From 26ff4720ee5c4246a4587c5fb7a6b83417a0851c Mon Sep 17 00:00:00 2001
From: wright13 <s.wright.618@gmail.com>
Date: Wed, 22 May 2024 16:22:57 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20national?=
 =?UTF-8?q?parkservice/imd-ccal@e51599c2dd10eac17da668ebf740705a91b2f395?=
 =?UTF-8?q?=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                                       | 2 +-
 authors.html                                   | 6 +++---
 index.html                                     | 2 +-
 pkgdown.yml                                    | 2 +-
 reference/getCCALData.html                     | 2 +-
 reference/imdccal-package.html                 | 2 +-
 reference/index.html                           | 2 +-
 reference/listParamsInData.html                | 2 +-
 reference/listParamsInQuestionableResults.html | 2 +-
 reference/machineReadableCCAL.html             | 2 +-
 reference/rangeToVector.html                   | 2 +-
 search.json                                    | 2 +-
 12 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/404.html b/404.html
index 6f66788..a609841 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="https://nationalparkservice.github.io/imd-ccal/index.html">imdccal</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 0f2865b..651c4b8 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">imdccal</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,13 +49,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Wright S (2024).
 <em>imdccal: Wrangle CCAL Data Into Machine Readable Format</em>.
-R package version 0.1.1, <a href="https://nationalparkservice.github.io/imd-ccal/">https://nationalparkservice.github.io/imd-ccal/</a>. 
+R package version 0.1.2, <a href="https://nationalparkservice.github.io/imd-ccal/">https://nationalparkservice.github.io/imd-ccal/</a>. 
 </p>
       <pre>@Manual{,
   title = {imdccal: Wrangle CCAL Data Into Machine Readable Format},
   author = {Sarah Wright},
   year = {2024},
-  note = {R package version 0.1.1},
+  note = {R package version 0.1.2},
   url = {https://nationalparkservice.github.io/imd-ccal/},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 1a655aa..ed59a0e 100644
--- a/index.html
+++ b/index.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="index.html">imdccal</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index aa543c0..72ac816 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-05-22T16:21Z
+last_built: 2024-05-22T16:22Z
 urls:
   reference: https://nationalparkservice.github.io/imd-ccal/reference
   article: https://nationalparkservice.github.io/imd-ccal/articles
diff --git a/reference/getCCALData.html b/reference/getCCALData.html
index 12ad779..9e27087 100644
--- a/reference/getCCALData.html
+++ b/reference/getCCALData.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">imdccal</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/imdccal-package.html b/reference/imdccal-package.html
index 2c7112d..73faa74 100644
--- a/reference/imdccal-package.html
+++ b/reference/imdccal-package.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">imdccal</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index df54c9b..00802e3 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">imdccal</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/listParamsInData.html b/reference/listParamsInData.html
index 311fa86..65b950a 100644
--- a/reference/listParamsInData.html
+++ b/reference/listParamsInData.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">imdccal</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/listParamsInQuestionableResults.html b/reference/listParamsInQuestionableResults.html
index 1da8692..bfbe3fa 100644
--- a/reference/listParamsInQuestionableResults.html
+++ b/reference/listParamsInQuestionableResults.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">imdccal</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/machineReadableCCAL.html b/reference/machineReadableCCAL.html
index 40e13bb..da47269 100644
--- a/reference/machineReadableCCAL.html
+++ b/reference/machineReadableCCAL.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">imdccal</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rangeToVector.html b/reference/rangeToVector.html
index ac6e0d3..d47a6f0 100644
--- a/reference/rangeToVector.html
