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Plant’net Overview | Michael Spratt

Plant’net Overview

Plant’net Overview

Climate change is going to stress the Phenological Fitness of plants, depending upon their geographical location and their adaptive relations to other plant species.

Our project is an Open Knowledge / Open Science / Community project to unit citizen field observations, scientifically obtained data  and  validated models to produce customized, open and simple tools to predict plant adaptation, interactions and long term Phenological Fitness.

This project has potential as a large scale cooperative effort for educational, professional and decisions support, which encourages scientific experimentation, mathematical literacy and personal development all within a supportive social group.  The scientific communities receives detailed in-field data which can validated their current methods and models.  While new models will be created and validated by motivated individuals, science education, environmentalists, etc. willing to observer, measure and note changes (budding, flowering, Leaf development, etc.), .

We have 3 basic elements to organize, Plant Data, Geological Data and Weather Data.  Currently the output is an Excel spreadsheet which uses a “INDIREXT” technique which presents daily weather and species data to the models and then stores corresponding results.  Thus models will calculate using any year or plant data.

Remember this is a project going online.

My advise is to :

Read some of the documentation   Overview ,Introduction  The Problem,  Current Status

The DataLocation

Technically, Daily Weather, ,  Models,,  Plant Species DetailsDownloads, video presentation and Links
Look over the demo and
download the project from the Github.

Overview     Daily Weather     Control     Work Area     Frost     Drought     Calculations     Download     Links

Overview

Simulating Phenological Fitness or Plant Survival Probability due to climate change depends upon daily weather data (ie. Centre Européen de Recherche et de Formation Avancée en Calcul Scientifique (CERFACS),)  for a given latitude and longitude.

For a given latitude and longitude there are 10 weather measurements(ie. min, max temperature, wind, precipitation, pressure, solar radiation, etc), for every day (365 days/year), for nearly 10,000 Latitude, Longitude combination.  Over 5,3  millions records

Other elements include :

Geological characteristics (slope, soil type/condition, infiltration considerations, etc.)

“User Selected” plants (indigenous, invasive, decorative, nutritional, etc.) all their parameters and

“User Selected Species Models” each plants has at least seven models for leaves, flower, fruit, seed, fire, drought, each model has several options.

Approx 75 data elements describing a plant’s reaction to climate, fires, frost, drought, etc.,

Roots and vegetation are classified into 3 straits each and adjusted to the latitude and longitude.

The species that produce the most viable flowers, fruits and seeds have better chances for survival.

The goal is to compare several species competing against each other for water, sunlight and root space over a long term (100+ year period).

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Simulation Excel

The objective this phase is to create a simulation with its data, models and calculations in Excel.

The original Phenofit had thousands or lines of code developed over decades by a variety of individuals

For example

o:=-5700*Top*(35*Top-950) / (19*Top*Top*Top*Top-1330* Top* Top* Top+ 15675* Top*Top +266000*Top+760000)

or

forcing:=d*(l-e); if forcing>700 then result:=0 else result:=1/(1+exp(forcing));”

There are several problems with (undocumented) code

formulas could be simplified

“magic numbers (eg. 5700, 700, etc.)” are to be replace with a descriptive variable names and default values (eg forcing_min = 700:)

There are several reasons for decomposing this simulation and scaling it down to an Excel version.

  1. Excel is pedagogic,  easier to understand, evolve, enhanced and adapted
  2. Excel is flexible, easier to re- structure for user control and data manipulation
  3. Excel has tools for outputs, graphics and documentation
  4. Excel has unexplored potential as more people can understand  Phenological fitness data and calculations
  5. Excel has greater calculation potential.

There are several major obstacles on the road to an Open Science application.  Using an object approach and Excel’s advanced features we can make considerable progress toward open and active community.

Excel techniques :

1 “black-box” or “function” approach –combining “Calculating building blocks”

  1. Each sheet (black-box) has input, outputs, local control and a buffer zone.

3 “Redirect” technique. Dynamically create pointers to different  data sets (ie. years 1, 2, 3. etc.) using an incremental counter

4 “Table lookup indexes” An index obtained from incremental counters, location or variable

5 “Retain-if” saves data (ie to a line) only when conditions (line number = year number) are met.

6 “Macro” used to increment a counter, in our case the year and species index, but also latitude and longitude.

7 “Color & comments” – ease of use and in-line documentation

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Site

A Site is a unique combination of Latitude and Longitude.

There are currently 9,989 Sites, with one or two other data elements.

The Site file is a GIS (ie. Open Street Map, Google map, etc.) which stores geological data like slope and water holding plus urban data, maps, satellite images, etc.

