From a699252c4fa9ee4e4574744ed08db8f086f5f00a Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 16:18:42 +0100 Subject: [PATCH 01/18] Update tutorial.md addf unding --- .../ecology/tutorials/biodiversity-data-exploration/tutorial.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.md b/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.md index 9d734f0421b051..a13d58af2b1bdb 100644 --- a/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.md +++ b/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.md @@ -24,6 +24,8 @@ contributions: - yvanlebras funding: - gallantries + - pndb + - fnso2019 --- From 52499970237393a1ce379995415e14bcecb10c7c Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 16:19:49 +0100 Subject: [PATCH 02/18] Update tutorial.md add funding --- topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md b/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md index 58933fd040273e..d7c32265f4e0f0 100644 --- a/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md +++ b/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md @@ -24,6 +24,9 @@ contributors: - ecoissac - fboyer - yvanlebras + funding: + - gallantries + - pndb --- From fcfa2a3b6d70439ee4ea26f1d5a66639c272e0be Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 16:20:20 +0100 Subject: [PATCH 03/18] Update tutorial.md --- topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md b/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md index fdc931dca4a875..455168b8dde4f6 100644 --- a/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md +++ b/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md @@ -32,6 +32,9 @@ contributors: - colineroyaux - yvanlebras - jbmihoub +funding: +- gallantries +- pndb --- From 109a1f2b2674b34963191b81e86b337e6fc5c65e Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 16:20:53 +0100 Subject: [PATCH 04/18] Update tutorial.md --- .../ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md b/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md index c0d2a511a6e25f..d337ef99b39cbf 100644 --- a/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md +++ b/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md @@ -21,6 +21,10 @@ contributors: - colineroyaux - Marie59 - yvanlebras + funding: + - gallantries + - fairease + - pndb --- From 5f040cf5857d92baa407db672f9e52d52ffd0771 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 16:21:19 +0100 Subject: [PATCH 05/18] Update tutorial.md --- .../tutorials/QGIS_Web_Feature_Services/tutorial.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md b/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md index d337ef99b39cbf..14d0ed15006ee5 100644 --- a/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md +++ b/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md @@ -21,10 +21,10 @@ contributors: - colineroyaux - Marie59 - yvanlebras - funding: - - gallantries - - fairease - - pndb +funding: +- gallantries +- fairease +- pndb --- From 571b3fc325ff58b3d6aeb71ea6b36bbffdfd5bee Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 16:22:09 +0100 Subject: [PATCH 06/18] Update tutorial.md --- topics/ecology/tutorials/champs-blocs/tutorial.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/topics/ecology/tutorials/champs-blocs/tutorial.md b/topics/ecology/tutorials/champs-blocs/tutorial.md index b6659aef72896d..a9057c79e6d7fc 100644 --- a/topics/ecology/tutorials/champs-blocs/tutorial.md +++ b/topics/ecology/tutorials/champs-blocs/tutorial.md @@ -19,6 +19,8 @@ contributors: - yvanlebras translations: - fr +funding: +- pndb --- From a8f9c32e5ca6037a87f1b08651c6f977c4c65a6a Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 16:22:39 +0100 Subject: [PATCH 07/18] Update tutorial.md --- topics/ecology/tutorials/gbif_cleaning/tutorial.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/topics/ecology/tutorials/gbif_cleaning/tutorial.md b/topics/ecology/tutorials/gbif_cleaning/tutorial.md index 42e407859277ee..0b37a36044e9ee 100644 --- a/topics/ecology/tutorials/gbif_cleaning/tutorial.md +++ b/topics/ecology/tutorials/gbif_cleaning/tutorial.md @@ -22,6 +22,8 @@ tags: contributors: - yvanlebras - sbenateau +funding: +- pndb --- From 72d88d4ab12706d322089141a86a01084a3929bd Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 16:23:18 +0100 Subject: [PATCH 08/18] Update tutorial.md --- topics/ecology/tutorials/obisindicators/tutorial.