version release

.Rbuildignore

@@ -3,3 +3,4 @@
 ^spirobankR\.Rproj$
 ^\.Rproj\.user$
 spiro_trash
+^LICENSE\.md$

DESCRIPTION

@@ -1,15 +1,14 @@
 Package: spirobankR
-Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
+Title: Read and Analyze Spirobank Data
+Version: 1.0.0
 Authors@R: 
-    person(given = "First",
-           family = "Last",
+    person(given = "Chris",
+           family = "Wolfe",
            role = c("aut", "cre"),
-           email = "first.last@example.com",
+           email = "wolfe.christopherlee@gmail.com",
            comment = c(ORCID = "YOUR-ORCID-ID"))
-Description: What the package does (one paragraph).
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
-    license
+Description: spirobanR includes funtions to read and summarize PDF and SQL Spirobank data.
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
@@ -20,4 +19,8 @@ Imports:
     DBI,
     dplyr,
     tidyr,
-    purrr
+    purrr,
+    lubridate,
+    tibble,
+    pdftools,
+    stringr

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2022
+COPYRIGHT HOLDER: spirobankR authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2022 spirobankR authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

R/get_summary_values.R

@@ -8,7 +8,7 @@
 #'
 #' @param df a data frame created by `read_spiro_sql()` or `read_spiro_pdf().`
 #' @param grp_vars character; string of column names to used to calculate maximum values by group (i.e. 'id', 'spiro_test', etc.).
-#' See \code{\link[dplyr]{dplyr::group_by()}}.
+#' See \link[dplyr]{group_by}.
 #' @param sum_fun character; summary function to be applied.  Must be one of c("max," "mean," "sd," "median," "min").
 #' @param basic_parameters logical; if TRUE, the default, only values for the following parameters are returned:
 #' - FEV1

R/read_ispiro_pdf.R

@@ -1,8 +1,8 @@
 
-#' Read iSpirometry PDF Export
+#' Read iSpirometry PDF Files
 #'
-#'`read_ispirometry_pdf()` reads exported PDF files from the iSpirometry phone app. Text is extracted using
-#'the Tesseract OCR engine ([Tesseract](https://cran.r-project.org/web/packages/tesseract/vignettes/intro.html))
+#'`read_ispirometry_pdf()` reads exported PDF files from the iSpirometry phone app. Text is
+#'extracted using the Tesseract OCR engine ([Tesseract](https://cran.r-project.org/web/packages/tesseract/vignettes/intro.html))
 #'
 #' @param pdf character; path of of iSpirometry PDF export.
 #' @param pages numeric; vector of page numbers to extract. If NULL, the default, all pages are extracted.
@@ -15,26 +15,29 @@
 #' data collection by individual patents. Default is NULL.
 #' @param sample_id user defined string to denote sample ID. If assigned, a
 #' value must also be supplied to `sample_col`. Default is NULL.
-#' @param test_threshold numeric; allows a user to partition Spirobank trials into discrete tests according to a user defined
-#' threshold value (seconds). If the time difference between the last trial and and a new trial exceeds the threshold value,
-#' the current trial is designated as belonging to a new test. For example, the threshold value is set at 600 seconds (10 minutes)
-#' and a patient performs 6 trials. The first 3 trials are done consecutively within 10 minutes. The fourth trial occurs
-#' about one hour after the third. The fifth and sixth trial are completed within 10 minutes of the fourth trial.
-#' These six trials represent two separate testing sessions according the user defined threshold. Spirobank test number is indicated
-#' under the column `spiro_test.`
+#' @param test_threshold numeric; allows a user to partition Spirobank trials into discrete
+#' tests according to a user defined threshold value (seconds). If the time difference
+#' between the last trial and and a new trial exceeds the threshold value, the current
+#' trial is designated as belonging to a new test. For example, the threshold value is
+#' set at 600 seconds (10 minutes) and a patient performs 6 trials. The first 3 trials are
+#' done consecutively within 10 minutes. The fourth trial occurs about one hour after the
+#' third. The fifth and sixth trial are completed within 10 minutes of the fourth trial. These
+#' six trials represent two separate testing sessions according the user defined threshold.
+#' Spirobank test number is indicated under the column `spiro_test.`
 #'#'
 #' @export
 #'
 #' @examples
 #'
 #' \dontrun{
-#' read_ispiro_pdf(pdf, pages = NULL, tzone = 'America/New_York', participant_id = NULL, sample_col = NULL,
-#'                 sample_id = NULL, test_threshold = NULL)
+#' read_ispiro_pdf(pdf, pages = NULL, tzone = 'America/New_York', participant_id = NULL,
+#'                 sample_col = NULL, sample_id = NULL, test_threshold = NULL)
 #' }
 #'
 #'
-read_ispirometry_pdf <- function(pdf, pages = NULL, tzone = 'America/New_York', participant_id = NULL, sample_col = NULL,
-                            sample_id = NULL, test_threshold = NULL) {
+read_ispirometry_pdf <- function(pdf, pages = NULL, tzone = 'America/New_York',
+                                 participant_id = NULL,sample_col = NULL, sample_id = NULL,
+                                 test_threshold = NULL) {
 
   if(sum(!is.null(sample_col), !is.null(sample_id)) == 1) {
     stop('  Both `sample_col` and `sample_id` must have values.', call. = FALSE)