Update Report Ch1

IPBES-Data · Nov 11, 2024 · 7122f37 · 7122f37
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diff --git a/.gitignore b/.gitignore
@@ -118,7 +118,6 @@ tca_corpus/input/List of papers_TSU Review Sebastian Villasante/Chapter 3/OneDri
 ### Ch 1 Evidence Causes  ###
 #############################
 
-ch1_evidence_causes/data
 
 #############################
 ### Ch 2 Technology       ###

diff --git a/IPBES_TCA_Ch1_evidence_causes.html b/IPBES_TCA_Ch1_evidence_causes.html
diff --git a/IPBES_TCA_Ch1_evidence_causes.qmd b/IPBES_TCA_Ch1_evidence_causes.qmd
@@ -158,27 +158,35 @@ if (file.exists(params$fn_corpus_6)) {
 }
 ```
 
+
 # Download of Data Files from Zenodo
 
-The `data` folder is not included in this deposit, but in a separate deposit at [10.5281/zenodo.11389148](https://doi.org/10.5281/zenodo.11389148).
-To guarantee reproducibility, =it is downloaded and extracted when the folder `data` does not exist. 
+The `data` folder is also available in a separate deposit at [10.5281/zenodo.11389148](https://doi.org/10.5281/zenodo.11389148).
+
+To guarantee reproducibility, it will be downloaded and extracted when the folder `ch1_evidence_causes/data` does not exist
+
+All code to re-generate the data is included but might take a long time to run and produce different numbers as OpenAlex is updated continously.
 
-All code to re-generate the data is included but might take a long time to run.
+Disable this block and delete all content in the folder `ch1_evidence_causes/data` to re-generate the data. The folder `ch1_evidence_causes/data` has to exist.
 
-Disable this block to re-generate the data. The folder `data` has to exist.
+This code will only work after the approval of the assessment by the plenary as the repository will remain confidential before.
 
 ```{r}
 #| label: download_data
-#|
+#| eval: true 
 
-if (!dir.exists("data")) {
-    dir.create("data")
+dn <- file.path("ch1_evidence_causes", "data")
+if (!dir.exists(dn)) {
+    dir.create(dn)
     url <- paste0("https://zenodo.org/record/", "11389148", "/files/data.zip")
     destfile <- tempfile(fileext = ".zip")
     download.file(url, destfile)
 
     unzip(destfile, exdir = "data")
-}## Working Title
+}
+```
+
+## Working Title
 IPBES_TCA_Ch1_evidence_causes
 
 ## Code repo
@@ -192,8 +200,16 @@ The BuidNo is automatically increased by one each time the report is rendered. I
 
 # Introduction
 
-All searches are done on all works in OpenAlex. The search in the TCA Corpus is not possibly at the moment, but we are working on it.
+## Overview Diagram
 
+![Overview of the analysis and results.](ch1_evidence_causes/figures/Ch1_evidence_causes.svg){width=100% height=100%}
+
+- To download png, [click here](ch1_evidence_causes/figures/Ch1_evidence_causes.png){target="_blank"}.
+- To download high resolution pdf, [click here](ch1_evidence_causes/figures/Ch1_evidence_causes.pdf){target="_blank"}.
+- To download high resolution svg, [click here](ch1_evidence_causes/figures/Ch1_evidence_causes.svg){target="_blank"}.
+
+All searches are done on OpenAlex directly. 
+The downloaded TCA Corpus is not used directly due to methodological and technical limitations.
 