Discussions, consultations and effort are required to obtain a data Site file.

Latitude and Longitude. are the site’s location while Latitude and Longitude, Year and Day are the keys to the Daily Weather file.

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Weather (Daily Weather Details)

Each Site (Latitude and Longitude), has a Meteorological (weather) Station.

Each day the station records the :

Day of Year _ day_no

  1. Relative humidity at 2 m  (Humidité relative à 2 m) [RH, %]
  2. Medium surface pressure (Pression moyenne au surface) [Press kPa]
  3. Daily precipitation (snow and rain) (Précipitation quotidienne (neige et pluie)) [P, mm]
  4. Daily sum of visible radiation (Somme quotidienne de rayonnement visible) [GLO, MJ/m²]
  5. Daily amount of infrared radiation (Somme quotidienne de rayonnement infra rouge [RAT, MJ/ m²]
  6.  Average specific humidity (Humidité spécifique moyenne) [Q, kg/kg]
  7. Daily minimum temperature at 2 m (Température minimalle quotidienne à 2 m) [TI, ° C]
  8. Average daily temperature at 2 m (Température moyenne quotidienne à 2 m) [T_a, °C]
  9. Daily maximum temperature at 2 m (Température maximalle quotidienne à 2 m) [T_i, °C]
  10. Average wind speed at 10m hight (Vitesse moyenne de vent à 10 m) [Vu, m/s]

There are 9,989 Sites with the 10 daily weather elements from 1951 to 2098 or approximately 55 million unique data elements.

Plus there are many other data elements which can be calculated based upon the Latitude / Longitude and the Daily Weather

Solar Declination – DEC, Day Length, Hours of light, etc

Daily Weather[/button

The file contains

[[spreadsheet?&id=4&autoheight=0&autowidth=0&width=600px&height=400px&color_scheme=salad&math=1]]

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Plant Species  (for more go to Plant Species Details)

Species data concerns its Provenance and reaction to Frost, Drought and Fires

Variables which on-line community member can note :

Member Input Calculations :
Leafing Date (Leaf Unfolding Date) – Dl

Flowering Date – Df

Ripening Date – Dr

Leaf Colouring Date – Dc

Dormancy Entrance (of the buds)

Hydric stress on fruit ripening

Leaves Surviving Frost – Il

Photosynthetic Index Depending on Temperature.

Frost injury of Leaves Index –  Il

Thermal Energy Available Since Flowering – Er

Frost Injury of Flowers Index – If

Fruit Ripening Index – Ir

Probability of Frost Survival – Sf

Probability of Drought Survival – St

Probability Fruits Reach Full Ripening (cumulated probability of the Gaussian distribution (Ec, sm))

Fitted Parameter of the Ripening Date Model – Etc

Plant Species Details

Plant Species data and calculations vary depending upon the plant but all Species data is placed in the “Species” sheet.

[[spreadsheet?&id=plant_species&autoheight=0&autowidth=0&width=600px&height=400px&color_scheme=salad&math=1]]

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Models   (for Models Details)

Models and their initial values are assigned to a Species.  Models calculate Site, Species and Climate

Models Evapor-Transportation Senescence

Frost

Leaf Habitat Fruit Maturation Drought

Compound

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Control  ( for Control Details)

User options and Initial values are grouped into a Control sheet.

Some user options are

Beginning Year    2010 Ending Year    2019

The 3 Species to calculate Species No.    Select Species No    Current Species 1                                   6                        Quercus_ilex_??? 2                                  7                         Quercus_ilex_7 3

Many other variables are also stored here :

Maximum Soil Depth

Soil Water Capacity

Air Psi for Saxton’s equation

Control

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Work Area  (Work Area Details)

This area groups all the initial values for the Species and Control variables and stores the results for each month or year.

The objective is to group, into one sheet all the initial and annual results.  As the year counter augments, the year number Daily-W

Work Area

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]

Calculations (Calculations Details)

Model calculation sheets like Sierra, Phenology, Evapotranspiration, etc. acquire their input data from the “Work” sheet, which collates the “Species”, “Daily Wheather_9999” (9999 is the year) and “Control” sheets.

This data is volatile as it updates every time the species changes (new model numbers and data). Plus the columns and their data are subject to changes. In order to protect sheets from species dynamics a “buffer area” (in yellow). Buffers take data from the “Work area”, in their sheet, in this case Frost. This makes it easier to cut and paste sheets as only the buffer area and calculations need to be copied and not the dynamic Species or “Work” data.