+++ b/reference/rangeToVector.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">imdccal</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index cc3118d..aa2df5b 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://nationalparkservice.github.io/imd-ccal/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sarah Wright. Author, maintainer.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Wright S (2024). imdccal: Wrangle CCAL Data Machine Readable Format. R package version 0.1.1, https://nationalparkservice.github.io/imd-ccal/.","code":"@Manual{,   title = {imdccal: Wrangle CCAL Data Into Machine Readable Format},   author = {Sarah Wright},   year = {2024},   note = {R package version 0.1.1},   url = {https://nationalparkservice.github.io/imd-ccal/}, }"},{"path":"https://nationalparkservice.github.io/imd-ccal/index.html","id":"imdccal","dir":"","previous_headings":"","what":"Wrangle CCAL Data Into Machine Readable Format","title":"Wrangle CCAL Data Into Machine Readable Format","text":"goal imdccal extract data water chemistry lab deliverables convert machine readable format.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Wrangle CCAL Data Into Machine Readable Format","text":"can install development version imdccal GitHub repository :","code":"# install.packages(\"remotes\") remotes::install_github(\"nationalparkservice/imd-ccal\")"},{"path":"https://nationalparkservice.github.io/imd-ccal/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Wrangle CCAL Data Into Machine Readable Format","text":"Read data single file CCAL lab data write machine-readable version Excel file set CSV files: Read data multiple files CCAL lab data write machine-readable version Excel files sets CSV files: Read tidy data work R, without writing data files:","code":"library(imdccal) # We'll assume that you have the CCAL file and a folder called \"ccal_tidy\" in your working directory machineReadableCCAL(\"LVLD_101118.xlsx\", destination_folder = \"ccal_tidy\")  # Write tidied data to a new .xlsx machineReadableCCAL(\"LVLD_101118.xlsx\", format = \"csv\", destination_folder = \"ccal_tidy\")  # Write tidied data to a folder of CSV files library(imdccal) # We'll assume that you have a folder full of CCAL files in a folder called \"ccal\", and a folder called \"ccal_tidy\" in your working directory all_files <- list.files(\"ccal\", pattern = \"*.xlsx$\", full.names = TRUE) machineReadableCCAL(all_files, destination_folder = \"ccal_tidy\")  # Write one file of tidied data per input file machineReadableCCAL(all_files, format = \"csv\", destination_folder = \"ccal_tidy\")  # Write one folder of tidied CSV data per input file library(imdccal) all_files <- list.files(\"ccal\", pattern = \"*.xlsx$\", full.names = TRUE) tidy_ccal <- getCCALData(all_files) lvld_18_data <- tidy_ccal$`LVLD_101118.xlsx`$data  # Get the data for a single set of lab results lvld_18_meta <- tidy_ccal$`LVLD_101118.xlsx`$metadata # Get the metadata for the same set of results"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/getCCALData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read CCAL Data — getCCALData","title":"Read CCAL Data — getCCALData","text":"Read CCAL Data","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/getCCALData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read CCAL Data — getCCALData","text":"","code":"getCCALData(files)"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/getCCALData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read CCAL Data — getCCALData","text":"files Path .xlsx file delivered CCAL. Use character vector specify multiple files.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/getCCALData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read CCAL Data — getCCALData","text":"nested list. list item corresponds one input file contains data frames data metadata.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/getCCALData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read CCAL Data — getCCALData","text":"","code":"if (FALSE) { my_folder <- \"ccal_results\" file_list <- list.files(my_folder, pattern = \"*.xlsx$\", full.names = TRUE) all_ccal_data <- getCCALData(file_list) }"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/imdccal-package.html","id":null,"dir":"Reference","previous_headings":"","what":"imdccal: Wrangle CCAL Data Into Machine Readable Format — imdccal-package","title":"imdccal: Wrangle CCAL Data Into Machine Readable Format — imdccal-package","text":"(maybe one line) Use four spaces indenting paragraphs within Description.","code":""},{"path":[]},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/imdccal-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"imdccal: Wrangle CCAL Data Into Machine Readable Format — imdccal-package","text":"Maintainer: Sarah Wright sarah_wright@nps.gov (ORCID)","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInData.html","id":null,"dir":"Reference","previous_headings":"","what":"List every parameter that occurs in the data — listParamsInData","title":"List every parameter that occurs in the data — listParamsInData","text":"List every parameter occurs data","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List every parameter that occurs in the data — listParamsInData","text":"","code":"listParamsInData(ccal_data)"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List every parameter that occurs in the data — listParamsInData","text":"ccal_data list object returned getCCALData","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List every parameter that occurs in the data — listParamsInData","text":"character vector parameter codes","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List every parameter that occurs in the data — listParamsInData","text":"","code":"my_folder <- \"ccal_results\" file_list <- list.files(my_folder, pattern = \"*.xlsx$\", full.names = TRUE) all_ccal_data <- getCCALData(file_list) parameters <- listParamsInData(all_ccal_data)"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInQuestionableResults.html","id":null,"dir":"Reference","previous_headings":"","what":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","title":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","text":"List every parameter name occurs questionable results","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInQuestionableResults.