From 574c2b1ed079ee7e39d191f6f2fae2c92cacfb7b Mon Sep 17 00:00:00 2001
From: npaterno <nicholas.paterno@gmail.com>
Date: Tue, 24 Jun 2025 10:50:02 -0700
Subject: [PATCH 1/4] dds.discr fix

---
 R/{data-dds.dscr.R => data-dds.discr.R} |  9 +++---
 man/dds.dscr.Rd                         | 43 -------------------------
 2 files changed, 4 insertions(+), 48 deletions(-)
 rename R/{data-dds.dscr.R => data-dds.discr.R} (84%)
 delete mode 100644 man/dds.dscr.Rd

diff --git a/R/data-dds.dscr.R b/R/data-dds.discr.R
similarity index 84%
rename from R/data-dds.dscr.R
rename to R/data-dds.discr.R
index ccf8d21f..9e6cdafd 100644
--- a/R/data-dds.dscr.R
+++ b/R/data-dds.discr.R
@@ -10,7 +10,7 @@
 #' protect the rights and privacy of specific individual consumers. The provided
 #' data set is based on actual attributes of consumers."
 #'
-#' @name dds.dscr
+#' @name dds.discr
 #' @docType data
 #' @format A dataframe with 1000 rows and 6 variables:
 #'    \describe{
@@ -27,10 +27,9 @@
 #'       \code{Multi Race}, \code{Native Hawaiian}, \code{Other},
 #'       \code{White not Hispanic}}
 #'   }
-#'   #' @references www.amstat.org/publications/jse/v22n1/mickel.pdf Taylor, Stanley A.,
-#'   and Amy E. Mickel. Simpson's paradox: A data set and discrimination case study
-#'   exercise. Journal of Statistics Education 22.1 (2014).
-#'   Data contained in supplement B of Taylor and Mickel.
+#'   @references Taylor, Stanley A., and Amy E. Mickel. Simpson's paradox: A data
+#'   set and discrimination case study exercise. Journal of Statistics Education
+#'   22.1 (2014). Data contained in supplement B of Taylor and Mickel.
 #'
 "dds.discr"
 
diff --git a/man/dds.dscr.Rd b/man/dds.dscr.Rd
deleted file mode 100644
index 90e3b47e..00000000
--- a/man/dds.dscr.Rd
+++ /dev/null
@@ -1,43 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data-dds.dscr.R
-\docType{data}
-\name{dds.dscr}
-\alias{dds.dscr}
-\alias{dds.discr}
-\title{A dataset on disbursements from the California Department of Developmental Services (DDS)}
-\format{
-A dataframe with 1000 rows and 6 variables:
-\describe{
-\item{\code{id}}{Numeric, Unique identification code for each resident}
-\item{\code{age.cohort}}{A factor, \code{0-5} years,
-\code{6-12} years, \code{13-17} years, \code{18-21} years, \code{22-50} years,
-and \code{51+} years}
-\item{\code{age}}{Numeric, Age measured in years}
-\item{\code{gender}}{A factor, with levels  \code{Female} or \code{Male}}
-\item{\code{expenditures}}{Numeric, Amount of expenditures spent by the
-State on an individual annually, measured in USD}
-\item{\code{ethnicity}}{Factor, Ethnic group, recorded as
-\code{American Indian},  \code{Asian}, \code{Black}, \code{Hispanic},
-\code{Multi Race}, \code{Native Hawaiian}, \code{Other},
-\code{White not Hispanic}}
-}
-#' @references www.amstat.org/publications/jse/v22n1/mickel.pdf Taylor, Stanley A.,
-and Amy E. Mickel. Simpson's paradox: A data set and discrimination case study
-exercise. Journal of Statistics Education 22.1 (2014).
-Data contained in supplement B of Taylor and Mickel.
-}
-\usage{
-dds.discr
-}
-\description{
-The dataset represents a sample of 1,000 DDS consumers (out of a total
-population of approximately 250,000),and includes information about age,
-gender, ethnicity, and the amount of financial support per consumer provided
-by the DDS.The dataset is based on recorded attributes of consumers, but has
-been altered to maintain consumer privacy.  From the Taylor and Mickel paper:
-"The data set originated from DDS’s Client Master File. In order to remain in
-compliance with California State Legislation, the data have been altered to
-protect the rights and privacy of specific individual consumers. The provided
-data set is based on actual attributes of consumers."
-}
-\keyword{datasets}

