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-rw-r--r--data_preparation_modeling/main.acn (renamed from data_preparation/main.acn)0
-rw-r--r--data_preparation_modeling/main.pdf (renamed from data_preparation/main.pdf)bin3320472 -> 3320472 bytes
-rw-r--r--data_preparation_modeling/main.tex (renamed from data_preparation/main.tex)0
-rw-r--r--deliverable/main.pdfbin4868517 -> 4876834 bytes
-rw-r--r--deliverable/main.tex7
l---------mysql_out1
l---------queries1
-rw-r--r--queries/data_per_assay_per_year_per_outcome17
-rw-r--r--queries/donor_demo11
-rw-r--r--queries/donors_list1
-rw-r--r--queries/donors_outcome_across_years18
-rw-r--r--queries/high_reponders4
-rw-r--r--queries/mike_repeat_visit23
-rw-r--r--queries/null_donors7
-rw-r--r--queries/repeat_investigation5
-rw-r--r--queries/simon_data_extra22
-rw-r--r--queries/simon_initial16
-rw-r--r--queries/simon_initial_check16
-rw-r--r--queries/visit_multiple_2111
-rw-r--r--queries/visits_all3
20 files changed, 160 insertions, 3 deletions
diff --git a/data_preparation/main.acn b/data_preparation_modeling/main.acn
index e69de29..e69de29 100644
--- a/data_preparation/main.acn
+++ b/data_preparation_modeling/main.acn
diff --git a/data_preparation/main.pdf b/data_preparation_modeling/main.pdf
index b7b9148..b7b9148 100644
--- a/data_preparation/main.pdf
+++ b/data_preparation_modeling/main.pdf
Binary files differ
diff --git a/data_preparation/main.tex b/data_preparation_modeling/main.tex
index 4b72ed4..4b72ed4 100644
--- a/data_preparation/main.tex
+++ b/data_preparation_modeling/main.tex
diff --git a/deliverable/main.pdf b/deliverable/main.pdf
index 9f2bd1c..5173bff 100644
--- a/deliverable/main.pdf
+++ b/deliverable/main.pdf
Binary files differ
diff --git a/deliverable/main.tex b/deliverable/main.tex
index 521be50..078533e 100644
--- a/deliverable/main.tex
+++ b/deliverable/main.tex
@@ -1137,7 +1137,12 @@ P values for all correlations shown in the correlation plots below were calculat
\subsection{Code and data availability}
-The code and data belonging to this project can be found in the \href{}{github repository}.
+The code and data belonging to this project can be found in the \href{https://github.com/Vinkage/fluprint_exploration}{github repository}.
+The repository contains the directories \lstinline{bussiness_understand}, \lstinline{data_understanding} and \lstinline{data_preparation_modeling} which contain all the \LaTeX source files for what was written during the project.
+However, the source files for the final pdf deliverable that is to be graded are in the \lstinline{deliverable} directory.
+The directory \lstinline{csv} contains all the flat data files that were generated in this work, \lstinline{queries} contains the SQL source files.
+As mentioned above, the import script for constructing the database is added as a submodule called \lstinline{fluprint}.
+Other files and directories are data files used in the latex source files.