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","text":"","code":"listParamsInQuestionableResults(ccal_data)"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInQuestionableResults.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","text":"ccal_data list object returned getCCALData","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInQuestionableResults.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","text":"character vector parameter names","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInQuestionableResults.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","text":"","code":"my_folder <- \"ccal_results\" file_list <- list.files(my_folder, pattern = \"*.xlsx$\", full.names = TRUE) all_ccal_data <- getCCALData(file_list) param_names <- listParamsInQuestionableResults(all_ccal_data)"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/machineReadableCCAL.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","title":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","text":"Takes data delivered CCAL, extracts , rewrites tabs xlsx file csv files folder.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/machineReadableCCAL.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","text":"","code":"machineReadableCCAL(   files,   format = c(\"xlsx\", \"csv\"),   destination_folder = \"./\",   overwrite = FALSE )"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/machineReadableCCAL.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","text":"files Path .xlsx file delivered CCAL. Use character vector specify multiple files. format File format export machine readable data - either \"xlsx\" \"csv\" destination_folder Folder save data . Defaults current working directory. Folder must already exist. overwrite Overwrite existing file (Defaults TRUE write.table)","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/machineReadableCCAL.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","text":"Invisibly returns list containing data written file.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/machineReadableCCAL.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","text":"","code":"if (FALSE) { ccal_folder <- \"ccal_results\" dest_folder <- \"ccal_results/tidied\" file_list <- list.files(ccal_folder, pattern = \"*.xlsx$\", full.names = TRUE) machineReadableCCAL(file_list, format = \"xlsx\", destination_folder = dest_folder) machineReadableCCAL(file_list, format = \"csv\", destination_folder = dest_folder) }"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/rangeToVector.html","id":null,"dir":"Reference","previous_headings":"","what":"Expand Number Range in Text to All Numbers in Range — rangeToVector","title":"Expand Number Range in Text to All Numbers in Range — rangeToVector","text":"Takes character vector containing number range (e.g. \"11 - 14\") replaces range numbers contained range (\"11 12 13 14\").","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/rangeToVector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expand Number Range in Text to All Numbers in Range — rangeToVector","text":"","code":"rangeToVector(numbers, separator = \" \")"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/rangeToVector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expand Number Range in Text to All Numbers in Range — rangeToVector","text":"numbers Character vector containing number range indicated dash (e.g. \"123 - 456\") separator Character string use separator numbers","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/rangeToVector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expand Number Range in Text to All Numbers in Range — rangeToVector","text":"character vector, number ranges removed replaced numbers range explicitly listed.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/rangeToVector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expand Number Range in Text to All Numbers in Range — rangeToVector","text":"","code":"rangeToVector(\"1 3 5-8 10\") #> [1] \"1 3 5 6 7 8 10\""}]