From d9644526d339bd1819c6f677b54ad0f7a78913c0 Mon Sep 17 00:00:00 2001
From: npaterno <nicholas.paterno@gmail.com>
Date: Tue, 24 Jun 2025 11:07:44 -0700
Subject: [PATCH 2/4] cdc data fixes

---
 R/data-cdc.R      |  5 +++--
 R/data-cdc.samp.R |  2 +-
 man/cdc.Rd        |  5 +++--
 man/cdc.samp.Rd   |  2 +-
 man/dds.discr.Rd  | 41 +++++++++++++++++++++++++++++++++++++++++
 5 files changed, 49 insertions(+), 6 deletions(-)
 create mode 100644 man/dds.discr.Rd

diff --git a/R/data-cdc.R b/R/data-cdc.R
index e7368c1d..032eeeb6 100644
--- a/R/data-cdc.R
+++ b/R/data-cdc.R
@@ -2,7 +2,8 @@
 #'
 #' A dataset from the 2000 Behavioral Risk Factors Surveillance System (BRFSS)
 #' conducted by the US Centers for Disease Control and Prevention used to
-#' illustrate inference on demographic data.
+#' illustrate inference on demographic data. The dataset is a random sample of 20,000
+#' participants drawn from 350,000 interviews from that year.
 #'
 #' @name cdc
 #' @docType data
@@ -22,6 +23,6 @@
 #'    \item{\code{age}}{Numeric;  respondent's age in years.}
 #'    \item{\code{gender}}{Factor with two levels \code{m} \code{f}}
 #'    }
-#' @source("https://www.cdc.gov/brfss/index.html")
+#' @source \url{https://www.cdc.gov/brfss/index.html}
 #'
 "cdc"
diff --git a/R/data-cdc.samp.R b/R/data-cdc.samp.R
index 19202156..8ce9137f 100644
--- a/R/data-cdc.samp.R
+++ b/R/data-cdc.samp.R
@@ -21,6 +21,6 @@
 #'    \item{\code{age}}{Numeric;  respondent's age in years.}
 #'    \item{\code{gender}}{Factor with two levels \code{m} \code{f}}
 #'    }
-#' @source("http://www.openintro.org/stat/data/cdc.R")
+#' @source \url{http://www.openintro.org/stat/data/cdc.R}
 #'
 "cdc.samp"
diff --git a/man/cdc.Rd b/man/cdc.Rd
index 59792761..22a7b7a6 100644
--- a/man/cdc.Rd
+++ b/man/cdc.Rd
@@ -23,7 +23,7 @@ cigarettes in their entire life and 0 otherwise.}
 }
 }
 \source{
-("https://www.cdc.gov/brfss/index.html")
+\url{https://www.cdc.gov/brfss/index.html}
 }
 \usage{
 cdc
@@ -31,6 +31,7 @@ cdc
 \description{
 A dataset from the 2000 Behavioral Risk Factors Surveillance System (BRFSS)
 conducted by the US Centers for Disease Control and Prevention used to
-illustrate inference on demographic data.
+illustrate inference on demographic data. The dataset is a random sample of 20,000
+participants drawn from 350,000 interviews from that year.
 }
 \keyword{datasets}
diff --git a/man/cdc.samp.Rd b/man/cdc.samp.Rd
index d3231fb5..e904f4d5 100644
--- a/man/cdc.samp.Rd
+++ b/man/cdc.samp.Rd
@@ -23,7 +23,7 @@ cigarettes in their entire life and 0 otherwise.}
 }
 }
 \source{
-("http://www.openintro.org/stat/data/cdc.R")
+\url{http://www.openintro.org/stat/data/cdc.R}
 }
 \usage{
 cdc.samp
diff --git a/man/dds.discr.Rd b/man/dds.discr.Rd
new file mode 100644
index 00000000..3ad98580
--- /dev/null
+++ b/man/dds.discr.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data-dds.discr.R
+\docType{data}
+\name{dds.discr}
+\alias{dds.discr}
+\title{A dataset on disbursements from the California Department of Developmental Services (DDS)}
+\format{
+A dataframe with 1000 rows and 6 variables:
+\describe{
+\item{\code{id}}{Numeric, Unique identification code for each resident}
+\item{\code{age.cohort}}{A factor, \code{0-5} years,
+\code{6-12} years, \code{13-17} years, \code{18-21} years, \code{22-50} years,
+and \code{51+} years}
+\item{\code{age}}{Numeric, Age measured in years}
+\item{\code{gender}}{A factor, with levels  \code{Female} or \code{Male}}
+\item{\code{expenditures}}{Numeric, Amount of expenditures spent by the
+State on an individual annually, measured in USD}
+\item{\code{ethnicity}}{Factor, Ethnic group, recorded as
+\code{American Indian},  \code{Asian}, \code{Black}, \code{Hispanic},
+\code{Multi Race}, \code{Native Hawaiian}, \code{Other},
+\code{White not Hispanic}}
+}
+@references Taylor, Stanley A., and Amy E. Mickel. Simpson's paradox: A data
+set and discrimination case study exercise. Journal of Statistics Education
+22.1 (2014). Data contained in supplement B of Taylor and Mickel.
+}
+\usage{
+dds.discr
+}
+\description{
+The dataset represents a sample of 1,000 DDS consumers (out of a total
+population of approximately 250,000),and includes information about age,
+gender, ethnicity, and the amount of financial support per consumer provided
+by the DDS.The dataset is based on recorded attributes of consumers, but has
+been altered to maintain consumer privacy.  From the Taylor and Mickel paper:
+"The data set originated from DDS’s Client Master File. In order to remain in
+compliance with California State Legislation, the data have been altered to
+protect the rights and privacy of specific individual consumers. The provided
+data set is based on actual attributes of consumers."
+}
+\keyword{datasets}

