tdjames1 / compadredb Goto Github PK
View Code? Open in Web Editor NEWThis project forked from jonesor/compadredb
Code and data for the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database
License: GNU General Public License v2.0
compadredb's People
Contributors
Watchers
compadredb's Issues
Resolve various queries in reprodStages()
There are various unresolved queries in this function relating to the way it should work. Summarising these:
- What is the best form for the output?
- How should we handle dormant stages?
- Is there any justification for stages to be combined/collapsed e.g. propagule and pre-reproductive or reproductive and post-reproductive?
More details are in the function documentation:
https://github.com/tdjames1/compadreDB/blob/master/Mage/R/reprodStages.R
Improve function documentation for collapse matrix functions
E.g. use descriptions of parameters matU, matF etc from lifetimeRepEvents() documentation.
extractVitalRates() shouldn't return NaN
Need to deal with degenerate matrices that create NaN values.
Example: matrix with juvenile survival and transition both specified as zero.
!> comadre$version
$Version
[1] "X.X.X"
$DateCreated
[1] "Jun_09_2017"
$NumberAcceptedSpecies
[1] 456
$NumberStudies
[1] 586
$NumberMatrices
[1] 2207
$Agreement
[1] "http://www.compadre-db.org/Page/UserAgreement"
!> comadre$mat[[454]]
$matA
A1 A2
[1,] 0 2.630585000
[2,] 0 0.002427184
$matU
U1 U2
[1,] 0 0.000000000
[2,] 0 0.002427184
$matF
F1 F2
[1,] 0 2.630585
[2,] 0 0.000000
$matC
C1 C2
[1,] 0 0
[2,] 0 0
Create example for rearrangeMatrix() where matrix contains non-reproductive stages
Create an example for rearrangeMatrix() that demonstrates the function's purpose, i.e. a matrix containing non-reproductive stages.
Decide what to do about standardizedVitalRates()
This function is supposed to handle the whole process of collapsing a matrix to standard form and calculating standardized vital rates. Need to figure out if it does what it's supposed to do.
https://github.com/tdjames1/compadreDB/blob/master/Mage/R/standardizedvitalrates.R
rearrangeMatrix() fails when matF contains NA
Example from Bernt-Erik Sæther, Øvind Bakke. 2000. Life history variation and contribution of different demographic traits to the population growth rate in birds: a comparative approach. Ecology 81: 642-653.
saetherMatrices$`Diomedea exulans`
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 NA
[2,] 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[3,] 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[4,] 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[5,] 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[6,] 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00
[7,] 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00
[8,] 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00
[9,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00
[10,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00
[11,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.92
Decomposed using values above the diagonal as the fecundity matrix, remaining values as growth/transition.
[1] "Species: Diomedea exulans"
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] 0 0 0 0 0 0 0 0 0 0 NA
[2,] 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0 0 0 0 0
[10,] 0 0 0 0 0 0 0 0 0 0 0
[11,] 0 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[2,] 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[3,] 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[4,] 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[5,] 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[6,] 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00
[7,] 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00
[8,] 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00
[9,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00
[10,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00
[11,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.92
Error in Rep[1]:Rep[length(Rep)] : argument of length 0
Fix example in extractVitalRates()
The structure of the matrix given in the example is not appropriate for the vital rate extraction procedure.
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.