-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.Rmd
589 lines (431 loc) · 25.4 KB
/
index.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
---
title: "Paul Melloy"
date: "`r Sys.Date()`"
---
`r htmltools::includeScript("./matamo.js")`
I am a Agroecologist at [CSIRO.](https://www.csiro.au/)
I specialise in modelling pest and diseases in agriculture and horticulture for
using in decision support tools.
Read about my recent research below, and if you are interested in collaborating
on a research topic, visit my [CSIRO profile page.](https://people.csiro.au/m/p/paul-melloy)
<br>
***
## Recent work
### cercopoRa 0.0.1 released on CRAN
#### December 2024
I am pleased to announce that the [cercopoRa](https://cran.r-project.org/web/packages/cercospoRa/index.html)
R package has been made available on the Comprehensive R Archive Network (CRAN).
I have enjoyed collaborating with [Rene Heim](https://reneheim.github.io/),
[Nathan Okole](https://orcid.org/0000-0002-5375-2420),
[Facundo Ispizua](https://www.researchgate.net/profile/Facundo-Ispizua-Yamati),
and [Anne-Katrin Mahlein](https://www.researchgate.net/profile/Anne-Katrin-Mahlein)
to produce this work as a foundation for further collaboration and development of
which I am looking forward to.
The `cercopoRa` package is designed to facilitate the integration of remote sensing
data into epidemiological models.
Its development builds on the research efforts of our team and aims to improve
the automation and accuracy of these models.
We invite researchers and practitioners interested in remote sensing and
epidemiology to explore `cercopoRa`'s capabilities lodge issues for discussion and
make pull requests to the
[Github repository](https://github.com/PaulMelloy/cercospoRa/) to further this
project.
You can install the package from CRAN in R with the `install.packages()` function
```r
install.packages("cercospoRa")
```
Access the documentation and tutorials from the pkgdown site
https://paul.melloy.com.au/cercospoRa/.
<br>
***
### LLMs for Decision Support
#### December 2024
Congratulations to [Dr Sandeep Dhakal](https://people.csiro.au/d/s/sandeep-dhakal)
and [Dr Hazel Parry](https://people.csiro.au/P/H/Hazel-Parry.aspx) for their
recent publication in [Nature Correspondance, *"Large language models can help to translate science into real-world impact"*](https://www.nature.com/articles/d41586-024-04059-w).
Many academics are hesitant to embrace the Large Language Model revolution, however
the genie can no longer be put back in the lamp and it is integrating itself in
our day-to-day life.
What this technology does well translate complex ideas and language
to a somewhat succinct summaries that are more readable.
This is what we as scientists are rather terrible at, communicating complex ideas
to the wider public, and we could gain a lot by using LLMs to enable this.
The latest models have come a long way and even though it is probably for the LLM
to include mistakes, we as scientists should be involved in the testing to ensure
improved accuracy.
<br>
***
### AusMac Macadamia Conference
#### 30 - 31 October 2024
The Pest READI project I'm working on focuses on horticultural industries in the
Northern Rivers area of Northern New South Wales. This region has been severely
impacted by recent disruptions, including [the 2022 floods](https://www.abc.net.au/news/2022-03-31/floods-lismore-byron-bay-northern-rivers-why-come-in-clusters/100954926)
and the [black summer bushfires in 2020](https://www.abc.net.au/news/backstory/2023-09-26/abc-emergency-black-summer-upcoming-bushfire-season/102871620).
The Pest READI team is conducting research on how this resilient community
implements integrated pest management practices and collaborates with them to
design tools that enhance preparedness and resilience for future changes.
The Northern Rivers region is home to significant horticultural industries,
including macadamias, which are one of the largest in the area.
Alongside avocados, these crops contribute significantly to the local economy.
The conference, which brings together industry professionals, growers, and
agronomists, featured a wide range of topics.
This year's event highlighted several key areas of focus.
**Machinery and automation** were well-represented, with many attendees seeking
solutions to reduce labor costs in the face of high demand for workers. However,
the investment required to adopt new machinery was a significant consideration
for farm businesses.
The conference also explored the importance of macadamia markets, which have
faced challenges from competitors in South Africa and China. **Spatial models**,
presented by [Andy Clark from UNE](https://www.une.edu.au/staff-profiles/science-and-technology/andy-clark),
demonstrated how earth observation can be used to identify and map tree crops.
These models also highlighted the potential for improved weather warning systems
and monitoring of seasonal phenology.