From 3f08f9be6aa899c079aaac5220f9d29f119fede8 Mon Sep 17 00:00:00 2001
From: npaterno <nicholas.paterno@gmail.com>
Date: Tue, 24 Jun 2025 11:16:21 -0700
Subject: [PATCH 3/4] danish fix

---
 R/data-danish.ed.primary.R |  2 +-
 man/danish.ed.primary.Rd   | 12 +++++++-----
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/R/data-danish.ed.primary.R b/R/data-danish.ed.primary.R
index 090a167a..b40c6dc7 100644
--- a/R/data-danish.ed.primary.R
+++ b/R/data-danish.ed.primary.R
@@ -46,7 +46,7 @@
 #'    \item{\code{icu.status}}{factor, patient admitted to ICU, values \code{yes},
 #'    \code{no}}
 #'    }
-#'    #' @references Kristensen, Michael, et al. "Routine blood tests are associated
+#' @references Kristensen, Michael, et al. "Routine blood tests are associated
 #' with short term mortality and can improve emergency department triage: a cohort
 #'  study of> 12,000 patients." Scandinavian Journal of Trauma, Resuscitation and
 #'  Emergency Medicine 25 (2017): 1-8.
diff --git a/man/danish.ed.primary.Rd b/man/danish.ed.primary.Rd
index 5ed00a36..dcaa07c4 100644
--- a/man/danish.ed.primary.Rd
+++ b/man/danish.ed.primary.Rd
@@ -40,11 +40,6 @@ value 99999 indicates patient not admitted to ICU}
 \item{\code{icu.status}}{factor, patient admitted to ICU, values \code{yes},
 \code{no}}
 }
-#' @references Kristensen, Michael, et al. "Routine blood tests are associated
-with short term mortality and can improve emergency department triage: a cohort
-study of> 12,000 patients." Scandinavian Journal of Trauma, Resuscitation and
-Emergency Medicine 25 (2017): 1-8.
-\url{https://sjtrem.biomedcentral.com/articles/10.1186/s13049-017-0458-x?report=reader}
 }
 \source{
 \url{doi:10.5061/dryad.m2bq5}
@@ -63,4 +58,11 @@ training data (called primary data in the original manuscript) used for model
 building. Some variable names have been changed for readability, but the data
 on 21 variables for the 6,249 participants are otherwise unchanged.
 }
+\references{
+Kristensen, Michael, et al. "Routine blood tests are associated
+with short term mortality and can improve emergency department triage: a cohort
+study of> 12,000 patients." Scandinavian Journal of Trauma, Resuscitation and
+Emergency Medicine 25 (2017): 1-8.
+\url{https://sjtrem.biomedcentral.com/articles/10.1186/s13049-017-0458-x?report=reader}
+}
 \keyword{datasets}