\printbibliography
diff --git a/mysql_out b/mysql_out
deleted file mode 120000
index f26dde7..0000000
--- a/mysql_out
+++ /dev/null
@@ -1 +0,0 @@
-/var/lib/mysql/fluprint \ No newline at end of file
diff --git a/queries b/queries
deleted file mode 120000
index 34efd61..0000000
--- a/queries
+++ /dev/null
@@ -1 +0,0 @@
-/home/mike/.local/share/db_ui/fluprint/ \ No newline at end of file
diff --git a/queries/data_per_assay_per_year_per_outcome b/queries/data_per_assay_per_year_per_outcome
new file mode 100644
index 0000000..2f8c063
--- /dev/null
+++ b/queries/data_per_assay_per_year_per_outcome
@@ -0,0 +1,17 @@
+SELECT donors.study_id AS study,
+ donors.id as donor,
+ donor_visits.visit_year AS year,
+ donor_visits.vaccine_resp AS outcome,
+ experimental_data.assay AS assay,
+ experimental_data.data AS data,
+ experimental_data.name_formatted as name,
+ experimental_data.units
+FROM donors
+ LEFT JOIN donor_visits
+ ON donors.id = donor_visits.donor_id
+ INNER JOIN experimental_data
+ ON donor_visits.id = experimental_data.donor_visits_id
+ AND experimental_data.donor_id = donor_visits.donor_id
+WHERE donors.gender IS NOT NULL
+ AND donor_visits.vaccine_resp IS NOT NULL
+ORDER BY donor_visits.visit_year ASC
diff --git a/queries/donor_demo b/queries/donor_demo
new file mode 100644
index 0000000..dd5077a
--- /dev/null
+++ b/queries/donor_demo
@@ -0,0 +1,11 @@
+SELECT donors.id as Donor,
+ donors.gender as Gender,
+ donor_visits.age_round as Age,
+ donors.race as Ethnicity,
+ donor_visits.cmv_status as 'CMV status',
+ donor_visits.vaccine_resp as Response
+from donors
+ LEFT JOIN donor_visits
+ ON donors.id = donor_visits.donor_id
+ AND donor_visits.visit_id = 1
+where donor_visits.vaccine_resp is not null
diff --git a/queries/donors_list b/queries/donors_list
new file mode 100644
index 0000000..e3610bd
--- /dev/null
+++ b/queries/donors_list
@@ -0,0 +1 @@
+SELECT * from `donors`
diff --git a/queries/donors_outcome_across_years b/queries/donors_outcome_across_years
new file mode 100644
index 0000000..1cbf55f
--- /dev/null
+++ b/queries/donors_outcome_across_years
@@ -0,0 +1,18 @@
+SELECT donors.id AS donor_id,
+ donor_visits.age AS age,
+ donor_visits.vaccine_resp AS outcome,
+ donor_visits.visit_id AS visit,
+ donor_visits.visit_day AS day,
+ donor_visits.visit_year AS year
+ # experimental_data.name_formatted AS data_name,
+ # experimental_data.data AS data,
+FROM donors
+ LEFT JOIN donor_visits
+ ON donors.id = donor_visits.donor_id
+ # AND donor_visits.visit_id = 1
+ # INNER JOIN experimental_data
+ # ON donor_visits.id = experimental_data.donor_visits_id
+ # AND experimental_data.donor_id = donor_visits.donor_id
+WHERE donors.gender IS NOT NULL
+ AND donor_visits.vaccine = 4
+ORDER BY donors.id DESC
diff --git a/queries/high_reponders b/queries/high_reponders
new file mode 100644
index 0000000..3f33373
--- /dev/null
+++ b/queries/high_reponders
@@ -0,0 +1,4 @@
+SELECT * from donor_visits
+where vaccine_resp is not null
+and donor_id = 166
+order by visit_year ASC
diff --git a/queries/mike_repeat_visit b/queries/mike_repeat_visit
new file mode 100644
index 0000000..c0bfbfd
--- /dev/null
+++ b/queries/mike_repeat_visit
@@ -0,0 +1,23 @@
+SELECT donors.id AS donor_id,
+ donors.study_id AS study,
+ donor_visits.age AS age,
+ donor_visits.vaccine_resp AS outcome,
+ donor_visits.visit_year AS year,
+ donor_visits.visit_type_hai as type,
+ donor_visits.d_geo_mean as hai_response,
+ experimental_data.name AS name,
+ experimental_data.name_formatted AS name_formatted,
+ experimental_data.assay AS assay,
+ experimental_data.data AS data
+FROM donors
+ LEFT JOIN donor_visits
+ ON donors.id = donor_visits.donor_id
+ INNER JOIN experimental_data
+ ON donor_visits.id = experimental_data.donor_visits_id
+ AND experimental_data.donor_id = donor_visits.donor_id
+WHERE donors.gender IS NOT NULL
+ AND donor_visits.vaccine_resp IS NOT NULL
+ AND donor_visits.vaccine = 4
+ AND donor_visits.visit_type_hai = "pre"
