From 40a3df132a301f39323ffd38d7c33874645494a5 Mon Sep 17 00:00:00 2001
From: Marty Oehme <marty.oehme@gmail.com>
Date: Tue, 5 Dec 2023 16:42:20 +0100
Subject: [PATCH] chore(repo): Fix links to bibtex file

Fixed any relative links to the bibtex file for generating annotations
or similar.
---
 00-notebooks/bibmanip.qmd | 117 ++++++++++++++++++++++++++++++++++++++
 notes.md                  |   2 +-
 scoping_review.qmd        |   2 +-
 3 files changed, 119 insertions(+), 2 deletions(-)
 create mode 100644 00-notebooks/bibmanip.qmd

diff --git a/00-notebooks/bibmanip.qmd b/00-notebooks/bibmanip.qmd
new file mode 100644
index 0000000..56f12e0
--- /dev/null
+++ b/00-notebooks/bibmanip.qmd
@@ -0,0 +1,117 @@
+---
+bibliography: ../02-data/supplementary/lib.bib
+csl: /home/marty/documents/library/utilities/styles/APA-7.csl
+papersize: A4
+linestretch: 1.5
+fontfamily: lmodern
+fontsize: "12"
+geometry:
+  - left=2.2cm
+  - right=3.5cm
+  - top=2.5cm
+  - bottom=2.5cm
+toc: false
+link-citations: true
+link-bibliography: true
+number-sections: false
+lang: en
+title: Scoping review on 'what works'
+subtitle: Addressing inequalities in the World of Work
+---
+
+```{python}
+#| echo: false
+from pathlib import Path
+data_dir=Path("../02-data")
+
+## standard imports
+from IPython.core.display import Markdown as md
+import numpy as np
+import pandas as pd
+from matplotlib import pyplot as plt
+import seaborn as sns
+from tabulate import tabulate
+```
+
+```{python}
+sns.set_style("whitegrid")
+```
+
+```{python}
+#| echo: false
+# load and parse overall bibtex sample
+import bibtexparser
+
+bib_string=""
+print(f"path: {data_dir.joinpath('raw/01_wos-sample_2023-11-02').absolute()}")
+for partial_bib in data_dir.joinpath("raw/01_wos-sample_2023-11-02").glob("*.bib"):
+    with open(partial_bib) as f:
+        bib_string+="\n".join(f.readlines())
+sample = bibtexparser.parse_string(bib_string)
+```
+
+## Description of results
+
+```{python}
+#| echo: false
+
+sample_size = len(sample.entries)
+md(f"""
+The exploratory execution of queries results in an initial sample of {sample_size} studies after the identification process.
+""")
+```
+
+yrs:
+
+```{python}
+reformatted = []
+for e in sample.entries:
+    reformatted.append([e["Year"], e["Author"], e["Title"], e["Type"], e["Times-Cited"], e["Usage-Count-Since-2013"]])
+bib_df = pd.DataFrame(reformatted, columns = ["Year", "Author", "Title", "Type", "Cited", "Usage"])
+bib_df["Date"] = pd.to_datetime(bib_df["Year"], format="%Y")
+bib_df["Year"] = bib_df["Date"].dt.year
+bib_df
+```
+
+```{python}
+# RESTRICT FOR NEWER STUDIES
+bib_df = bib_df[bib_df["Year"] >= 2000]
+```
+
+Publications per year:
+
+```{python}
+ax = sns.countplot(bib_df[bib_df["Year"] >= 2000], x="Year")
+ax.tick_params(axis='x', rotation=45)
+plt.tight_layout()
+plt.show()
+```
+
+By type:
+
+```{python}
+bib_df["Type"].value_counts()
+bib_df["Literature"] = np.where(bib_df["Type"].str.contains("article", case=False, regex=False), "white", "gray")
+bib_df["Literature"] = bib_df["Literature"].astype("category")
+```
+
+Per type:
+
+```{python}
+ax = sns.countplot(bib_df[bib_df["Year"] >= 2000], x="Year", hue="Literature")
+ax.tick_params(axis='x', rotation=45)
+# ax.set_xlabel("")
+plt.tight_layout()
+plt.show()
+```
+
+Avg num of citations:
+
+```{python}
+bib_df["Cited"] = bib_df["Cited"].astype("int")
+grpd = bib_df.groupby(["Year"], as_index=False)["Cited"].mean()
+ax = sns.barplot(grpd, x="Year", y="Cited")
+ax.tick_params(axis='x', rotation=45)
+plt.tight_layout()
+plt.show()
+```
diff --git a/notes.md b/notes.md
index 37f546e..a5f7b38 100644
--- a/notes.md
+++ b/notes.md
@@ -1,5 +1,5 @@
 ---
-bibliography: 03-supplementary_data/lib.bib
+bibliography: 02-data/supplementary/lib.bib
 csl: /home/marty/documents/library/utilities/styles/APA-7.csl
 papersize: A4
 linestretch: 1.5
diff --git a/scoping_review.qmd b/scoping_review.qmd
index abd2cc1..c0aa270 100644
--- a/scoping_review.qmd
+++ b/scoping_review.qmd
@@ -1,5 +1,5 @@
 ---
-bibliography: 03-supplementary_data/lib.bib
+bibliography: 02-data/supplementary/lib.bib
 csl: /home/marty/documents/library/utilities/styles/APA-7.csl
 papersize: A4
 linestretch: 1.5