The **Trade displays** offered a wealth of information on novel AgTech products
targeting agricultural and horticultural production.
Farm management platforms, such as [InformAg](https://www.informag.com.au/) and
[FieldIn](https://fieldin.com/), were showcased as tools to organize farm tasks
and improve record-keeping for compliance.
The importance of pollination was emphasized in several talks and at related
stalls.
[Bee Hero](https://www.beehero.io/) presented acoustic monitoring technology to
understand bee activity, while [Wheen Bee](https://www.wheenbeefoundation.org.au/)
offered grants for planting insect-friendly habitats.
[Biological Services](https://www.biologicalservices.com.au/) supplied beneficial
insects to suppress pests.
> [Read more about our round-up on our Pest READI website](https://research.csiro.au/pestreadi/pest-readi-team-at-ausmac-2024/)
<br>
***
### UQ Agronomy student workshop on decision support tools
#### 10 October 2024
A workshop to introduce the benefits of consulting decision support tools (DSTs)
in Agriculture.
[Class resources](https://paulmelloy.github.io/DST_Workshop.html)
<br>
***
### GRDC Soil-borne disease workshop
#### August 2024
Early this month I visited Sydney to talk at the GRDC soil-borne diseases workshop.
There were some interesting discussions about the complexity to manage soil and
stubble borne diseases in grain crops.
A primary concern was, despite heroic efforts by our Aussie plant pathologists,
that past research was not easily able to translate to measurable impact.
Additionally growers are not aware of the increasing chronic disease impact as a
result of increased stubble retention and zero till farming in Australia.
Overwhelmingly there seems to be strong support for digital tools to help translate
research to impact and simplify disease management options with decision support
tools.
However, will the rest of the GRDC research managers and regional panels agree???
Thank you to [Colare](https://www.colere.com.au/) group for the invitation to talk.
<br>
***
### Starting a new job at CSIRO!!!
#### July 2024
I am super excited to start a new role back with CSIRO as a Senior Research Scientist.
I will be working in a wider capacity on insect pests and diseases, engaging with
the horticultural industry and agri-tech platforms to integrate spatial models as
decision support tools.
I am working in the [agroecology team](https://research.csiro.au/agroecology/)
with the [Pest READI](https://research.csiro.au/pestreadi/) and the [canola allies](https://research.csiro.au/agroecology/canola-allies/) project.
**Update:** [A short blog post](https://research.csiro.au/agroecology/meet-our-new-team-members/) on myself and [Jessa Thurnman](https://people.csiro.au/t/j/jessa-thurman), starting with the
agroecology team at CSIRO.
<br>
***
### Australian Spors Turf Managers Association conference
#### June 2024
What a treat giving a presentation on ERI diseases to a packed room at the ASTMA
Conference in Brisbane.
<center>
</center>
<br>
<br>
### weatherOz: API client for weather and climate data in R
#### June 2024
Congratulations to [Dr Rodrigo Pires](https://www.agric.wa.gov.au/rodrigo-pires)
and [Prof. Adam Sparks](https://www.ccdm.com.au/people/adam-sparks/)
with this latest publication of which I am a co-author.
[weatherOz: An API Client for Australian Weather and Climate Data Resources in R. (2024) \n Journal of Open Source Software, 9(98), 6717, \n https://doi.org/10.21105/joss.06717](https://joss.theoj.org/papers/10.21105/joss.06717)
<br>
***
### [13th International Epidemiology Workshop](https://iew13.netlify.app/)
#### April 2024
What a fantastic workshop hosted by the [Socidedade Brasileira de Gitopatologia](https://sbfitopatologia.org.br/)
(Brazilian Phytopathological Society).
The workshop took place in Iguasu and was a great opportunity to meet plant
epidemiologists from around the world.
I was able to speak on the first day of the workshop introducing the idea that
farmers might not be interested in JAFAs (Just another F___ *?fone?* App) and that
using APIs to serve decision support tools to farm management software could reach
more stake-holders.
I will look forward to the next workshop and seeing many of the same good folk and
new friends.
<center>
{width=60%}
</center>
***
### GRDC updates - Goondiwindi and Dubbo
#### February/March 2024
I presented a talk at "Efficiently limiting yield loss from net-blotch in barley
– a meta-analysis" at the GRDC updates in Goondiwindi and Dubbo.
This described the results of a meta-analysis of fungicide trials across Australia
to determine the best fungicide timing to maximise yield protection.