Site data is stored in variable such as :

Daily Mean Temperature – Ta

Daily Minimum Temperature – Ti

Monthly Precipitations – Pm

Total Holding Water Capacity (in mm) – Wh

Monthly Ground Water (in mm) – Wm

Monthly potential evapotranspiration – Em

Monthly actual evapotranspiration – Am

Monthly Index of Moisture – Ia

Soil Moisture – Sm

Calculations

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Conclusion

As you can imagine there are several problems associated with taking this project to the next level

Phenofit represent an enormous investment in scientific research and public money. The investment could be leveraged  to yield greater returns. .  The Phenofit model is a gold mine of data, their relationships and  their calculations

The most important element, with even greater potential, is applied knowledge.  I’m proposing converting Phenofit  into an Open working tools for all humanity.  I have a plan, a road map, a Project.

Click here for A video presentation

Phenofit (was written in Pascal, over a period of 2 decades)

Difficult to understand, enhance and adapt

Impossible to Democratize and evolve.

The Daily Weather data requires re-structuring

Lacks technical documentation, user support and project development potential

The Solution

A 3 step plan :

1)  Create a simulation of Phenofit’s models and calculations in Excel and use it as a working tool.

2) Transport Phenofit Excel  to web technologies (RISK,  GUI, Widgets, etc.)

3 Create an open / on-line community project.

Discussion

There are several reasons for decomposing Phenofit and scaling it down to an Excel version.

It’s easier to understand thus we can evolve, enhance and adapt it It easier to structure Phenofit for user control and data manipulation The outputs are already in Excel and graphics and documentation

Greater potential as it opens Phenofit’s data and calculations to more people

Here are some site which maybe interested. Links

.

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Under Construction

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Overview     Daily Weather     Control     Work Area     Frost     Drought     Calculations     Download     Links

      Demonstration     

Download 
Details Simulating Phenological ‎Adaptation

Click here for A video presentation Links

 

The Data

Location

10,000 Geographical locations (lat/long), 30Km long squares, soil types, slope, etc.

Earth

Daily Weather from 1951 to 2098 147 years consisting of ..

Daily Weather provides 10 weather elements from which another 20+ values can be calculate.

  1. Relative humidity at 2 m  (Humidité relative à 2 m) [RH, %]
  2. Medium surface pressure (Pression moyenne au surface) [Press kPa]
  3. Daily precipitation (snow and rain) (Précipitation quotidienne (neige et pluie)) [P, mm]
  4. Daily sum of visible radiation (Somme quotidienne de rayonnement visible) [GLO, MJ/m²]
  5. Daily amount of infrared radiation (Somme quotidienne de rayonnement infra rouge [RAT, MJ/ m²]
  6.  Average specific humidity (Humidité spécifique moyenne) [Q, kg/kg]
  7. Daily minimum temperature at 2 m (Température minimalle quotidienne à 2 m) [TI, ° C]
  8. Average daily temperature at 2 m (Température moyenne quotidienne à 2 m) [T_a, °C]
  9. Daily maximum temperature at 2 m (Température maximalle quotidienne à 2 m) [T_i, °C]
  10. Average wind speed at 10m hight (Vitesse moyenne de vent à 10 m) [Vu, m/s]
Daily Weather

Weather

 

 

 

 

Evapo-transpiration

There are 4 models for calculating the daily Evapo-transpiration , of a plant

1- Thornwaite  – 2- Penman_FAO  – 3- Priestley_Taylor, 4- Penman,

Evapor-Transportation

Species entails the values required to model a species' response to daily weather and it's location.

Plant development, 10+ models (leaves, bud, flowers, fruits, etc) under drought, frost and other climatic conditions.

Plant Species Details

Tree

 

 

 

 

Buds (simple, compound)

 

 

 

 

 

 

 

 

Roots

Roots

 

 

 

Buds/Leaf Frost Models

Buds / Leaf Frost Models are : 1) Unified 2) Unichill 3) Uniforc 4) Spring_WarmingFrost

Drought Models

Drought and their Length are classified as Mild, Moderate, Severe and ExtremeDrought

Flowers

under construction
flowers

Leaves

Leaves

 

 

 

Fruit Maturation

 

 

fruits-in-trees

Fruits (seeds)

Senescence

 

 

Overview     Daily Weather     Control     Work Area     Frost     Drought     Calculations     Download     Links

 

The goal is to compute and compare several species all competing against each other for water, sunlight and root and canopy space over the long term (100+ year period) using input from people all around the world..

We will create an on-line Open Source / Open Communities Internet Platform (ie. Github, Social Network Manager etc.) and develop the tools and social network which impact decision making.

Let me demonstrate… Follow the visit