 ## The following steps will be done in documented in this report:
 
@@ -223,7 +239,7 @@ count$tca_corpus <- openalexR::oa_fetch(
 
 ## 1. Ethical arguments for transformative change
 
-The search terms is [ethical](input/ethical.txt){target=_blank}
+The search terms is [ethical](ch1_evidence_causes/input/ethical.txt){target=_blank}
 on **OpenAlex**.
 
 ```{r}
@@ -238,7 +254,7 @@ count$ethical <- openalexR::oa_fetch(
 )$count
 ```
 
-The search terms is [ethical](input/ethical.txt){target=_blank}
+The second search terms is [ethical](ch1_evidence_causes/input/ethical.txt){target=_blank} [ethical](ch1_evidence_causes/input/ethical.txt){target=_blank}
 on **TCA Corpus**.
 
 ```{r}
@@ -257,10 +273,10 @@ count$ethical_tca <- openalexR::oa_fetch(
 
 ## 2. Assessing broader biodiversity concepts
 
-The search terms is [concepts_1](input/concepts_1.txt){target=_blank}
+The search terms is [concepts_1](ch1_evidence_causes/input/concepts_1.txt){target=_blank}
 Open Alex search.
 
-The [concepts_1](input/concepts_1.txt){target=_blank} search returns a subset of the [nature corpus](input/tca_corpus/search terms/nature.txt){target=_blank} as `biodiversity` is a subset of the nature corpus. Therefore, it is not nbecessary to subset the nature corpus and the search can be done on the complete OpenAlex corpus
+The [concepts_1](ch1_evidence_causes/input/concepts_1.txt){target=_blank} search returns a subset of the [nature corpus](tca_corpus/input/search terms/nature.txt){target=_blank} as `biodiversity` is a subset of the nature corpus. Therefore, it is not nbecessary to subset the nature corpus and the search can be done on the complete OpenAlex corpus
 .
 ```{r}
 #| label: get_concepts_1_count
@@ -289,7 +305,7 @@ count$concepts_2 <- openalexR::oa_fetch(
 )$count
 ```
 
-Assessing the broader biodiversity concepts by searching for [concepts_1 corpus](input/concepts_1.txt){target=_blank} AND [concepts_2 corpus](input/concepts_2.txt){target=_blank}
+Assessing the broader biodiversity concepts by searching for [concepts_1 corpus](ch1_evidence_causes/input/concepts_1.txt){target=_blank} AND [concepts_2 corpus](ch1_evidence_causes/input/concepts_2.txt){target=_blank}
 
 ```{r}
 #| label: get_concepts_1_2_nature_count
@@ -308,11 +324,11 @@ count$concepts_1_2 <- openalexR::oa_fetch(
 
 ## 3. Assessing disciplinary bias in the nature corpus
 
-To be discussed
+Skipped
 
 ## 4. Narrowed transformative change corpus
 
-Here the term [narrowed_tca](input/narrowed_tca.txt){target=_blank} is used to narrow down the TCA corpus.
+Here the term [narrowed_tca](ch1_evidence_causes/input/narrowed_tca.txt){target=_blank} is used to narrow down the TCA corpus.
 
 ```{r}
 #| label: get_narrowed_tca_count
@@ -384,10 +400,10 @@ count$narrowed_tca_nature <- openalexR::oa_fetch(
 ## 5. Assessing criteria in the narrowed TFC corpus
 
 Here the terms about criteria are used:
-- [criteria_1](input/criteria_1.txt){target=_blank}
-- [criteria_2](input/criteria_2.txt){target=_blank}
-- [criteria_3](input/criteria_3.txt){target=_blank}
-- [criteria_4](input/criteria_4.txt){target=_blank}
+- [criteria_1](ch1_evidence_causes/input/criteria_1.txt){target=_blank}
+- [criteria_2](ch1_evidence_causes/input/criteria_2.txt){target=_blank}
+- [criteria_3](ch1_evidence_causes/input/criteria_3.txt){target=_blank}
+- [criteria_4](ch1_evidence_causes/input/criteria_4.txt){target=_blank}
 
 ```{r}
 #| label: get_narrowed_tca_criteria_criteria_count
@@ -587,11 +603,11 @@ rm(data)
 
 Here the terms about criteria are used:
 
