Creating Home Range (KDE 50% and 95%) with Barriers in QGIS
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MercedesEhrhardt
Dec 17, 2019, 7:54:56 AM12/17/19
to GIS In Ecology Forum
Hi,
I am very new to QGIS (and any similar type of software/programme and programming) and am currently teaching myself to use it for my bachelor dissertation (I am studying an Animal Behaviour and Welfare degree in the UK). Coming across this forum was amazing, and it has helped me a lot so far! So thank you all for that.
For my project, I am working with data on a small dolphin population in southern Brazil (around 60 individuals). I have assisted researchers in their fieldwork and I am now working on mapping out the home ranges for the population, but at the moment I am stuck.
I have managed to make heatmaps for the whole population as well as for males and females, but only 'general' ones - not specifically 50% and 95%, which is what I need to assess the data in more detail. I have the 'Introduction to using GIS in marine biology' book and workbooks, and have found help to other steps on this forum and on youtube, but I can't seem to find this particular question on here.
As the dolphins live in a lagoon area, the land areas that need to be taken into consideration when producing the heatmaps (I have not included any barriers in the heatmaps I have made so far), but I cannot seem to figure out the way to do it in QGIS, as the tutorial I have found (in the books and also online) are for ArcGIS or other. I have a shapefile for the lagoon area (land area) which one of my colleagues from Brazil already had made previously - but I am unsure how to make an empty layer to use as a barrier?
I have tried to follow the tutorial for ArcGIS (from workbook 4, chapter 5) to see if I could suss my way to the functions in QGIS, but so far I haven't succeeded.
I am using a Mac with an OSMojave system, and QGIS 3.4.9 Madeira.
If anyone knows a way to do this I would greatly appreciate the help. I can, of course, send pictures of the things I have made so far if that helps.
Thank you!
Emilie
cdma...@gisinecology.com
Dec 17, 2019, 8:16:24 AM12/17/19
to gis-in-eco...@googlegroups.com
Hi Emilie,
Thanks for your post. At the moment, there is no easy way to take
complex barriers to movement (like areas of land for your dolphins) into
account when creating kernel density estimates (KDEs - also known as
heatmaps) while using QGIS rather than ArcGIS. This is because there are
currently no equivilant tools in QGIS to the ones you'd use in ArcGIS to
do this
There are four possible ways round this.
The first is to use one of the home range tools in R to create a KDE
with barriers to movement (I think there is one in the adehabitat
package). The main issues with this approach is that you'd have to learn
how to use R, and that it only allows you to incorporate very simple
barriers to movement (too simple to represent most real-world barriers
to movement).
The second option is to make your KDE using the heatmap tool in QGIS and
then clip it to remove any areas that fall on land. This will remove the
areas from land from it. The biggest issue here is that it is only
appropriate to use this if your barrier represents a closed polygon with
no concave angles in its outline and with a relatively simple shape. I
your case, this would only work if your lagoon is more or less
circular/oval/polygonal and the animals never move out of it.
The third option is to use ArcGIS to generate your KDEs with barriers.
The biggest limitation here is that you have to use ArcGIS (and
potentially learn a different GIS software packagage). You can get a
trial licence for ArcGIS for free, but it will only last a few months,
and this can be an issue if you wish to re-do your analysis at a later
point. Given this, it is a far from ideal solution.
The final option is to use a Python Script that has been written that
specifically allows you to replicate the workflow for creating a KDE
with barriers from ArcGIS in QGIS. This script was put together a few
years ago based on the workbook you mention (Supplementary Workbook 4),
and I would need to check that I can share this before passing it on to
you. In addition, it may be quite complicated to work out how to
actually use it (I've not personally used it myself). However, at the
moment, it is the only way I know of being able to create KDEs for
animals with barriers to movement in QGIS.
Since this topic has come up, I am currently working on an updated
version 'An Introduction To USing GIS In Marine Biology Supplementary
Workbook 4' that will be specific to QGIS, and I am hoping I'm going to
be able to include full instructions on how to use this Python script to
create KDEs with barriers in QGIS (this is by no means certain yet).
However, this will not be available until the middle of next year at the
earliest, which is probably not much use for your project.
I hope this helps, and if you need any clarification of the above, or
would like a copy of the Python script I mentioned abobe, just post back
on this thread.
