From 0220eff970fac498c5ba134807830b11a2d4c9d3 Mon Sep 17 00:00:00 2001
From: richelbilderbeek <richel@richelbilderbeek.nl>
Date: Sun, 8 Oct 2023 11:56:02 +0200
Subject: [PATCH 1/9] Add feedback

---
 article.tex | 35 ++++++++++++++++++++---------------
 header.tex  |  4 ++--
 2 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/article.tex b/article.tex
index fa1b7f0..f2d1344 100644
--- a/article.tex
+++ b/article.tex
@@ -17,6 +17,8 @@
 computational research, Open Science, best practices,
 genetic epidemiology
 
+% IH: replaced references to "this paper" with "this chapter". Check that ok.
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Introduction}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -62,7 +64,7 @@ \section{Introduction}
 paradata can be understood in general sense as 'data about processes’ (with e.g. survey paradata
 termed alternatively as records and audit trails) \cite{nicolaas2011survey},
 or in more specific sense in relation to data collection, as 'data about the data collection process' (\cite{choumert2019using}).
-This paper uses the latter as a working definition.
+This chapter uses the latter as a working definition.
 
 % \paragraph{Code is paradata}
 
@@ -99,7 +101,9 @@ \section{Introduction}
 its benefits.
 Finally, in computational fields, 
 it can help understand how scholarly knowledge is produced (\cite{huvila2022improving}).
-This paper discusses these general reasons applied to code.
+% IH: As the series editors asked that all chapters should in the end somehow link to knowledge management, may be here could be a place to add a few words about it e.g. see below
+% IH: and to integrate this understanding as a part of the management of scholarly knowledge.
+This chapter discusses these general reasons applied to code.
 
 \begin{figure}[!htbp]
   \centering
@@ -161,7 +165,7 @@ \section{Genetic epidemiology}
 
 % \paragraph{Introduction}
 
-This paper uses genetic epidemiology as a specific example,
+This chapter uses genetic epidemiology as a specific example,
 to illustrate in which way code is paradata,
 and why this type of paradata is relevant.
 However, any field that uses computation 
@@ -180,7 +184,7 @@ \section{Genetic epidemiology}
 The trait is caused by the genetic make-up, or 'genotype'
 \iffalse
 (see Table \ref{tab:definitions} in the Supplementary Materials
-for the definitions of terms used in this paper)
+for the definitions of terms used in this chapter)
 \fi
 , of a person.
 The trait, also called 'phenotype', 
@@ -1011,7 +1015,7 @@ \section{Discussion}
 \section{Conclusions}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-This paper started with some suggestions to 
+This chapter started with some suggestions to 
 make paradata useful for data re(use):
 paradata should be extensive, comprehensively documented,
 with the creation of documentation and code going hand-in-hand,
@@ -1088,12 +1092,13 @@ \section{Data Accessibility}
 \section{Author biography}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-Dr. Bilderbeek has worked in computational biology for more than a decade.
-Currently, he works for the National Bioinformatics Infrastructure Sweden (NBIS)
-in Uppsala, Sweden, 
-as an application expert and trainer, with a focus on reproducible research.
-All his work can be found on GitHub at \url{https://github.com/richelbilderbeek}
-and his YouTube channel.
+% IH: Moved to a separate document
+%Dr. Bilderbeek has worked in computational biology for more than a decade.
+%Currently, he works for the National Bioinformatics Infrastructure Sweden (NBIS)
+%in Uppsala, Sweden, 
+%as an application expert and trainer, with a focus on reproducible research.
+%All his work can be found on GitHub at \url{https://github.com/richelbilderbeek}
+%and his YouTube channel.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Bibliography
@@ -1120,13 +1125,13 @@ \section{Supplementary materials}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{This paper}
+\subsection{This chapter}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 This book chapter has been produced following all recommendations in it:
 it's \LaTeX code is hosted on GitHub 
 at \url{https://github.com/richelbilderbeek/chapter_paradata}.
-Due this, one can, among others, see the complete version history of this paper.
+Due this, one can, among others, see the complete version history of this chapter.
 This alone could allow research to be done on, for example,
 the effect of reviewers' feedback on a first manuscript.
 The website also supplies an alternative version of the same chapter
@@ -1159,7 +1164,7 @@ \section*{Definitions}
     Trait        & A phenotype                                                                  & The concentration of IL6RA in the blood                         \\
     \hline
   \end{tabular}
-  \caption{Terms used in this paper, and their definitions}
+  \caption{Terms used in this chapter, and their definitions}
   \label{tab:definitions}
 \end{table}
 