-- [biodiv_loss_3_1](input/biodiv_loss_3_1.txt){target=_blank}
-- [biodiv_loss_3_2](input/biodiv_loss_3_2.txt){target=_blank}
-- [biodiv_loss_3_3](input/biodiv_loss_3_3.txt){target=_blank}
-- [biodiv_loss_3_4](input/biodiv_loss_3_4.txt){target=_blank}
-- [biodiv_loss_3_5](input/biodiv_loss_3_5.txt){target=_blank}
+- [biodiv_loss_3_1](ch1_evidence_causes/input/biodiv_loss_3_1.txt){target=_blank}
+- [biodiv_loss_3_2](ch1_evidence_causes/input/biodiv_loss_3_2.txt){target=_blank}
+- [biodiv_loss_3_3](ch1_evidence_causes/input/biodiv_loss_3_3.txt){target=_blank}
+- [biodiv_loss_3_4](ch1_evidence_causes/input/biodiv_loss_3_4.txt){target=_blank}
+- [biodiv_loss_3_5](ch1_evidence_causes/input/biodiv_loss_3_5.txt){target=_blank}
 
 These need to be `AND` with
 - Nature Corpus
@@ -1338,10 +1354,4 @@ There are the following numbers of wotks in the Nature Corpus AND Narrowed TCA C
 - **`r count$biodiv_loss_nat_narrowed_s_4 `** works in the Nature Corpus AND Narrowed TFC Corpus that discuss the `Topic 4`, which is **`r round(100 * count$biodiv_loss_nat_narrowed_s_4 / count$narrowed_tca_nature, digits = 2)`%**
 - **`r count$biodiv_loss_nat_narrowed_s_5 `** works in the Nature Corpus AND Narrowed TFC Corpus that discuss the `Topic 5`, which is **`r round(100 * count$biodiv_loss_nat_narrowed_s_5 / count$narrowed_tca_nature, digits = 2)`%**
 
-## Diagram
 
-![Overview of the analysis and results.](ch1_evidence_causes/figures/Ch1_evidence_causes.svg){width=100% height=100%}
-
-- To download png, [click here](ch1_evidence_causes/figures/Ch1_evidence_causes.png){target="_blank"}.
-- To download high resolution pdf, [click here](ch1_evidence_causes/figures/Ch1_evidence_causes.pdf){target="_blank"}.
-- To download high resolution svg, [click here](ch1_evidence_causes/figures/Ch1_evidence_causes.svg){target="_blank"}.
diff --git a/ch1_evidence_causes/buildNo b/ch1_evidence_causes/buildNo
@@ -1 +1 @@
-417
+424
diff --git a/ch1_evidence_causes/data/corpus_6.rds b/ch1_evidence_causes/data/corpus_6.rds
diff --git a/ch1_evidence_causes/data/corpus_6_all.xlsx b/ch1_evidence_causes/data/corpus_6_all.xlsx
diff --git a/ch1_evidence_causes/data/count.rds b/ch1_evidence_causes/data/count.rds
diff --git a/ch1_evidence_causes/data/samples_4.2_narrowed_tca.xlsx b/ch1_evidence_causes/data/samples_4.2_narrowed_tca.xlsx
diff --git a/ch1_evidence_causes/data/samples_5.1_narrowed_criteria1.xlsx b/ch1_evidence_causes/data/samples_5.1_narrowed_criteria1.xlsx
diff --git a/ch1_evidence_causes/data/samples_5.2_narrowed_criteria2.xlsx b/ch1_evidence_causes/data/samples_5.2_narrowed_criteria2.xlsx
diff --git a/ch1_evidence_causes/data/samples_5.3_narrowed_criteria3.xlsx b/ch1_evidence_causes/data/samples_5.3_narrowed_criteria3.xlsx
diff --git a/ch1_evidence_causes/data/samples_5.4_narrowed_criteria4.xlsx b/ch1_evidence_causes/data/samples_5.4_narrowed_criteria4.xlsx
diff --git a/ch1_evidence_causes/figures/Ch1_evidence_causes.pdf b/ch1_evidence_causes/figures/Ch1_evidence_causes.pdf
diff --git a/ch1_evidence_causes/figures/Ch1_evidence_causes.png b/ch1_evidence_causes/figures/Ch1_evidence_causes.png
diff --git a/ch1_evidence_causes/figures/Ch1_evidence_causes.svg b/ch1_evidence_causes/figures/Ch1_evidence_causes.svg