+ AND donor_visits.visit_id != 1
+ORDER BY donors.study_donor_id DESC
diff --git a/queries/null_donors b/queries/null_donors
new file mode 100644
index 0000000..4646677
--- /dev/null
+++ b/queries/null_donors
@@ -0,0 +1,7 @@
+SELECT * from donors
+where donors.id is NULL or
+donors.study_donor_id is NULL or
+donors.study_id is NULL or
+donors.study_internal_id is NULL or
+donors.gender is NULL or
+donors.race is NULL
diff --git a/queries/repeat_investigation b/queries/repeat_investigation
new file mode 100644
index 0000000..293e21c
--- /dev/null
+++ b/queries/repeat_investigation
@@ -0,0 +1,5 @@
+SELECT *
+from `donor_visits`
+left join donors on
+ donors.id = donor_visits.donor_id
+where study_id = 15
diff --git a/queries/simon_data_extra b/queries/simon_data_extra
new file mode 100644
index 0000000..ea97abb
--- /dev/null
+++ b/queries/simon_data_extra
@@ -0,0 +1,22 @@
+SELECT donors.id AS donor_id,
+ donors.study_id AS study,
+ donor_visits.age AS age,
+ donor_visits.vaccine_resp AS outcome,
+ donor_visits.visit_year AS year,
+ donor_visits.visit_type_hai as type,
+ donor_visits.d_geo_mean as hai_response,
+ experimental_data.name AS name,
+ experimental_data.name_formatted AS data_name,
+ experimental_data.assay AS assay,
+ experimental_data.data AS data
+FROM donors
+ LEFT JOIN donor_visits
+ ON donors.id = donor_visits.donor_id
+ AND donor_visits.visit_id = 1
+ INNER JOIN experimental_data
+ ON donor_visits.id = experimental_data.donor_visits_id
+ AND experimental_data.donor_id = donor_visits.donor_id
+WHERE donors.gender IS NOT NULL
+ AND donor_visits.vaccine_resp IS NOT NULL
+ AND donor_visits.vaccine = 4
+ORDER BY donors.study_donor_id DESC
diff --git a/queries/simon_initial b/queries/simon_initial
new file mode 100644
index 0000000..f7ae18a
--- /dev/null
+++ b/queries/simon_initial
@@ -0,0 +1,16 @@
+SELECT donors.id AS donor_id,
+ donor_visits.age AS age,
+ donor_visits.vaccine_resp AS outcome,
+ experimental_data.name_formatted AS data_name,
+ experimental_data.data AS data
+FROM donors
+ LEFT JOIN donor_visits
+ ON donors.id = donor_visits.donor_id
+ AND donor_visits.visit_id = 1
+ INNER JOIN experimental_data
+ ON donor_visits.id = experimental_data.donor_visits_id
+ AND experimental_data.donor_id = donor_visits.donor_id
+WHERE donors.gender IS NOT NULL
+ AND donor_visits.vaccine_resp IS NOT NULL
+ AND donor_visits.vaccine = 4
+ORDER BY donors.study_donor_id DESC
diff --git a/queries/simon_initial_check b/queries/simon_initial_check
new file mode 100644
index 0000000..703a685
--- /dev/null
+++ b/queries/simon_initial_check
@@ -0,0 +1,16 @@
+SELECT donors.id AS donor_id,
+ donor_visits.age AS age,
+ donor_visits.vaccine_resp AS outcome,
+ # experimental_data.name_formatted AS data_name,
+ # experimental_data.data AS data,
+ donor_visits.visit_year AS year
+FROM donors
+ LEFT JOIN donor_visits
+ ON donors.id = donor_visits.donor_id
+ # AND donor_visits.visit_id = 1
+ # INNER JOIN experimental_data
+ # ON donor_visits.id = experimental_data.donor_visits_id
+ # AND experimental_data.donor_id = donor_visits.donor_id
+WHERE donors.gender IS NOT NULL
+ AND donor_visits.vaccine = 4
+ORDER BY donors.id DESC
diff --git a/queries/visit_multiple_21 b/queries/visit_multiple_21
new file mode 100644
index 0000000..d8a16fa
--- /dev/null
+++ b/queries/visit_multiple_21
@@ -0,0 +1,11 @@
+SELECT * from `donor_visits`
+join(
+select donor_visits.donor_id
+from donor_visits
+group by donor_visits.donor_id
+having count(*) > 1) s on donor_visits.donor_id = s.donor_id
+join donors
+on donors.id = donor_visits.donor_id
+where study_id = 21
+and donor_visits.donor_id = 166
+order by donor_visits.donor_id, visit_id
diff --git a/queries/visits_all b/queries/visits_all
new file mode 100644
index 0000000..0a6dcfa
--- /dev/null
+++ b/queries/visits_all
@@ -0,0 +1,3 @@
+SELECT * from `donor_visits`
+where donor_id = 779
+order by visit_year
generated by cgit v1.2.3 (git 2.25.1) at 2026-02-12 06:53:27 +0000