All the best,
Colin
On 2019-12-16 21:47, MercedesEhrhardt wrote:
> Hi,
>
> I am very new to QGIS (and any similar type of software/programme and
> programming) and am currently teaching myself to use it for my
> bachelor dissertation (I am studying an Animal Behaviour and Welfare
> degree in the UK). Coming across this forum was amazing, and it has
> helped me a lot so far! So thank you all for that.
>
> For my project, I am working with data on a small dolphin population
> in southern Brazil (around 60 individuals). I have assisted
> researchers in their fieldwork and I am now working on mapping out the
> home ranges for the population, but at the moment I am stuck.
>
> I have managed to make heatmaps for the whole population as well as
> for males and females, but only 'general' ones - not specifically 50%
> and 95%, which is what I need to assess the data in more detail. I
> have the '_Introduction to using GIS in marine biology_' book and
> --
> ======================================================================
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> [1].
>
>
> Links:
> ------
> [1]
> https://groups.google.com/d/msgid/gis-in-ecology-forum/6af62bc4-110f-4be3-a6c1-c8aed0c1a796%40googlegroups.com?utm_medium=email&utm_source=footer
Thanks for your post. At the moment, there is no easy way to take
complex barriers to movement (like areas of land for your dolphins) into
account when creating kernel density estimates (KDEs - also known as
heatmaps) while using QGIS rather than ArcGIS. This is because there are
currently no equivilant tools in QGIS to the ones you'd use in ArcGIS to
do this
There are four possible ways round this.
The first is to use one of the home range tools in R to create a KDE
with barriers to movement (I think there is one in the adehabitat
package). The main issues with this approach is that you'd have to learn
how to use R, and that it only allows you to incorporate very simple
barriers to movement (too simple to represent most real-world barriers
to movement).
The second option is to make your KDE using the heatmap tool in QGIS and
then clip it to remove any areas that fall on land. This will remove the
areas from land from it. The biggest issue here is that it is only
appropriate to use this if your barrier represents a closed polygon with
no concave angles in its outline and with a relatively simple shape. I
your case, this would only work if your lagoon is more or less
circular/oval/polygonal and the animals never move out of it.
The third option is to use ArcGIS to generate your KDEs with barriers.
The biggest limitation here is that you have to use ArcGIS (and
potentially learn a different GIS software packagage). You can get a
trial licence for ArcGIS for free, but it will only last a few months,
and this can be an issue if you wish to re-do your analysis at a later
point. Given this, it is a far from ideal solution.
The final option is to use a Python Script that has been written that
specifically allows you to replicate the workflow for creating a KDE
with barriers from ArcGIS in QGIS. This script was put together a few
years ago based on the workbook you mention (Supplementary Workbook 4),
and I would need to check that I can share this before passing it on to
you. In addition, it may be quite complicated to work out how to
actually use it (I've not personally used it myself). However, at the
moment, it is the only way I know of being able to create KDEs for
animals with barriers to movement in QGIS.
Since this topic has come up, I am currently working on an updated
version 'An Introduction To USing GIS In Marine Biology Supplementary
Workbook 4' that will be specific to QGIS, and I am hoping I'm going to
be able to include full instructions on how to use this Python script to
create KDEs with barriers in QGIS (this is by no means certain yet).
However, this will not be available until the middle of next year at the
earliest, which is probably not much use for your project.
I hope this helps, and if you need any clarification of the above, or
would like a copy of the Python script I mentioned abobe, just post back
on this thread.
All the best,
Colin
On 2019-12-16 21:47, MercedesEhrhardt wrote:
> Hi,
>
> I am very new to QGIS (and any similar type of software/programme and
> programming) and am currently teaching myself to use it for my
> bachelor dissertation (I am studying an Animal Behaviour and Welfare
> degree in the UK). Coming across this forum was amazing, and it has
> helped me a lot so far! So thank you all for that.
>
> For my project, I am working with data on a small dolphin population
> in southern Brazil (around 60 individuals). I have assisted
> researchers in their fieldwork and I am now working on mapping out the
> home ranges for the population, but at the moment I am stuck.
>
> I have managed to make heatmaps for the whole population as well as
> for males and females, but only 'general' ones - not specifically 50%
> and 95%, which is what I need to assess the data in more detail. I
> workbooks, and have found help to other steps on this forum and on
> youtube, but I can't seem to find this particular question on here.