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/topics/ecology/tutorials/obisindicators/tutorial.md b/topics/ecology/tutorials/obisindicators/tutorial.md index 15223d6f7ef3fe..e254b37abd0e92 100644 --- a/topics/ecology/tutorials/obisindicators/tutorial.md +++ b/topics/ecology/tutorials/obisindicators/tutorial.md @@ -16,6 +16,8 @@ contributions: - yvanlebras funding: - gallantries + - fairease + - pndb --- From f0b5555d696dd2bb7ad82ce23575241d4cf91e50 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 16:24:04 +0100 Subject: [PATCH 09/18] Update tutorial.md --- topics/ecology/tutorials/panoply_ebv/tutorial.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/topics/ecology/tutorials/panoply_ebv/tutorial.md b/topics/ecology/tutorials/panoply_ebv/tutorial.md index ad9fdefa2b4180..4052f3cf97f51b 100644 --- a/topics/ecology/tutorials/panoply_ebv/tutorial.md +++ b/topics/ecology/tutorials/panoply_ebv/tutorial.md @@ -24,7 +24,10 @@ contributors: - colineroyaux - Marie59 - annefou - +funding: +- gallantries +- fairease +- pndb --- From 379b5c7065482c06ffe4bd89fd3f97d1f23cde0b Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 16:24:43 +0100 Subject: [PATCH 10/18] Update tutorial.md --- topics/ecology/tutorials/remote-sensing/tutorial.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/topics/ecology/tutorials/remote-sensing/tutorial.md b/topics/ecology/tutorials/remote-sensing/tutorial.md index cdee05efadf9b0..b6aa25c17151b4 100644 --- a/topics/ecology/tutorials/remote-sensing/tutorial.md +++ b/topics/ecology/tutorials/remote-sensing/tutorial.md @@ -22,7 +22,8 @@ contributions: authorship: - Marie59 - yvanlebras - + funding: + - pndb --- From 99bc07fdb84131c7d32ff13494e7dd8b84b31b1c Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 22:08:57 +0100 Subject: [PATCH 11/18] Update topics/ecology/tutorials/gbif_cleaning/tutorial.md Co-authored-by: Helena --- topics/ecology/tutorials/gbif_cleaning/tutorial.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/topics/ecology/tutorials/gbif_cleaning/tutorial.md b/topics/ecology/tutorials/gbif_cleaning/tutorial.md index 0b37a36044e9ee..cb755e709004c4 100644 --- a/topics/ecology/tutorials/gbif_cleaning/tutorial.md +++ b/topics/ecology/tutorials/gbif_cleaning/tutorial.md @@ -19,11 +19,12 @@ tags: - gbif - data management - data cleaning -contributors: -- yvanlebras -- sbenateau -funding: -- pndb +contributions: + authorship: + - yvanlebras + - sbenateau + funding: + - pndb --- From a75b30c2db7e9d774db84af3d1f029a0c98a467c Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 22:10:12 +0100 Subject: [PATCH 12/18] Update tutorial.md --- .../tutorials/Obitools-metabarcoding/tutorial.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md b/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md index d7c32265f4e0f0..5eebd37487c662 100644 --- a/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md +++ b/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md @@ -18,13 +18,14 @@ tags: - EBV workflow - eDNA - Metabarcoding -contributors: -- colineroyaux -- onorvez -- ecoissac -- fboyer -- yvanlebras - funding: +contributions: +- authorship: + - colineroyaux + - onorvez + - ecoissac + - fboyer + - yvanlebras +- funding: - gallantries - pndb From 2d3429790cbed355aec357b0ccad383dd5aafa75 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 22:11:12 +0100 Subject: [PATCH 13/18] Update tutorial.md --- topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md b/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md index 5eebd37487c662..1b477a338240a7 100644 --- a/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md +++ b/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.md @@ -19,13 +19,13 @@ tags: - eDNA - Metabarcoding contributions: -- authorship: + authorship: - colineroyaux - onorvez - ecoissac - fboyer - yvanlebras -- funding: + funding: - gallantries - pndb From 26e69707bb46c5703816b6a767c0c36a1adcada5 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 22:13:15 +0100 Subject: [PATCH 14/18] Update tutorial.md --- .../PAMPA-toolsuite-tutorial/tutorial.