From 68f64be3564be5cfad4b3acf9ee473d1f111fb26 Mon Sep 17 00:00:00 2001
From: npaterno <nicholas.paterno@gmail.com>
Date: Tue, 24 Jun 2025 11:30:10 -0700
Subject: [PATCH 4/4] remaining fixes

---
 R/data-forest.birds.R | 2 +-
 R/data-prevend.R      | 2 +-
 R/data-prevend.samp.R | 2 +-
 R/data-swim.R         | 2 +-
 R/data-thermometry.R  | 2 +-
 man/forest.birds.Rd   | 2 +-
 man/prevend.Rd        | 2 +-
 man/prevend.samp.Rd   | 2 +-
 man/swim.Rd           | 4 +++-
 man/thermometry.Rd    | 2 +-
 10 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/R/data-forest.birds.R b/R/data-forest.birds.R
index d443b1a3..bfe01851 100644
--- a/R/data-forest.birds.R
+++ b/R/data-forest.birds.R
@@ -35,6 +35,6 @@
 #'     Saunders DA, Arnold GW, Burbridge AA, and Hopkins AJM eds. Surrey Beatty and Sons,
 #'     Chipping Norton, NSW, 65-77, 1987.  Logan, M 2011 Biostatistical Design and
 #'     Analysis Using R.  Wiley-Blackwell, Chapter 9
-#' @source https://users.monash.edu.au/~murray/BDAR/  Listed under chapter 9 datasets
+#' @source \url{https://users.monash.edu.au/~murray/BDAR/}  Listed under chapter 9 datasets
 #'
 "forest.birds"
diff --git a/R/data-prevend.R b/R/data-prevend.R
index 1479cc22..ccab87cf 100644
--- a/R/data-prevend.R
+++ b/R/data-prevend.R
@@ -62,7 +62,7 @@
 #'   \item{\code{Match_2}}{Numeric, statin users and non-users matched 1:1 on Framingham risk score.
 #'   Matched pairs share a common integer label. -1 indicates participant not matched}
 #' }
-#' @references{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115755}
+#' @references \url{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115755}
 #' @source \url{http://doi.org/10.5061/dryad.6qs53}
 