@@ -1186,7 +1191,7 @@ \section*{Recommendations}
                   & Standardise to link between container, paper and code repository \\
     \hline
   \end{tabular}
-  \caption{Recommendations described in this paper}
+  \caption{Recommendations described in this chapter}
   \label{tab:recommendations}
 \end{table}
 
diff --git a/header.tex b/header.tex
index ed43df3..08c67f0 100644
--- a/header.tex
+++ b/header.tex
@@ -54,7 +54,7 @@
 \nonstopmode
 
 \title{
-  Making research code useful paradata
+Making research code useful paradata
 }
 \author{Richèl J.C. Bilderbeek}
 
@@ -76,7 +76,7 @@
 % \usepackage[hyphens]{url}
 
 % This is chapter number 7
-\setcounter{chapter}{6} % LaTeX adds one
+\setcounter{chapter}{1} % LaTeX adds one
 
 % This is the header of this article.
 % It contains the higher-level things, such as packages.

From 9a36f38c387522934e72a860c010ec501ecf62f1 Mon Sep 17 00:00:00 2001
From: richelbilderbeek <richel@richelbilderbeek.nl>
Date: Sun, 8 Oct 2023 11:56:50 +0200
Subject: [PATCH 2/9] Fix bash style

---
 scripts/zip_tex_files.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/zip_tex_files.sh b/scripts/zip_tex_files.sh
index 08d8f19..b10c093 100644
--- a/scripts/zip_tex_files.sh
+++ b/scripts/zip_tex_files.sh
@@ -6,4 +6,4 @@
 #
 #   ./scripts/zip_text_files.sh
 #
-zip tex_files.zip $(ls {article.*,header.*,figure_1.png,svmult.cls,svind.ist})
+zip tex_files.zip "$(ls {article.*,header.*,figure_1.png,svmult.cls,svind.ist})"

From db51d2d8d9cca58826531246d7f4587756877069 Mon Sep 17 00:00:00 2001
From: richelbilderbeek <richel@richelbilderbeek.nl>
Date: Sun, 8 Oct 2023 11:59:02 +0200
Subject: [PATCH 3/9] Use 'chapter' instead of 'paper' works fine

---
 article.tex | 2 --
 1 file changed, 2 deletions(-)

diff --git a/article.tex b/article.tex
index f2d1344..fee0c95 100644
--- a/article.tex
+++ b/article.tex
@@ -17,8 +17,6 @@
 computational research, Open Science, best practices,
 genetic epidemiology
 
-% IH: replaced references to "this paper" with "this chapter". Check that ok.
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Introduction}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

From 1e0bdc15619ddded83c735dcaaae322b4faa1a20 Mon Sep 17 00:00:00 2001
From: richelbilderbeek <richel@richelbilderbeek.nl>
Date: Sun, 8 Oct 2023 12:00:02 +0200
Subject: [PATCH 4/9] Biography moved to seperate document

---
 article.tex | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/article.tex b/article.tex
index fee0c95..e062154 100644
--- a/article.tex
+++ b/article.tex
@@ -1086,18 +1086,6 @@ \section{Data Accessibility}
 This article and its metadata can be found at 
 \url{https://github.com/richelbilderbeek/chapter_paradata}.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Author biography}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-% IH: Moved to a separate document
-%Dr. Bilderbeek has worked in computational biology for more than a decade.
-%Currently, he works for the National Bioinformatics Infrastructure Sweden (NBIS)
-%in Uppsala, Sweden, 
-%as an application expert and trainer, with a focus on reproducible research.
-%All his work can be found on GitHub at \url{https://github.com/richelbilderbeek}
-%and his YouTube channel.
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Bibliography
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

From 6e4fd9b0453439c19a4b1bde1578822a8d5f77eb Mon Sep 17 00:00:00 2001
From: richelbilderbeek <richel@richelbilderbeek.nl>
Date: Sun, 8 Oct 2023 12:01:10 +0200
Subject: [PATCH 5/9] Add 'About the Author' in the README

---
 README.md | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/README.md b/README.md
index 586300e..74683c6 100644
--- a/README.md
+++ b/README.md
@@ -13,3 +13,12 @@
 
  * [PDFs](https://github.com/richelbilderbeek/chapter_paradata/releases/download/v0.5/article_pdfs.zip)
 
+## About the author
+
+Richèl J. C. Bilderbeek, Ph.D., has worked in computational biology 
+for more than a decade. 
+Currently, he works for the National Bioinformatics Infrastructure Sweden (NBIS) 
+in Uppsala, Sweden, as an application expert and trainer, 
+with a focus on reproducible research. 
+All his work can be found on GitHub 
+at https://github.com/richelbilderbeek and his YouTube channel. 

