DV-129 ⁃ Refine the Reports feature within Descriptive Stats

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The suggestions that used to be here have been moved to a comment.

All the suggestions from all comments on this task have been compiled in the following excel document (duplicates consolidated, suggestions that are not applicable removed, etc.)

[^ReportsFeatureSuggestions.xlsx]

┆Issue is synchronized with this Jira Task by Unito ┆Attachments: 2019 Inventaire des mammiferes terrestre Momba.pdf | ACC6E81E26604A659AF2A4B8D36B923B.png | Africa_V2_cadre.tiff | Ithala_dscrptv_stts_rprt_2021.10.13_11.12.23.html | MoukalabaWakaMonkey.jpg | Rapport Mayumba Conkouati .pdf | ReportsFeatureSuggestions.xlsx | ReportsFeatureSuggestions (10f34991-f51d-4941-abb8-e914f1373527).xlsx | Screenshot 2021-06-18 at 14.35.44.png | Screenshot 2021-06-18 at 14.37.44.png | Timbavati_Leopard_Monitoring_Report_2021_v1.docx

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➤ Shannon Dubay commented:

Data Science ( https://pantheradatascience.atlassian.net/jira/people/team/61a6dbc3-8e98-4200-ab42-bd46246ce00b?ref=jira$&src=issue ) (Shannon Dubay Christopher MaraisRoss Tyzack Pitman Valentine Tawira)

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➤ Shannon Dubay commented:

Linking this task with the other Report-related task, as it might be easiest for the same person to do both.

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➤ Shannon Dubay commented:

Thabied Majal something to consider when re-vamping this feature: Recently in a training for Malaysia projects, users asked if it was possible to add capability to encrypt/password protect the files that are produced in this feature. Upon speaking to Ross about it, he found this package, which might allow us to do this: https://cran.r-project.org/web/packages/encryptedRmd/readme/README.html ( https://cran.r-project.org/web/packages/encryptedRmd/readme/README.html|smart-link ) (although I’m sure there are also other ways) Ross Tyzack Pitman , chime in here too, but if this proves to be too difficult to incorporate into IDS, then we will just recommend a third party app for them to encrypt the files they need.

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➤ Shannon Dubay commented:

Shannon: Marike sent me this html file ( https://pantheraids.org/forum.html?p=post%2Finterpreting-individual-capture-locations-different-symbols-11982317%3Fpid%3D1328885744 ) (uploading it to this task) that she created in the Reports feature- the map markers/icons/symbols don’t seem to make sense. They should reflect the different numbers of captures per station, but that doesn't appear to be the case since stations with the same number of captures will have different symbols. For instance, two stations that each have 2 captures will be shown differently. Ross: Those yellow/orange markers are based on the number of captures, but they render in a weird way that I've never been able to figure out. I recall it being because the captures are just too small given the scale. Something like that. We may just need to ditch it completely, as I remember we couldn't find a better solution back then.

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➤ Shannon Dubay commented:

Sasi has mentioned on the forum ( https://pantheraids.org/forum.html?p=%2Fpost%2Fcan-we-create-mcp-for-each-individual-12047278%3Fpid%3D1330242876 ) that her team uses MCPs (maximum convex polygons) in most of their reports, and wanted to show specific species captures as MCPs and specific individual captures as MCPs. We do have a way to see this information in the Maps module and (I believe) the Reports tool, but only as markers/icons/symbols and not MCPs. If it isn’t a complete mission, it might be nice to allow the user to see the captures MCP for their specified species/individuals too.

NB: probably get Ross' thoughts on this before implementing

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➤ Shannon Dubay commented:

More input (sorry for dropping this all here, Thabied Majal , I just don’t know where else to record all the suggestions for this section- people have a lot of opinions and requests.

One thing people would like to be included in auto-generated reports is: Principal investigator and email (both attributes in the database).