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md b/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md index 455168b8dde4f6..02cc69ef44bf6c 100644 --- a/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md +++ b/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md @@ -28,13 +28,14 @@ tags: - EBV dataset - EBV workflow - modeling -contributors: -- colineroyaux -- yvanlebras -- jbmihoub -funding: -- gallantries -- pndb +contributions: + authorship: + - colineroyaux + - yvanlebras + - jbmihoub + funding: + - gallantries + - pndb --- From 92498e0ff79c064283b514232105f9ae59493001 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 22:14:19 +0100 Subject: [PATCH 15/18] Update tutorial.md --- .../QGIS_Web_Feature_Services/tutorial.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md b/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md index 14d0ed15006ee5..594af133d82568 100644 --- a/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md +++ b/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.md @@ -17,14 +17,15 @@ tags: - QGIS - Maps - OGC -contributors: -- colineroyaux -- Marie59 -- yvanlebras -funding: -- gallantries -- fairease -- pndb +contributions: + authorship: + - colineroyaux + - Marie59 + - yvanlebras + funding: + - gallantries + - fairease + - pndb --- From fa6ce3b101355397bb6ae308f59966caf8eb4f6a Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 22:17:03 +0100 Subject: [PATCH 16/18] Update tutorial.md --- topics/ecology/tutorials/champs-blocs/tutorial.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/topics/ecology/tutorials/champs-blocs/tutorial.md b/topics/ecology/tutorials/champs-blocs/tutorial.md index a9057c79e6d7fc..c97536b1d518e7 100644 --- a/topics/ecology/tutorials/champs-blocs/tutorial.md +++ b/topics/ecology/tutorials/champs-blocs/tutorial.md @@ -14,13 +14,14 @@ key_points: - Diversity indicators - Champs Blocs - Boulder Fields -contributors: -- Marie59 -- yvanlebras +contributions: + authorship: + - Marie59 + - yvanlebras + funding: + - pndb translations: - fr -funding: -- pndb --- From 13a2f255a9387796a69eaa648dcb753228dcd70c Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 19 Jan 2024 22:18:23 +0100 Subject: [PATCH 17/18] Update tutorial.md --- .../ecology/tutorials/panoply_ebv/tutorial.md | 20 ++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/topics/ecology/tutorials/panoply_ebv/tutorial.md b/topics/ecology/tutorials/panoply_ebv/tutorial.md index 4052f3cf97f51b..32c44112cb167e 100644 --- a/topics/ecology/tutorials/panoply_ebv/tutorial.md +++ b/topics/ecology/tutorials/panoply_ebv/tutorial.md @@ -19,15 +19,17 @@ tags: - interactive-tools - EBV cube - Data visualization -contributors: -- yvanlebras -- colineroyaux -- Marie59 -- annefou -funding: -- gallantries -- fairease -- pndb +contributions: + authorship: + - pndb + - yvanlebras + - colineroyaux + - Marie59 + - annefou + funding: + - gallantries + - fairease + - pndb --- From 4dbcdcbef2f7fb8e07a743d4731cef4b52a243ff Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Sat, 20 Jan 2024 08:36:38 +0100 Subject: [PATCH 18/18] Update tutorial.md fix bold headers errors --- topics/ecology/tutorials/obisindicators/tutorial.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/topics/ecology/tutorials/obisindicators/tutorial.md b/topics/ecology/tutorials/obisindicators/tutorial.md index e254b37abd0e92..a92c17cfe0fb40 100644 --- a/topics/ecology/tutorials/obisindicators/tutorial.md +++ b/topics/ecology/tutorials/obisindicators/tutorial.md @@ -113,7 +113,7 @@ This first step consist of downloading and uploading obis data onto galaxy. You are now all set to use your obis data in order to do a diversity analysis. -## **Ocean biodiversity indicators** +## Ocean biodiversity indicators > Ocean biodiversity indicators > @@ -184,13 +184,13 @@ Maxp is the maximum of the total number of records for the ith-species ni divide ## Hill -### **Hill 1** +### Hill 1 The Hill biodiversity index accounts for species’ relative abundance (number of records in OBIS) and Hill1 can be roughly interpreted as the number of species with “typical” abundances, and is a commonly used indicator for marine biodiversity richness. It is defined as: Warning: The Simpson index has the same assumptions as the Shannon index. -### **Hill 2** +### Hill 2 The Hill biodiversity index accounts for species’ relative abundance (number of records in OBIS) and discounts rare species, so Hill2 can be interpreted as the equivalent to the number of more dominant species and so is less sensitive to sample size than Hill1. The Hill index is a commonly used indicator for marine biodiversity richness. It is defined as: