Formatted help file

markhogue · Apr 11, 2024 · 2b445ac · 2b445ac
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,4 +3,4 @@
 ^CRAN-RELEASE$
 ^cran-comments.md$
 ^README.Rmd$
-^NEWS.Rmd$
+^NEWS.Rmd$
diff --git a/.Rhistory b/.Rhistory
@@ -148,3 +148,25 @@ devtools::check_win_devel()
 devtools::check_rhub()
 devtools::release()
 devtools::release()
+# build and release
+roxygen2::roxygenise()
+devtools::spell_check()
+library(RadData)
+library(RadData)
+# build and release
+roxygen2::roxygenise()
+devtools::spell_check()
+devtools::check_win_devel()
+devtools::check_rhub()
+devtools::release()
+library(RadData)
+library(RadData)
+# build and release
+roxygen2::roxygenise()
+devtools::spell_check()
+devtools::check_win_devel()
+devtools::check_rhub()
+devtools::release()
+library(devtools)
+library(roxygen2)
+session_info()
diff --git a/CRAN-RELEASE b/CRAN-RELEASE
@@ -1,2 +1,2 @@
 This package was submitted to CRAN on 2021-04-12.
-Once it is accepted, delete this file and tag the release (commit 1cf40c2).
+Once it is accepted, delete this file and tag the release (commit 7f20f9b).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,29 +1,29 @@
-Package: RadData
-Version: 1.0.1
-Type: Package
-Title: Nuclear Decay Data for Dosimetric Calculations - ICRP 107
-Authors@R: c(person("Mark", "Hogue", role = c("aut", "cre"), email = "[email protected]"), person("KF", "Eckerman", role = c("dtc", "cph")), person("A", "Endo", role = c("dtc", "cph"))) 
-Description: Nuclear Decay Data for Dosimetric Calculations from the 
-    International Commission on Radiological Protection from ICRP 
-    Publication 107. Ann. ICRP 38 (3). Eckerman, Keith and Endo, Akira 2008 
-    <doi:10.1016/j.icrp.2008.10.004> 
-    <https://www.icrp.org/publication.asp?id=ICRP%20Publication%20107>. 
-    This is a database of the physical data needed in calculations of 
-    radionuclide-specific protection and operational quantities. The 
-    data is prescribed by the ICRP, the international authority on 
-    radiation dose standards, for estimating dose from the intake of or 
-    exposure to radionuclides in the workplace and the environment. 
-    The database contains information on the half-lives, decay chains, 
-    and yields and energies of radiations emitted in nuclear transformations 
-    of 1252 radionuclides of 97 elements. 
-License: GPL-2
-Copyright: Source data from ICRP 107 copyright 2008 Eckerman and Endo. 
-    See the file license.txt file for details.
-Encoding: UTF-8
-LazyData: true
-LazyDataCompression: xz
-RoxygenNote: 7.1.1
-Depends: R (>= 3.5.0)
-Suggests: radsafer
-URL: https://github.com/markhogue/RadData
-BugReports: https://github.com/markhogue/RadData/issues
+Package: RadData
+Version: 1.0.2
+Type: Package
+Title: Nuclear Decay Data for Dosimetric Calculations - ICRP 107
+Authors@R: c(person("Mark", "Hogue", role = c("aut", "cre"), email = "[email protected]"), person("KF", "Eckerman", role = c("dtc", "cph")), person("A", "Endo", role = c("dtc", "cph"))) 
+Description: Nuclear Decay Data for Dosimetric Calculations from the 
+    International Commission on Radiological Protection from ICRP 
+    Publication 107. Ann. ICRP 38 (3). Eckerman, Keith and Endo, Akira 2008 
+    <doi:10.1016/j.icrp.2008.10.004> 
+    <https://www.icrp.org/publication.asp?id=ICRP%20Publication%20107>. 
+    This is a database of the physical data needed in calculations of 
+    radionuclide-specific protection and operational quantities. The 
+    data is prescribed by the ICRP, the international authority on 
+    radiation dose standards, for estimating dose from the intake of or 
+    exposure to radionuclides in the workplace and the environment. 
