceedance probability, estimated by
+#'         the proportion of threshold exceedances,
+#'       \item \eqn{N_0} is the number of uncensored sample \eqn{K}-gaps that
+#'         are equal to zero,
+#'       \item (apart from an adjustment for the contributions of \eqn{S_0}
 #'         and \eqn{S_N}) \eqn{N_1} is the number of positive sample
-#'         \eqn{K}-gaps,}
-#'       \item{specifically, if \code{inc_cens = TRUE} then \eqn{N_1} is equal
+#'         \eqn{K}-gaps,
+#'       \item specifically, if \code{inc_cens = TRUE} then \eqn{N_1} is equal
 #'         to the number of \eqn{S_1, ..., S_{N-1}}{S_1, ..., S_(N-1)}
 #'         that are positive plus \eqn{(I_0 + I_N) / 2}, where \eqn{I_0 = 1} if
 #'         \eqn{S_0} is greater than zero and \eqn{I_0 = 0} otherwise, and
-#'         similarly for \eqn{I_N}.}
+#'         similarly for \eqn{I_N}.
 #'     }
 #'    The differing treatment of uncensored and right-censored \eqn{K}-gaps
 #'    reflects differing contributions to the likelihood.  Right-censored

R/spm_rcpp.R

@@ -100,12 +100,12 @@
 #'   \strong{no warning will be given until the returned object is printed} and,
 #'   for the affected estimator (\code{"N2015"} or \code{"BB2018/BB2018b"}),
 #'     \itemize{
-#'       \item{the corresponding estimated standard errors using sliding
-#'             blocks will be missing in \code{se_sl} in the returned object,}
-#'       \item{if \code{bias_adjust == "BB3"} then bias-adjustment
+#'       \item the corresponding estimated standard errors using sliding
+#'             blocks will be missing in \code{se_sl} in the returned object,
+#'       \item if \code{bias_adjust == "BB3"} then bias-adjustment
 #'             based on \code{bias_adjust == "BB1"} will instead be performed
 #'             when using sliding blocks, because the former relies on the
-#'             estimated variances of the estimators.}
+#'             estimated variances of the estimators.
 #'     }
 #'  Similarly, bias adjustment under \code{adjust = "BB3"} and/or subtraction
 #'  of \eqn{1 / b} in the \code{"BB2018b"} case may, rare cases, produce a