 "prevend"
diff --git a/R/data-prevend.samp.R b/R/data-prevend.samp.R
index f178fe67..1203954f 100644
--- a/R/data-prevend.samp.R
+++ b/R/data-prevend.samp.R
@@ -59,7 +59,7 @@
 #'   \item{\code{Match_2}}{Numeric, statin users and non-users matched 1:1 on Framingham risk score.
 #'   Matched pairs share a common integer label. -1 indicates participant not matched}
 #' }
-#' @references{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115755}
+#' @references \url{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115755}
 #' @source \url{http://doi.org/10.5061/dryad.6qs53}
 #'
 "prevend.samp"
diff --git a/R/data-swim.R b/R/data-swim.R
index 6c1b5d9f..20bd1098 100644
--- a/R/data-swim.R
+++ b/R/data-swim.R
@@ -21,7 +21,7 @@
 #'     \item{\code{velocity.diff}}{Numeric, \code{wet.suit.velocity
 #'          - swim.suit.velocity}}
 #'  }
-#'  #' @source \url{https://doi.org/10.1016/S1440-2440(00)80042-0}
+#' @source \url{https://doi.org/10.1016/S1440-2440(00)80042-0}
 #' @references Table 3 of De Lucas, Ricardo Dantas, et al. The effects of wet
 #'       suits on physiological and biomechanical indices during swimming.
 #'       Journal of Science and Medicine in Sport 3.1 (2000): 1-8.
diff --git a/R/data-thermometry.R b/R/data-thermometry.R
index 6a1b94cb..7d89efd3 100644
--- a/R/data-thermometry.R
+++ b/R/data-thermometry.R
@@ -14,7 +14,7 @@
 #'      \code{female}, \code{male}}
 #'    \item{\code{heart.rate}}{Numeric, heart rate, in beats per minute}
 #'    }
-#' @source{http://jse.amstat.org/v4n2/datasets.shoemaker.html}
+#' @source \url{http://jse.amstat.org/v4n2/datasets.shoemaker.html}
 #' @references Mackowiak, P. A., Wasserman, S. S., and Levine, M. M. (1992),
 #'      A Critical Appraisal of 98.6 Degrees F, the Upper Limit of the
 #'      Normal Body Temperature, and Other Legacies of Carl Reinhold August Wunderlich,
diff --git a/man/forest.birds.Rd b/man/forest.birds.Rd
index ec5da0a5..bc92326a 100644
--- a/man/forest.birds.Rd
+++ b/man/forest.birds.Rd
@@ -26,7 +26,7 @@ time study was conducted (1983).Computed as 1983 - year.of.isolation}
 }
 }
 \source{
-https://users.monash.edu.au/~murray/BDAR/  Listed under chapter 9 datasets
+\url{https://users.monash.edu.au/~murray/BDAR/}  Listed under chapter 9 datasets
 }
 \usage{
 forest.birds
diff --git a/man/prevend.Rd b/man/prevend.Rd
index 70be0643..37c9e1e1 100644
--- a/man/prevend.Rd
+++ b/man/prevend.Rd
@@ -74,6 +74,6 @@ which participants completed in 2003-2006;
 data are provided for 4,095 individuals who completed cognitive testing with RFFT.
 }
 \references{
-{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115755}
+\url{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115755}
 }
 \keyword{datasets}
diff --git a/man/prevend.samp.Rd b/man/prevend.samp.Rd
index a3d491eb..a6822762 100644
--- a/man/prevend.samp.Rd
+++ b/man/prevend.samp.Rd
@@ -71,6 +71,6 @@ Random sample of size 500 from the 4,095 cases in the prevend dataset with all
 31 variables.
 }
 \references{
-{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115755}
+\url{https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115755}
 }
 \keyword{datasets}
diff --git a/man/swim.Rd b/man/swim.Rd
index 6ebf33c1..9cbb46af 100644
--- a/man/swim.Rd
+++ b/man/swim.Rd
@@ -18,7 +18,9 @@ a swim suit, in meters/sec}
 \item{\code{velocity.diff}}{Numeric, \code{wet.suit.velocity
          - swim.suit.velocity}}
 }
-#' @source \url{https://doi.org/10.1016/S1440-2440(00)80042-0}
+}
+\source{
+\url{https://doi.org/10.1016/S1440-2440(00)80042-0}
 }
 \usage{
 swim
diff --git a/man/thermometry.Rd b/man/thermometry.Rd
index e639682d..4563fb24 100644
--- a/man/thermometry.Rd
+++ b/man/thermometry.Rd
@@ -15,7 +15,7 @@ A tibble with 130 rows and 3 variables:
 }
 }
 \source{
-{http://jse.amstat.org/v4n2/datasets.shoemaker.html}
+\url{http://jse.amstat.org/v4n2/datasets.shoemaker.html}
 }
 \usage{
 thermometry