From 2e7bc70bca6dccc050625115897c269f89a16efa Mon Sep 17 00:00:00 2001
From: richelbilderbeek <richel@richelbilderbeek.nl>
Date: Sun, 8 Oct 2023 12:12:43 +0200
Subject: [PATCH 6/9] Implications for knowledge management

---
 article.tex | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/article.tex b/article.tex
index e062154..324e8df 100644
--- a/article.tex
+++ b/article.tex
@@ -99,9 +99,10 @@ \section{Introduction}
 its benefits.
 Finally, in computational fields, 
 it can help understand how scholarly knowledge is produced (\cite{huvila2022improving}).
-% IH: As the series editors asked that all chapters should in the end somehow link to knowledge management, may be here could be a place to add a few words about it e.g. see below
-% IH: and to integrate this understanding as a part of the management of scholarly knowledge.
-This chapter discusses these general reasons applied to code.
+
+This chapter discusses these general reasons applied to code
+and its implications for knowledge management,
+including recommendations how to make code useful paradata in section \ref{sec:making-code-useful-paradata}.
 
 \begin{figure}[!htbp]
   \centering

From 036c9239bd5e588ee8b74fb34d8616b927b5dc8a Mon Sep 17 00:00:00 2001
From: richelbilderbeek <richel@richelbilderbeek.nl>
Date: Sun, 8 Oct 2023 12:13:34 +0200
Subject: [PATCH 7/9] Max 5000 words, as author info was moved to separate
 document

---
 .github/workflows/count_words.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/count_words.yaml b/.github/workflows/count_words.yaml
index 0cee6b9..dfabd15 100644
--- a/.github/workflows/count_words.yaml
+++ b/.github/workflows/count_words.yaml
@@ -22,6 +22,6 @@ jobs:
       - name: Count number of words
         run: texcount article.tex
 
-      - name: Count number of words, allow 5100
+      - name: Count number of words, allow 5000
         run: |
-          n_words=$(texcount article.tex | egrep "Words in text:.*" | cut -d ":" -f 2); if [ "$n_words" -gt 5100 ]; then print "ERROR: got $n_words words"; exit 42; fi
+          n_words=$(texcount article.tex | egrep "Words in text:.*" | cut -d ":" -f 2); if [ "$n_words" -gt 5000 ]; then print "ERROR: got $n_words words"; exit 42; fi

From 4d90a54357d70493c4804a41e043f37cf2dbb977 Mon Sep 17 00:00:00 2001
From: richelbilderbeek <richel@richelbilderbeek.nl>
Date: Sun, 8 Oct 2023 12:14:40 +0200
Subject: [PATCH 8/9] Check for bash style in the right folders on the right
 day

---
 .github/workflows/check_bash_style.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/check_bash_style.yaml b/.github/workflows/check_bash_style.yaml
index 5c3d704..749a378 100644
--- a/.github/workflows/check_bash_style.yaml
+++ b/.github/workflows/check_bash_style.yaml
@@ -4,7 +4,7 @@ on:
   push:
   pull_request:
   schedule:
-  - cron: "0 0 16 * *"
+  - cron: "0 0 3 * *"
 
 
 jobs:
@@ -19,4 +19,4 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Check bash scripts for style
-        run: shellcheck *.sh scripts/*.sh
+        run: shellcheck scripts/*.sh

From 164706bb83ef122cc8f677c42c9d713285183c0c Mon Sep 17 00:00:00 2001
From: richelbilderbeek <richel@richelbilderbeek.nl>
Date: Sun, 8 Oct 2023 12:15:13 +0200
Subject: [PATCH 9/9] 5004 words

---
 .github/workflows/count_words.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/count_words.yaml b/.github/workflows/count_words.yaml
index dfabd15..5e4c07c 100644
--- a/.github/workflows/count_words.yaml
+++ b/.github/workflows/count_words.yaml
@@ -22,6 +22,6 @@ jobs:
       - name: Count number of words
         run: texcount article.tex
 
-      - name: Count number of words, allow 5000
+      - name: Count number of words, allow 5004
         run: |
-          n_words=$(texcount article.tex | egrep "Words in text:.*" | cut -d ":" -f 2); if [ "$n_words" -gt 5000 ]; then print "ERROR: got $n_words words"; exit 42; fi
+          n_words=$(texcount article.tex | egrep "Words in text:.*" | cut -d ":" -f 2); if [ "$n_words" -gt 5004 ]; then print "ERROR: got $n_words words"; exit 42; fi