Read about the results in the [GRDC GroundCover article](https://grdc.com.au/resources-and-publications/grdc-update-papers/tab-content/grdc-update-papers/2024/02/efficiently-limiting-yield-loss-from-net-blotch-in-barley-a-meta-analysis).
<center>
{width=60%}
</center>
<br>
***
### `Extract` from nested lists in R
#### November 2023
`Extract`ing from lists and nested lists using the "[[" function is always a bit
of syntax I forget and can never seem to google the answer to easily.
So I post it here for myself to easily reference in the future.
*Edit - more information can be obtained from* `?Extract`.
Wearing my programming and data-science hats, lists can be a extremely useful
way to store and organise data.
This is especially true for epidemiological model outputs.
Yet newcomers will find lists can be difficult to understand and find it even more
difficult to easily retrieve data from especially for nested lists.
This is a short-hand way to easily retrieve the same element within a nested list.
First lets create a nested list.
```{r, R.options=list(max.print=20)}
# set random seed for reproducibility
set.seed(28)
nested_list <- lapply(1:3, function(x) {
return(list(
capitals = sample(LETTERS),
smallcaps = sample(letters),
numbers = sample(1:50)
))
})
#head(nested_list)
```
Here we have created a list with a length of 3 with three lists nested inside each
list with names "capitals", "smallcaps" and "numbers".
Frequently we only want to pull all of one nested list.
To do this we use two opening square brackets `"[["` as the function, followed by
the name of the list.
```{r, R.options=list(max.print=20)}
lapply(nested_list,"[[", "capitals")
```
This also works by indicating the integer of the nested list i.e `lapply(list1,"[[", 2)`.
<br>
<br>
***
### OnPrime
#### November 2023
Through October and November I had the opportunity to develop my industry engagement
skills.
The OnPrime program run by CSIRO provides researchers with coaching on how to improve
their engagement with industry and ensure improved outcomes for researchers and
industry investors.
This program taught me how to develop a research project that is tailored to the
needs of industry to ensure research gains are focused on what is novel and needed.
Our team researched the opportunity for developing a turf breeding program to support
the turf industry.
I was surprised on the importance of turf in our culture, society and economy.
We learned it can cost approximately $700k to import new varieties to Australia from
the US.
These varieties may not even be suitable for Australia's varied and harsh climate.
Sporting turf surfaces are at capacity, and with the rise in women's sport, demand
is still growing placing a lot of pressure on sporting surfaces.
We could save sporting clubs money by developing a wear tolerant grass which reduces
the chance of cancelled games.
In addition a more tolerant turf for stadiums might increase the opportunity for
more frequent games, concerts and events.
Boosting revenue for the stadiums, local businesses and tourism.
[Contact our team for more infomation about this project](https://paulmelloy.github.io/OnprimeContact.html)
<center>
{width=60%}
</center>
<br>
***
### International Conference of Plant Pathology (ICPP)
#### August 2023
It was a long time coming but this was my first International conference overseas.
The [ICPP was held in Lyon](https://www.icpp2023.org/) and it was a scorcher!
The city was experiencing a heat wave which placed a topical spin on the conference
and how to manage plant diseases in a future experiencing the effects of climate
change.
<center>
{width=43.5%}
</center>
The highlight for me was the [episense satellite meeting](https://www.icpp2023.org/sites/default/files/2023-08/Abstract_book_wtitpage_v8.7_030823_0.pdf)
held on the preceding weekend.
The air-conditioning could barely cope with the temperatures outside and despite the
amazing talks, my attention could not help to wander to the Rhone river visable through
the window behind the speakers.
The attendees of the Episense satellite meeting were genuinely good company and
not only provided stimulating phytopathological discussions, but also extended a
collaborative effort into robust research of the Lyonnaise cultural pursuits.
{width=43.5%}
{width=43.5%}
The conference was well attended by Aussies with the close of the meeting providing
an opportunity to reflect on the conference insights and how they could be applied
in Australia.
<br>
***
### UQ Agri-Food Innovation Alliance grant
#### May 2023
A quick visit to [Cauldron Distillery and Winery](https://www.cauldrondistillery.com.au/)
to take soil and leaf samples for the UQ Industry Kick-starter project.
<center>
While it was late in the season and the vines entering dormancy, we found, (Left)
possible phosphorus deficiency in the ferrosol soils, and (Right) Possible downy mildew.
{width=43.5%}
{width=55%}
<br>
Leaf samples revealed downy mildew _Plasmopara viticola_.