Also, whenever they are editing the text for a section, it would be helpful if they can see the plots/maps they are supposed to be writing about.

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➤ Ross Tyzack Pitman commented:

Thabied Majal– I see this task is in progress, have you done much with it?. I think this entire topic is a massize can of worms, though it’s one we have to address and develop very soon. Guy frequently asks on the status of this tool. Thabied, lets sit down together and map out a plan for this. I believe this task is too big for one person, so I’ll jump on it with you.

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➤ Thabied Majal commented:

Ross Tyzack Pitman I haven’t done any work on it at all. Just created the branch to start working on it and then other work popped up. Definitely keen on mapping out a plan on tackling it together

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➤ Ross Tyzack Pitman commented:

Thabied Majal let’s move this back to To Do if it’s not yet started.

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➤ Shannon Dubay commented:

Feedback from Roberto (rsalom@panthera.org ( mailto:rsalom@panthera.org )) on the topic:

{quote}I would say that on top of what you already have, to be able to generate an editable file (e.g. word doc) so that one can incorporate things or translate the document.{quote}

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➤ Shannon Dubay commented:

Feedback from Chris O (corbell@panthera.org ( mailto:corbell@panthera.org )) on the topic:

{quote}I have attached two “recent” example of reports. These are the type of reports I’m writing at the end of a field survey, after classifying images but before starting occupancy analysis.{quote}

[^Rapport Mayumba Conkouati .pdf] [^2019 Inventaire des mammiferes terrestre Momba.pdf]

{quote}What I usually export from IDS :

• Independent capture csv and effort/detection for occupancy analysis to work on R. and ArcGIS.

• Information from a survey statistic summary (trap night, area covered …) to put in my field report.

• Activity patterns like in the 2019 Momba report (screenshot actually, I didn’t found how to change the html into a jpeg or pdf to insert in a word document).

What I would like to be able to export :

• Capture rate by station for specific species to create maps like Figure 18 in Mayumba Conkouati report. I usually calculate it manually based on independent capture csv export and camera active ; being able to get a csv with station number, gps and capture rates for all the different species would be really helpful.

• The MCP displayed in the statistic summary as a shapefile to use it on ArcGIS. Being able to get MCP for specific species would be great to investigate natural or anthropogenic barrier, and be more explicit than the map I’ve attached (coming from a 2017 field report).

• I like the species accumulation curve, but would prefer to have the possibility of a total camera-day as x-axis.

As more general suggestion : multiple export format for graphical features (jpeg, pdf, shp) and choice in species names (scientific, common in different language).{quote}

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➤ Shannon Dubay commented:

Feedback from Sasi (ssuksavate@panthera.org ( mailto:ssuksavate@panthera.org )) on the topic:

{quote}The reports I send to the conservation area generally include:

-Table of species list group by order, family with IUCN red list status

-The proportion chart of wildcat species

-The proportion chart of ungulate species

-Distribution/PCRI map of species

-Time activity overlap of human and tiger

-Overlapping map of home range for tigers

-Independence event of tiger's prey and threat

-Timeline movement map of tiger, and a further explanation of each graph/map in statistical terms

These are helpful to our reports and help us to work faster. Please add it if it looks appropriate. I'm glad to be a part of IDS!{quote}

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➤ Shannon Dubay commented:

Feedback from Robin (rhorion@panthera.org ( mailto:rhorion@panthera.org )) on the topic:

{quote}Anyway to summarize some of our need for reports :

1. Being able to change the name of IDS categories (using French for example). I’m Simply using a reference table with a key column.

2. Being able to choose the species for each figure. Eg : we should remove birds in the accumulation curve

3. Basic pie plot with : number of blank, number of mammals, number of other species (birds, reptiles…), number of human

4. I like to take a look at the % of NA, 0, 1 in the camera active. It’s useless for a report but nice to compare between surveys.

5. In report we generally use 2 maps. First one is continent-sub region (west Africa)-Country-Park (eg :map attached). And second one is focused on the park with the grid and location of camera traps.