+    The database contains information on the half-lives, decay chains, 
+    and yields and energies of radiations emitted in nuclear transformations 
+    of 1252 radionuclides of 97 elements. 
+License: GPL-2
+Copyright: Source data from ICRP 107 copyright 2008 Eckerman and Endo. 
+    See the file license.txt file for details.
+Encoding: UTF-8
+LazyData: true
+LazyDataCompression: xz
+RoxygenNote: 7.3.1
+Depends: R (>= 3.5.0)
+Suggests: radsafer
+URL: https://github.com/markhogue/RadData
+BugReports: https://github.com/markhogue/RadData/issues
diff --git a/NEWS.Rmd b/NEWS.Rmd
@@ -13,5 +13,5 @@ knitr::opts_chunk$set(
   out.width = "100%"
 )
 ```
-# RadData (version 1.0.1 )
-Added `LazyDataCompression: xz` to Description to help with file download size. Fixed the name of branch_4 in "ICRP_07.NDX". It was previously without the number at the end (branch_).  
+# RadData (version 1.0.2 )
+Changed formats in data.R file to improve readability of help file.  
diff --git a/News.md b/News.md
@@ -1,8 +1,6 @@
 
 <!-- News.md is generated from News.Rmd. Please edit that file -->
 
-# RadData (version 1.0.1 )
+# RadData (version 1.0.2 )
 
-Added `LazyDataCompression: xz` to Description to help with file
-download size. Fixed the name of branch\_4 in “ICRP\_07.NDX”. It was
-previously without the number at the end (branch\_).
+Changed formats in data.R file to improve readability of help file.
diff --git a/R/data.R b/R/data.R
@@ -4,37 +4,69 @@
 #'
 #' @format A \code{tibble} with 32 variables, 31 original variables from ICRP, plus the derived decay_constant variable.
 #' \describe{
+#' 
 #' \code{RN} Name of nuclide; e.g. Am-241, Tc-99m
+#' 
 #' \code{half_life} Half-life of nuclide. Caution - units vary.
+#' 
 #' \code{units} Half-life units: ls, microsecond; ms, millisecond; s, second; m, minute; d, day; y, year
+#' 
 #' \code{decay_mode} A, alpha; B-, beta minus; B+, beta plus; EC, electron capture; IT, isomeric transition; SF, spontaneous fission
+#' 
 #' \code{pointer_rad} Not functional. Originally, location of nuclide in the ICRP_07.RAD file
+#' 
 #' \code{pointer_bet}  Not functional. Originally, location of nuclide in ICRP_07.BET file
+#' 
 #' \code{pointer_ack}  Not functional. Originally, location of nuclide in ICRP_07.ACK file
+#' 
 #' \code{pointer_nsf}  Not functional. Originally, location of nuclide in ICRP_07.NSF file
+#' 
 #' \code{progeny_1}  Radioactive progeny number 1
+#' 
 #' \code{pointer_1}  Location of progeny number 1 in RN dataset
+#' 
 #' \code{branch_1}  Branching fraction to progeny number 1
+#' 
 #' \code{progeny_2}  Radioactive progeny number 2
+#' 
 #' \code{pointer_2}  Location of progeny number 2 in RN dataset
+#' 
 #' \code{branch_2}  Branching fraction to progeny number 2
+#' 
 #' \code{progeny_3}  Radioactive progeny number 3
+#' 
 #' \code{pointer_3}  Location of progeny number 3 in RN dataset
+#' 
 #' \code{branch_3}  Branching fraction to progeny number 3
+#' 
 #' \code{progeny_4}  Radioactive progeny number 4
+#' 
 #' \code{pointer_4}  Location of progeny number 4 in RN dataset
+#' 
 #' \code{branch_4}  Branching fraction to progeny number 4
+#' 
 #' \code{E_alpha}  Energy of alpha emissions (MeV/nuclear transformation)
+#' 
 #' \code{E_electron}  Energy of electrons, including beta (MeV/nuclear transformation)
+#' 
 #' \code{E_photon}  Energy of photon emission (MeV/nuclear transformation)
+#' 
 #' \code{num_phot_lt_10k}  Number of photons of energy less than 10 keV
+#' 
 #' \code{num_phot_gt_10k}  Number of photons of energy greater than 10 keV
+#' 
 #' \code{num_betas}  Number of beta transitions
+#' 
 #' \code{num_mono_e}  Number of mono-energetic electrons
+#' 
 #' \code{num_alpha}  Number of alpha transitions
+#' 
 #' \code{AMU}  Atomic mass of radionuclide (Audi et al., 2003)
+#' 
 #' \code{air_kerma_rate_const}  Air-kerma rate constant (Gy-m^2/Bq s)
+#' 
 #' \code{air_kerma_coef} Point source air-kerma coefficient (Gy-m^2/Bq s)
+#' 
 #' \code{decay_constant} Decay constant in inverse seconds.