Below: (Left) Sporangiophore, (Right) Sporangia
{width=45%}
{width=50%}
</center>
<br>
***
### UQ Agri-Food Innovation Alliance grant
#### April 2023
I am extremely excited to announce [Dr Anthony Young](https://agriculture.uq.edu.au/profile/4625/anthony-young)
and myself were successful in an [Industry Kickstarter grant](https://agriculture.uq.edu.au/research/research-centres-and-groups/uq-agri-food-innovation-alliance/find-funding-or-research-partners)
to develop a "Decision support tool to support speciality smallholders and farm-gate
producers."
We are working with [Cauldron Distillery and Winery](https://www.cauldrondistillery.com.au/)
in Mt Tamborine, south of Brisbane, to assess the efficacy of organic and synthetic
fungicide timing on foliar grape vine diseases, powdery mildew and downy mildew.
The field trial will assist in refining a decision support tool which will help
smaller farm gate producer manage disease with lower costs and fungicide applications.
<br>
***
### [The influence of temperature and vapour pressure deficit on conidial germination and germ tubes production in an Australian _Podosphaera xanthii_ isolate.](https://paulmelloy.github.io/P_xanthii_titlepage.html)
#### March 2023
This paper has been accepted and published in the European Journal of Plant Pathology.
[https://doi.org/10.1007/s10658-023-02664-5](https://doi.org/10.1007/s10658-023-02664-5)
<br>
***
### Sampling Ascochyta rabaeii for field experiment
#### February 2023
Following the Goondiwindi GRDC updates I drove home via the Eastern Darling Downs
to collect some Ascochyta infested chickpea stubble.
This will be used for inoculum in a field trial we are planning later this year.
<center>
{width=60%}
</center>
Stay tuned!!!
<br>
***
### [The influence of temperature and vapour pressure deficit on conidial germination and germ tubes production in an Australian _Podosphaera xanthii_ isolate.](https://paulmelloy.github.io/P_xanthii_titlepage.html)
#### November 2022
I am pleased to share a pre-print of a paper I have been assisting with, titled,
"The influence of temperature and vapour pressure deficit on conidial germination
and germ tubes production in an Australian _Podosphaera xanthii_ isolate."
The paper has been submitted for review at the [European Journal of Plant Pathology](https://www.springer.com/journal/10658). The work was undertaken as part
of Zaiton Sapak's PhD and furthers our understanding on the temperature and vapour
pressure conditions which influence germination rate and infection success of
_P. xanthii_ on cucurbit leaves.
Powdery mildew is at a high risk of evolving fungicide resistance and improper
applications can be costly, hastening the evolution of fungicide resistance.
Understanding the conditions at which the crop is at risk of infection will lead
to the development of models and decisions support tools which increase the lead
time to prepare for fungicide applications and timing sprays for maximum efficacy,
reducing excessive spray applications or the immediate cost of applying ineffective
poorly timed sprays.
The results from this paper show the optimum conditions for rapid conidia germination
and the production of secondary and tertiary germ-tubes (a proxy for successful
infection) was 28°C at saturated vapour pressure. Germination was prevented at
temperatures above 34°C and below 8°C and reduced at other temperatures. As vapour
pressure deficit increased germination and germ tube production decreased in a
non-linear relationship and never completely prevented conidial germination or
germ-tube production.
I assisted with statistical analysis and final drafts of the paper. If you wish
to read the pre-print, you can download it from Zenodo.
[](https://doi.org/10.5281/zenodo.7349124)
[You can also find the full statistical analysis and code at the research compendium here.](https://paulmelloy.github.io/P_xanthii_titlepage.html).
<br>
***
### National Pulse Pathology Meeting & Ascochyta blight Workshop
#### October 2022
An amazing week of presentations and discussions around pulse pathology and ascochyta
blight research in chickpea.
I had a great time learning about chickpea breading efforts and disease epidemiology
research.
I came away with some excellent insights that I wish to apply as improvements to
the `ascotraceR` model. Watch this space.
</center>
<br>
***
### GRDC Update - Miles - Pitsworth - Goondiwindi
#### July 2022
At the end of July, I travelled around South East Queensland to the GRDC Updates
to present the decision support tools which have been developed on the GRDC funded
project I am involved with. A second la nina at the start of 2022 has provided a
lot of moisture which are likely to lead to heavy losses to foliar diseases if crops
are not managed well for disease.
The main apps we were presenting for the Northern grains region were
[StripeRustWM](https://www.agric.wa.gov.au/apps/striperustwm)
and [YellowSpotWM](https://www.agric.wa.gov.au/apps/yellowspotwm-yellow-leaf-spot-management).
