2017-08-24

Workplan Until May 1, 2018

Review and Discuss

Functions count in CTFS R Package and forestr

In CTFS R Package: 373

Selected for forestr: 157 (42%)

forestr: functions count per module.
folder n
recruitment 2
biomass 3
demogchange 3
map 4
speciesarea 4
mortality 5
topography 6
growth 7
abundance 8
spatial 22
utilities 92

Task Listed in the Job Description

* Build forestr. Produce and maintain a package sensu stricto.

* Host on GitHub. Set up a fully documented and active code repository.

* Document functions. Fully document the functions including help files.

* Optimize for speed. Optimize code for speed.

* Add contributions. Integrate code written by other researchers.

! Interact with database. Write functions to interact directly with output tables from the MySQL database.

! Wrangle data. Write functions to pre-process and format CTFS-ForestGEO data.

! Please clarify.

Timeline of tasks listed in job description

Example: functions in the module abundance

folder file fun decision priority
abundance abundance abund.manycensus key a
abundance abundance abundance key a
abundance abundance abundance.spp key a
abundance abundance abundanceperquad key a
abundance abundance ba keep b
abundance abundance basum keep b
abundance abundance pop.change keep b
abundance abundance pop.change.dbh keep b

Example: dependencies of abundanceperquad()

Example of some extra tasks

Thanks for helping and sharing your ideas!

end

Leftovers

Example: functions in the module mortality

folder file fun decision priority
mortality mortality find.climits high a
mortality mortality mortality high a
mortality mortality mortality.calculation high a
mortality mortality mortality.dbh high a
mortality mortality mortality.eachspp high a

Example: dependencies of mortality()

Excluded functions of priority c

#> [1] "AGB.dbtable, AGB.ind, agb.model, AGB.tree, biomass.CTFSdb, Chave.AGB, predht.asym, abundmodel.fit, bad.asymexp.param, bad.asympower.param, find.xaxis.hist, fitSeveralAbundModel, full.abundmodel.llike, graph.abundmodel, hyper.abundGibbs, hyper.mortGibbs, model.littleR.Gibbs, prob.N1, spmean.mort.abundGibbs, lmerMortFixedTime, lmerMortLinear, binGraphManySpecies, binGraphManySpecies.Panel, binGraphSampleSpecies, compare.growthbinmodel, graph.growthmodel, graph.growthmodel.spp, graph.outliers, graph.outliers.spp, overlay.growthbinmodel, map1species, map2species, Annuli, CalcRingArea, circlearea, partialcirclearea, RipUvK, graph.quadrats, distance.to.side, fullplot.imageJ, imageJ.to.lxly, SectionCorrection, readelevdata, rarefy.diversity, arrangeParam.Gibbs, arrangeParam.llike, autoregression, BadParam, bootconf, bootstrap.corr, border.distance"

Excluded functions of priority d

#> [1] "trim.growth, assembleBinOutput, bad.binparam, bad.binsdpar, calculateBinModel.AIC, calculateBinModel.bestpred, calculateBinModel.BIC, defineBinBreaks, defineSDpar, enoughSamplePerBin, extract.growthdata, growth.flexbin, llike.linearbin.optim, run.growthbin.manyspp, run.growthfit.bin, wideEnoughBins, define.graphwindow, get.filename, pdf.allplot, png.allplot, setsize, draw.axes, image_dataframe, imageGraph, plot_wavelet, rasterize, wavelet.allsp, wavelet.bivariate, wavelet.univariate, coverage.diag, startCTFS, getTopoLinks, rearrangeSurveyData, solve_topo, calcalpha, calcS.alpha, d.calcS.alpha, addBinParam, asymp.ht, asymp.ht.fixmax, asymptote.exp, bad.paretopar, beta.normalized, beta.total, betaproduct, center.predictors, constant, constant.bin, constant.linear, dasymexp, dasymnorm, dasympower, dbeta.reparam, dbinomrev, default.badpar, dexp.sin, dgamma.mean, dgamma.meansd, dgamma.scale, dgammadexp, dgammaMinusdexp, dgammaPlusdexp, discrete.model, discrete.mortmodel, dmixnorm, dnormprod0, dnormrev, doublenormal, dpois.max, dpois.maxtrunc, dpois.rearrange, dpois.trunc, dpower, dsymexp, dweibull.3param, exp_2par, expon.model, exponential.sin, fit.beta.normal, fit.logistic, fit.pdf, fitnorm, graph.mvnorm, invlogit, linear.model, linear.model.ctr, linear.mortmodel, linearmodel.bin, linearmodel.bin.set, log_model, logistic.ctr, logistic.inter, logistic.multiplicative, logistic.power, logistic.power.mode, logistic.power_simple, logistic.standard, logistic.sum.squares, logisticmodel.bin, logit, minum.beta.normal, minum.mixnorm, minum.normal, mvrnormRC, normalproduct, pexp.sin, pospower, psymexp, pweibull.3param, qasymexp, qasympower, rasympower, rgamma.meansd, rmixnorm, rpois.max, rpois.trunc, rpower, rsymexp, simple, simple.model, weibull.mean.3param, weibull.median.3param, weibull.sd.3param, angleBisector, are.ptsinside, cartesian.to.polar, circle, drawrectangle, ellipse, fullcircle, fullellipse, inside.rect, insideRectangle, intersection.line.curve, intersection.of.lines, is.between, ispt.inside, line.intersection.pts, parallel.line, perpendicular.distance, perpendicular.line, polar.to.cartesian, pts.to.interceptslope, segmentPt, xydist, xydistmat, xydistvect, arrangeParam.Gibbs.2D, arrangeParam.llike.2D, badSD, covTocorr, full.likelihood.lmerBayes, llike.model.lmer, lmerBayes, lmerBayes.hyperllike.mean, lmerBayes.hyperllike.sigma, recalculate.lmerBayesllike, resetParam, residual.llike.lmerBayes, restoreParamFile, saveParamFile, summaryMCMC, modelBayes, residual.llike.modelBayes, summaryModelMCMC"