 #' }
 "ICRP_07.NDX"
@@ -45,11 +77,17 @@
 #'
 #' @format A \code{tibble} with 6 variables.
 #' \describe{
+#' 
 #' \code{RN}  Nuclide name, e.g. Tc-99m
+#' 
 #' \code{code_AN}  Short alphanumeric code for radiation type. See rad_codes for description.
+#'  
 #' \code{E_MeV}  Numeric. Energy of the radiation in MeV
+#' 
 #' \code{prob}  Numeric. Yield of the radiation (/nuclear transformation)
+#' 
 #' \code{code_num}  Numeric code for radiation type. See rad_codes for description.
+#' 
 #' \code{is_photon} Logical. Allows selection of all photons.
 #' }
 "ICRP_07.RAD"
@@ -60,18 +98,25 @@
 #'
 #' @format A \code{tibble} with 3 variables.
 #' \describe{
-#' \code{code_num}  Numeric code for radiation type. See rad_codes for description.
-#' \code{code_AN}  Short alphanumeric code for radiation type. See rad_codes for description.
-#' \code{description}  Short textual description
+#' A table used for cross-linking  numerical, alphabetical and textual references for a radiation emission type, such as: 1, G, Gamma Rays.
+#' 
+#' \code{code_num}  Numeric code for radiation type. 
+#' 
+#' \code{code_AN}  Alphabetical abbreviation, some with + or -.
+#' 
+#' \code{description} Description of radiation emission type.   
 #' }
 "rad_codes"
 
 #' Beta data
 #'
 #' @format A \code{tibble} with 3 variables.
 #' \describe{
+#' 
 #' \code{RN}  Nuclide name, e.g. Tc-99m
+#' 
 #' \code{E_MeV}  Energy grid point (MeV)
+#' 
 #' \code{A} Number of beta particles per MeV per nuclear transformation at this energy
 #' }
 "ICRP_07.BET"
diff --git a/README.Rmd b/README.Rmd
@@ -39,7 +39,7 @@ The development version from GitHub:
 devtools::install_github("markhogue/RadData")
 ```
 
-## Oveview
+## Overview
 To start using the installed package: 
 
 ```{r}

diff --git a/README.md b/README.md
@@ -1,22 +1,30 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-RadData <img src='man/figures/RadData.png' align="right" height="139" />
-========================================================================
 
-This package contains data from the International Commission on Radiological Protection (ICRP) Publication 107, Nuclear Decay Data for Dosimetric Calculations. The data sets were converted from the original to a tidy data set. The files include:
+# RadData <img src='man/figures/RadData.png' align="right" height="139" />
 
--   ICRP-07.NDX The index file has 32 variables, including 31 original variables from ICRP. The 32nd variable is a derived decay\_constant variable in inverse seconds, to allow activity computation without unit conversion issues.
+This package contains data from the International Commission on
+Radiological Protection (ICRP) Publication 107, Nuclear Decay Data for
+Dosimetric Calculations. The data sets were converted from the original
+to a tidy data set. The files include:
 
--   ICRP-07.RAD Data on the energy and yield of each radiation emitted in nuclear transformations of the radionuclide.
+- ICRP-07.NDX The index file has 32 variables, including 31 original
+  variables from ICRP. The 32nd variable is a derived decay_constant
+  variable in inverse seconds, to allow activity computation without
+  unit conversion issues.
