To do - Lasso approach

[bniebuhr]

Preparation:

1. function to add strata in RSF setup, for sampling purposes
2. Implement function explore_blocks()

Fitting:
3. Predictor standardization: implement unstandardization of coefficients in bag_models() or bag_fit_net_(c)logit() if standardize = "external"
4. put cumulative type (nearest, cum), zoi shape, infrastructure type, and radius as input
5. Concordance: add continuous Boyce index/SomersD - for no strata present
6. Go for the clogit implementation to be coherent with the logit - all functions

After
7. Variable importance: what if removing variables leads to higher validation score than the full model for drop = TRUE?
8. Separate bag_plot_response into two - prediction and then plotting - more customizable, and also a fast plot like it is
9. weighted quantile prediction is not working
10. Variable importance vs weighted coefficients - how to interpret? What does the variable importance mean?
11. How to plot effects of all ZOI (both cumulative and nearest) by incorporating the number of features?

General:
12. Define final datasets in the package (rsf, SSF) and document them - check data contributors as well

[bniebuhr]

plot_coef:

• add possibility to rescale the coefficients (standardize them) within the function.
• add different types of plots (histogram, bar plots, barplot side-by-side)
• add order to terms, both type of infra/variable and ZOI radius

[bniebuhr]

variable_importance:

• add recognition of type of validation (habitat or not), and habitat only prediction for evaluating variable importance

[bniebuhr]

Add function to make a spatial prediction

[bniebuhr]

1. Function to add strata was included in a separate issue: #21
2. Function explore_blocks() included in 0de9212 and improved in 8a5c499
3. Predictor standardization: implement unstandardization of coefficients in bag_models() or bag_fit_net_(c)logit() if standardize = "external": included in a separate issue: #22
4. Not sure what was that, ignored for now.
5. Boyce and SomersD without strata - not included now, include if required
6. Correspondence of logit - clogit functions: they were kept correspondent in a series of different commits. One function to be added to the logit context: bag_load_net_logit (could be the same?). Opened in a different issue in #23
7. Variable importance: ignored for now, check later
8. Separate bag_plot_response into two: it is now possible to return either the plot or the dataset if ggplot = FALSE.
9. Weighted quantile prediction now working, but it is highly variable
10. Variable importance is proportional to the standardized coefficients, to be shown in a supplementary material in the methods paper.
11. How to plot effects of all ZOI (both cumulative and nearest) by incorporating the number of features? Good question to be discussed, opened in a new issue now in #24
12. Documentation of SSF and RSF datasets opened in a new issue in #25
13. plot_coef:
    • standardized coefficients: addressed in a74d178
    • different plots implemented in a0add50
    • order of terms included in a1ee553
14. variable_importance: add recognition of type of validation (habitat or not), and habitat only prediction for evaluating variable importance: opened in a different issue in #26
15. bag_predict_spat: first implementation for data.frame in 0d4257c