>
> As the dolphins live in a lagoon area, the land areas that need to be
> taken into consideration when producing the heatmaps (I have not
> included any barriers in the heatmaps I have made so far), but I
> cannot seem to figure out the way to do it in QGIS, as the tutorial I
> have found (in the books and also online) are for ArcGIS or other. I
> have a shapefile for the lagoon area (land area) which one of my
> colleagues from Brazil already had made previously - but I am unsure
> how to make an empty layer to use as a barrier?
>
> I have tried to follow the tutorial for ArcGIS (from workbook 4,
> chapter 5) to see if I could suss my way to the functions in QGIS, but
> so far I haven't succeeded.
> I am using a Mac with an OSMojave system, and QGIS 3.4.9 Madeira.
>
> If anyone knows a way to do this I would greatly appreciate the help.
> I can, of course, send pictures of the things I have made so far if
> that helps.
>
> Thank you!
> Emilie
>
> --
> youtube, but I can't seem to find this particular question on here.
>
> As the dolphins live in a lagoon area, the land areas that need to be
> taken into consideration when producing the heatmaps (I have not
> included any barriers in the heatmaps I have made so far), but I
> cannot seem to figure out the way to do it in QGIS, as the tutorial I
> have found (in the books and also online) are for ArcGIS or other. I
> have a shapefile for the lagoon area (land area) which one of my
> colleagues from Brazil already had made previously - but I am unsure
> how to make an empty layer to use as a barrier?
>
> I have tried to follow the tutorial for ArcGIS (from workbook 4,
> chapter 5) to see if I could suss my way to the functions in QGIS, but
> so far I haven't succeeded.
> I am using a Mac with an OSMojave system, and QGIS 3.4.9 Madeira.
>
> If anyone knows a way to do this I would greatly appreciate the help.
> I can, of course, send pictures of the things I have made so far if
> that helps.
>
> Thank you!
> Emilie
>
> --
> ======================================================================
> You received this message because you are subscribed to the "GIS In
> Ecology Forum" discussion group
> (http://www.gisinecology.com/GIS_in_Ecology_forum.htm).
>
> To control how often you get emails from this group, go to
> http://groups.google.com/group/gis-in-ecology-forum/subscribe (you
> will need to log on to get to this page).
>
> To post to this group, either log onto the group's home page or send
> an email to
> gis-in-eco...@googlegroups.com.
>
> The rules for posting to this group can be found here:
> http://groups.google.com/group/gis-in-ecology-forum/browse_thread/thread/df31a0822742203f#.
>
> To unsubscribe from this group, email:
> gis-in-ecology-f...@googlegroups.com
>
> All information on this forum is provided on an 'as is' basis. GIS In
> Ecology is not responsible for checking the accuracy or suitability of
> any posting or response.
> ======================================================================
> ---
> You received this message because you are subscribed to the Google
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> To view this discussion on the web visit
> https://groups.google.com/d/msgid/gis-in-ecology-forum/6af62bc4-110f-4be3-a6c1-c8aed0c1a796%40googlegroups.com
> [1].
>
>
> Links:
> ------
> [1]
> https://groups.google.com/d/msgid/gis-in-ecology-forum/6af62bc4-110f-4be3-a6c1-c8aed0c1a796%40googlegroups.com?utm_medium=email&utm_source=footer
MercedesEhrhardt
Jan 17, 2020, 4:55:05 AM1/17/20
to GIS In Ecology Forum
Hi Colin,
I just wanted to say thank you again for your reply, and let you know that I in the end decided to try it out with an R script - luckily, I have some friends who are working with R software, and could help me tweak an R script previously used for something similar.
Currently working on that now.
Just wanted to let you know what way I took it, in case you wondered. Also, sorry for the very slow response.
Cheers
Emilie
>
> All information on this forum is provided on an 'as is' basis. GIS In
> Ecology is not responsible for checking the accuracy or suitability of
> any posting or response.
> ======================================================================
> ---
> You received this message because you are subscribed to the Google
> Groups "GIS In Ecology Forum" group.
> To unsubscribe from this group and stop receiving emails from it, send
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GIS in Ecology
Jan 23, 2020, 7:06:41 AM1/23/20
to GIS In Ecology Forum
HI Emilie,
Thanks for letting us know how you solved this issue. This is always useful to know (and is helpful for other people who may come across this thread while trying to solve a similar problem).
All the best,
Colin
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