 
--   rad\_codes A small table providing descriptions of the codes used in ICRP-07.RAD.
+- ICRP-07.RAD Data on the energy and yield of each radiation emitted in
+  nuclear transformations of the radionuclide.
 
--   ICRP-07.BET Beta decay spectra for beta emitters.
+- rad_codes A small table providing descriptions of the codes used in
+  ICRP-07.RAD.
 
-Installation
-------------
+- ICRP-07.BET Beta decay spectra for beta emitters.
 
-You can install the released version of RadData from [CRAN](https://CRAN.R-project.org) (after it has been released) with:
+## Installation
+
+You can install the released version of RadData from
+[CRAN](https://CRAN.R-project.org) (after it has been released) with:
 
 ``` r
 install.packages("RadData")
@@ -29,28 +37,43 @@ The development version from GitHub:
 devtools::install_github("markhogue/RadData")
 ```
 
-Oveview
--------
+## Overview
 
 To start using the installed package:
 
 ``` r
 library(RadData)
 ```
 
-Functions for selecting and filtering data for health physics computations will be included in the package `radsafer`.
+Functions for selecting and filtering data for health physics
+computations will be included in the package `radsafer`.
 
-Source Data
------------
+## Source Data
 
-Source data is from ICRP 107 copyright 2008 Eckerman and Endo. This data is provided with the following text in the license.txt file:
+Source data is from ICRP 107 copyright 2008 Eckerman and Endo. This data
+is provided with the following text in the license.txt file:
 
 ICRP-07 Data Files Copyright Notice
 
-Copyright (C) 2008 A. Endo and K.F. Eckerman, Authors. All Rights Reserved.
-
-Permission is hereby granted to any person obtaining a copies of the ICRP-07 data files and associated documentation to use, copy, and distribute these materials and the documentation for educational, research, and not-for-profit purposes, without fee and without a signed licensing agreement provided that the file LICENSE.TXT containing the above copyright notice, this paragraph and the following two paragraphs appears in all copies, modifications, and distributions.
-
-IN NO EVENT SHALL THE AUTHORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THE SOFTWARE, ITS DATA FILES, AND THE DOCUMENTATION.
-
-THE AUTHORS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE, DATA FILES AND ACCOMPANYING DOCUMENTATION PROVIDED HEREUNDER IS PROVIDED "AS IS". THE AUTHORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, FUTURE UPDATES, ENHANCEMENTS, OR MODIFICATIONS TO THE SOFTWARE.
+Copyright (C) 2008 A. Endo and K.F. Eckerman, Authors. All Rights
+Reserved.
+
+Permission is hereby granted to any person obtaining a copies of the
+ICRP-07 data files and associated documentation to use, copy, and
+distribute these materials and the documentation for educational,
+research, and not-for-profit purposes, without fee and without a signed
+licensing agreement provided that the file LICENSE.TXT containing the
+above copyright notice, this paragraph and the following two paragraphs
+appears in all copies, modifications, and distributions.
+
+IN NO EVENT SHALL THE AUTHORS BE LIABLE TO ANY PARTY FOR DIRECT,
+INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST
+PROFITS, ARISING OUT OF THE USE OF THE SOFTWARE, ITS DATA FILES, AND THE
+DOCUMENTATION.
+
+THE AUTHORS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE. THE SOFTWARE, DATA FILES AND ACCOMPANYING
+DOCUMENTATION PROVIDED HEREUNDER IS PROVIDED “AS IS”. THE AUTHORS HAVE
+NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, FUTURE UPDATES,
+ENHANCEMENTS, OR MODIFICATIONS TO THE SOFTWARE.
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,5 @@
 ## Test environments
-* local Windows 10 home version 1803, R 3.5.3
-* Fedora 29 (on R-hub builder), R 4.0.5
+* local Windows 11 Home version 22H2, R 4.3.3
 
 ## R CMD check results
 There were no errors, warnings or notes.

diff --git a/man/ICRP_07.BET.Rd b/man/ICRP_07.BET.Rd