+[{"path":"https://nationalparkservice.github.io/imd-ccal/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sarah Wright. Author, maintainer.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Wright S (2024). imdccal: Wrangle CCAL Data Machine Readable Format. R package version 0.1.2, https://nationalparkservice.github.io/imd-ccal/.","code":"@Manual{,   title = {imdccal: Wrangle CCAL Data Into Machine Readable Format},   author = {Sarah Wright},   year = {2024},   note = {R package version 0.1.2},   url = {https://nationalparkservice.github.io/imd-ccal/}, }"},{"path":"https://nationalparkservice.github.io/imd-ccal/index.html","id":"imdccal","dir":"","previous_headings":"","what":"Wrangle CCAL Data Into Machine Readable Format","title":"Wrangle CCAL Data Into Machine Readable Format","text":"goal imdccal extract data water chemistry lab deliverables convert machine readable format.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Wrangle CCAL Data Into Machine Readable Format","text":"can install development version imdccal GitHub repository :","code":"# install.packages(\"remotes\") remotes::install_github(\"nationalparkservice/imd-ccal\")"},{"path":"https://nationalparkservice.github.io/imd-ccal/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Wrangle CCAL Data Into Machine Readable Format","text":"Read data single file CCAL lab data write machine-readable version Excel file set CSV files: Read data multiple files CCAL lab data write machine-readable version Excel files sets CSV files: Read tidy data work R, without writing data files:","code":"library(imdccal) # We'll assume that you have the CCAL file and a folder called \"ccal_tidy\" in your working directory machineReadableCCAL(\"LVLD_101118.xlsx\", destination_folder = \"ccal_tidy\")  # Write tidied data to a new .xlsx machineReadableCCAL(\"LVLD_101118.xlsx\", format = \"csv\", destination_folder = \"ccal_tidy\")  # Write tidied data to a folder of CSV files library(imdccal) # We'll assume that you have a folder full of CCAL files in a folder called \"ccal\", and a folder called \"ccal_tidy\" in your working directory all_files <- list.files(\"ccal\", pattern = \"*.xlsx$\", full.names = TRUE) machineReadableCCAL(all_files, destination_folder = \"ccal_tidy\")  # Write one file of tidied data per input file machineReadableCCAL(all_files, format = \"csv\", destination_folder = \"ccal_tidy\")  # Write one folder of tidied CSV data per input file library(imdccal) all_files <- list.files(\"ccal\", pattern = \"*.xlsx$\", full.names = TRUE) tidy_ccal <- getCCALData(all_files) lvld_18_data <- tidy_ccal$`LVLD_101118.xlsx`$data  # Get the data for a single set of lab results lvld_18_meta <- tidy_ccal$`LVLD_101118.xlsx`$metadata # Get the metadata for the same set of results"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/getCCALData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read CCAL Data — getCCALData","title":"Read CCAL Data — getCCALData","text":"Read CCAL Data","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/getCCALData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read CCAL Data — getCCALData","text":"","code":"getCCALData(files)"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/getCCALData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read CCAL Data — getCCALData","text":"files Path .xlsx file delivered CCAL. Use character vector specify multiple files.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/getCCALData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read CCAL Data — getCCALData","text":"nested list. list item corresponds one input file contains data frames data metadata.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/getCCALData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read CCAL Data — getCCALData","text":"","code":"if (FALSE) { my_folder <- \"ccal_results\" file_list <- list.files(my_folder, pattern = \"*.xlsx$\", full.names = TRUE) all_ccal_data <- getCCALData(file_list) }"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/imdccal-package.html","id":null,"dir":"Reference","previous_headings":"","what":"imdccal: Wrangle CCAL Data Into Machine Readable Format — imdccal-package","title":"imdccal: Wrangle CCAL Data Into Machine Readable Format — imdccal-package","text":"(maybe one line) Use four spaces indenting paragraphs within Description.","code":""},{"path":[]},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/imdccal-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"imdccal: Wrangle CCAL Data Into Machine Readable Format — imdccal-package","text":"Maintainer: Sarah Wright sarah_wright@nps.gov (ORCID)","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInData.html","id":null,"dir":"Reference","previous_headings":"","what":"List every parameter that occurs in the data — listParamsInData","title":"List every parameter that occurs in the data — listParamsInData","text":"List every parameter occurs data","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List every parameter that occurs in the data — listParamsInData","text":"","code":"listParamsInData(ccal_data)"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List every parameter that occurs in the data — listParamsInData","text":"ccal_data list object returned getCCALData","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List every parameter that occurs in the data — listParamsInData","text":"character vector parameter codes","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List every parameter that occurs in the data — listParamsInData","text":"","code":"my_folder <- \"ccal_results\" file_list <- list.files(my_folder, pattern = \"*.xlsx$\", full.names = TRUE) all_ccal_data <- getCCALData(file_list) parameters <- listParamsInData(all_ccal_data)"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInQuestionableResults.html","id":null,"dir":"Reference","previous_headings":"","what":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","title":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","text":"List every parameter name occurs questionable results","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInQuestionableResults.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","text":"","code":"listParamsInQuestionableResults(ccal_data)"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInQuestionableResults.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","text":"ccal_data list object returned getCCALData","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInQuestionableResults.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","text":"character vector parameter names","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/listParamsInQuestionableResults.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List every parameter name that occurs in the questionable results — listParamsInQuestionableResults","text":"","code":"my_folder <- \"ccal_results\" file_list <- list.files(my_folder, pattern = \"*.xlsx$\", full.names = TRUE) all_ccal_data <- getCCALData(file_list) param_names <- listParamsInQuestionableResults(all_ccal_data)"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/machineReadableCCAL.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","title":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","text":"Takes data delivered CCAL, extracts , rewrites tabs xlsx file csv files folder.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/machineReadableCCAL.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","text":"","code":"machineReadableCCAL(   files,   format = c(\"xlsx\", \"csv\"),   destination_folder = \"./\",   overwrite = FALSE )"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/machineReadableCCAL.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","text":"files Path .xlsx file delivered CCAL. Use character vector specify multiple files. format File format export machine readable data - either \"xlsx\" \"csv\" destination_folder Folder save data . Defaults current working directory. Folder must already exist. overwrite Overwrite existing file (Defaults TRUE write.table)","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/machineReadableCCAL.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","text":"Invisibly returns list containing data written file.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/machineReadableCCAL.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrangle CCAL data into a machine-readable format — machineReadableCCAL","text":"","code":"if (FALSE) { ccal_folder <- \"ccal_results\" dest_folder <- \"ccal_results/tidied\" file_list <- list.files(ccal_folder, pattern = \"*.xlsx$\", full.names = TRUE) machineReadableCCAL(file_list, format = \"xlsx\", destination_folder = dest_folder) machineReadableCCAL(file_list, format = \"csv\", destination_folder = dest_folder) }"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/rangeToVector.html","id":null,"dir":"Reference","previous_headings":"","what":"Expand Number Range in Text to All Numbers in Range — rangeToVector","title":"Expand Number Range in Text to All Numbers in Range — rangeToVector","text":"Takes character vector containing number range (e.g. \"11 - 14\") replaces range numbers contained range (\"11 12 13 14\").","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/rangeToVector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Expand Number Range in Text to All Numbers in Range — rangeToVector","text":"","code":"rangeToVector(numbers, separator = \" \")"},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/rangeToVector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Expand Number Range in Text to All Numbers in Range — rangeToVector","text":"numbers Character vector containing number range indicated dash (e.g. \"123 - 456\") separator Character string use separator numbers","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/rangeToVector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Expand Number Range in Text to All Numbers in Range — rangeToVector","text":"character vector, number ranges removed replaced numbers range explicitly listed.","code":""},{"path":"https://nationalparkservice.github.io/imd-ccal/reference/rangeToVector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Expand Number Range in Text to All Numbers in Range — rangeToVector","text":"","code":"rangeToVector(\"1 3 5-8 10\") #> [1] \"1 3 5 6 7 8 10\""}]