There was a lot of interest in the applications and many were not yet familiar with
the available suit of decision support tools (DST). With a full moisture profile across
many of the cropping areas those who were able to sow had more options. With seemingly
more growers from the Goondiwindi region going into canola. Some farm managers were
therefore interested in the canola DSTs [SclerotiniaCM](https://www.agric.wa.gov.au/apps/sclerotiniacm-sclerotinia-management-app),
and [UCI BlackLegCM](https://www.agric.wa.gov.au/apps/uci-blacklegcm-blackleg-upper-canopy-infection-management-app).
<br>
***
### Farms Advice - Plant disease modelling interview
#### June 2022
I had a great chat with ABC rural trailblazer [Jack Cresswell](https://twitter.com/jcressw3) on his [Farms Advice](https://farmsadvice.com.au/) pod-cast.
[Follow this link to the interview.](https://anchor.fm/farmsadviceau/episodes/Plant-Disease-Modelling-in-Broadacre--Paul-Melloy-e1ji1kl)
Or search for 'Farms Advice' in your pod-cast app.
<br>
***
### Simulation model for ascochyta blight
#### May 2022
`ascotraceR` is an R package which simulates ascochyta blight epidemics in chickpea
crops.
You can find `ascotraceR` on CRAN, and a resource announcement in *Phytopathology*.
[ascotraceR: An R Package Resource to Simulate the Spatiotemporal Spread of Ascochyta Blight in a Chickpea Field Over a Growing Season](https://apsjournals.apsnet.org/doi/10.1094/PHYTO-01-22-0016-A)
<br>
***
### Is UniSuper's Defined Benefit Division fund worthwhile Shiny App
#### May 2022
Choice of superannuation is not the first type of research people like to do when starting a new job.
Most people want to finish the induction paperwork and financial forms as quickly as possible so they can commence diligently working for their new employer.
Therefore I gather most people would not fully dedicate their time to trying to understand 'What is a defined benefit division?' and 'Is it the best super product for me?'.
I certainly did not when I started work with the University of Southern Queensland almost four years ago.
I was coerced into UniSuper's DBD and only 3 years down the track I realise it was not for me.
When checking up on my super balance, shortly after starting work at The University of Queensland,
I noticed that the total contributions I made from my salary after tax exceeded the fund balance.
Suffice to say, I liken the DBD to a pyramid scheme which only benefits people who are over the age of 50.
In fact it is almost impossible to have a positive net return if you exit the fund before the age of 46.
To help people understand how the DBD is calculated I created a shiny app which can be found at the following link
[https://paulmelloy.shinyapps.io/UniSuperDBD/](https://paulmelloy.shinyapps.io/UniSuperDBD/)
<br>
***
### 2022 Election shiny app
#### May 2022
I have been working on a shiny app to help a political party I am a member of,
the [Fusion Party, *Science, Pirate, Secular and Climate Emergency Parties*](https://www.fusionparty.org.au/)
The shiny app was made to easily convert electoral boundaries data from shape file
to `KML` file so they could be uploaded on a shared Google maps.
Needless to say the app expanded monstrously when I found more data on the [AEC website](https://results.aec.gov.au/24310/Website/HouseDownloadsMenu-24310-Csv.htm).
I included some analysis of voting preferences by division and voting booth, including
expected voter turnout to booths.
Check out the app at https://paulmelloy.shinyapps.io/22_electoralboundaries/
<br>
***
### Estimating leaf temperature from NASA satellite data
#### April 2022
I wrote a blog, published on OpenPlantPathology's website, for how to use R to
estimate leaf temperatures from data retrieved using the `nasapower` R package.
Then plugging the data into functions from the R package `tealeaves`.
The result is being able to estimate the leaf temperature for any where on the planet.
[Click here to read the blog post](https://openplantpathology.netlify.app/posts/2022-04-01-powerful-tea-using-nasapower-and-tealeaves-to-obtain-leaf-temperatures/)
<br>
***
### Efficient control of powdery mildew in mungbeans
#### November 2021
This paper uses meta-analytic methods to examine 16 field trials over eight seasons assessing fungicide spray timing for control of powdery mildew.
[Read the paper in *Plant Disease*](https://apsjournals.apsnet.org/doi/10.1094/PDIS-06-21-1256-RE).
[Recreate the analysis by following the research compendium.](https://openplantpathology.github.io/Mungbean_PM/preliminary-analysis.html)