6. Sometimes we use a map showing the IDW (inverse distance weight) using the RAI for a specie at each station. It’s not “super scientifically” accurate, it’s not a real distribution map for the specie but it’s a nice map to plot areas where the specie was the most captured.

7. In the keys information : number of images and independent capture for each felids, number of specie (without birds, human or other selected)

8. To add more details to accumulative curve Marine suggest that it would be nice to have the observer and estimated species richness with chao, jackknife…{quote}

!Africa_V2_cadre.tiff|width=1280,height=905!

!ACC6E81E26604A659AF2A4B8D36B923B.png|width=567,height=295!

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➤ Shannon Dubay commented:

Feedback from Beckie (rgarbett@panthera.org ( mailto:rgarbett@panthera.org )) on the topic:

{quote}So this is REALLY pertinent to the leopard monitoring work in SA in particular. Being able to generate reports in IDS would make a HUGE difference to the project workload.

I’ve worked to standardise the reports that we sent last year – I’ve attached a copy of the Timbavati one.

To summarise, the key components that we would REALLY like are:

-Standard (but editable) intro, methods, and results sections  

-Capture frequency map (number of leopard captures per station mapped out) – we currently do this manually in GIS – can you imagine.

-Pie chart showing age composition of individually ID’d leopards

-Graph (with SE) of density estimates each year

-Summary of ALL species captured during the survey (omitting unidentified ones)

In addition to this, it would be amazing to have an automated process for identifying (and reporting on) individuals that have been recaptured in each year from previous years – does that make sense?{quote}

[^Timbavati_Leopard_Monitoring_Report_2021_v1.docx]

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➤ Shannon Dubay commented:

Unfortunately I haven’t had the time to consolidate everyone’s feedback yet, but I hope to do this next week. For now, I have simply added the raw feedback.

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➤ Shannon Dubay commented:

I am moving my suggestions into this comment here and removing them from the general description of this task. This is because most of my suggestions are specific to the current tool, and may not be applicable to the future tool:

While overall the tool works, there are some specific plots and text sections that need more work. The following are things I have noticed:

• This feature should probably be removed from the Descriptive Stats module and into its own module

• The default for “Include density plot” should be “No”

• When selecting additional plots or maps to include, IDS renders them at the bottom of the window- during this process a status bar should show in the bottom right corner (like in all other steps within IDS when data is loading) in order for the user to know IDS isn’t unresponsive but in fact compiling information.

• There should be a “none” option for “Plots to include in report” like there is for “Text boxes to include in report” and “Mapping to include in report”

• The name of the “Mapping to include in report” setting should be “Map+s+ to include in report”… like “Plot+s+ to include in report”

• The relative abundance indices plot doesn’t work in the preview at the bottom of the window; see screenshot. (NB: it DOES work in the final HTML report though)

• Within the “Report editor” popup (after clicking Generate Report), the text should say “Review and edit report information.” instead of “Review and edit descriptive statistics report information.“

  • In fact, that entire popup might benefit from a re-formatting.

• I am not sure it is clear that you need to add additional text for the plots in the preview at the bottom of the page, but you need to add additional text for the text boxes in the Report Editor popup.

• The text for “Introduction” and “Methods” and “Results” are exactly the same.

  • There is an issue with the reporting of the “range” in this text- two dashes included; see screenshot

• The text for the “Individual capture locations” maps needs to be written- if any (it is still the latin filler).

• When I chose just “Methods” and “Acknowledgements” as “Text boxes to include in report“, the report still includes “Introduction” and “Discussion” even though I didn’t want them.

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➤ Shannon Dubay commented:

Here is everyone’s raw feedback (mentioned in the previous comments here), compiled and consolidated in one file.

[^ReportsFeatureSuggestions (10f34991-f51d-4941-abb8-e914f1373527).xlsx]