splitrepo.md

In sustainablefarms/sflddata: Data Extraction Methods for the Linking Data Project

Mapping How to Split This Repo By Purpose

1) data access, extraction and preparation + SQL reading 2) generic model fitting tools (including standardising input data, simulating, likelihood and residuals, extracting predictions and more) + also ViF analysis functions, avoid multicollinearity stuff + model assessment 3) other? + plotting tools + reference documents

Work To Do

Name new package: msod

Shift files

In data access, extraction and preparation

• all of analysis/
• all of side_projects/
• all of vignettes/
• inst/climate_names_table.rds
• references/
• scripts/

In model fitting package

• inst/modeldescriptions/*
• inst/rmarkdown/*
• R
• as_list_format
• avoid_multicollinearity
• bugsdataconversion
• calcpredictions
• calcspeciesprobs_singlesitetheta
• DS_residuals *
• elpd_compare
• Enum_compare
• expected_biodiversity *
• extend_detectionoccupancy
• get_theta
• likelihood
• LV_covar_plots
• model_quality_stats
• numspec_fulldistribution
• pdetection_occupied
• poccupy
• predoccupancy_standalone
• preddesignmat *
• run_detectionoccupancy
• RVofrandomselectRV
• simulate_fit

• vif_analysis

• tests/testthat/

• benchmark_identicalsitesmodel.Rdata
• En_condLV.txt
• En_margLV.txt Especrich_condLV.txt Especrich_margLV.txt lkl_sites.txt pdet_theta01.txt pocc_theta01_condLV.txt pocc_theta01_margLV.txt test-bugsvar2array.R test-calcs_saved_fit.R test-DS_residuals.R test-expectedbiodiversity.R test-fulldistribution_numspecies.R test-likelihoods.R test-predcalculations.R test-prepdesignmat.R test-rundetectionoccupancy.R test-simulationmethods.R test-standalone.R test-whole-identical-sites.R test-whole-noiterations.R test-whole-variety-nolv.R test-whole-variety-wlv-60species.R test-whole-variety-wlv.R

Changes to files

• version number for msod
• modeldescription files names
• variable description names
• dependencies
• for msod:
  • suggest: arrangements, Rfast, parallel, runjags, car
• for data extraction:
  • suggest: all others

sustainablefarms/sflddata documentation built on April 19, 2022, 11:19 a.m.