Man pages for wpetry/IPMpack2
Builds and analyses Integral Projection Models (IPMs).
| addPdfGrowthPic | Adds probability density functions of density function of... |
| coerceGrowthObj | Function to coerce growth or survival objects, i.e., impose... |
| convergeIPM | Iterates until obtaining the number of bins required so that... |
| convertIncrement | Convert size increment according to time elapsed between... |
| dataIPMpackCryptantha.csv | Cryptantha Perennial Dataset with Covariates |
| dataIPMpackHypericumCov.csv | Hypericum Perennial Dataset with covariates |
| dataIPMpackHypericum.csv | Hypericum Perennial Dataset |
| dataIPMpackSilwood.csv | Silwood Monocarp Dataset |
| dataIPMpackSuccisa2.csv | Succisa pratensis Dataset |
| dataIPMpackSuccisa.csv | Succisa pratensis Dataset |
| diagnosticsPmatrix | Creates a series of diagnostic graphs for a P matrix. |
| discreteTrans-class | Class '"discreteTrans"' |
| discreteTransInteger-class | Class '"discreteTransInteger"' |
| elas | Estimates matrix element sensitivities and elasticities. |
| envMatrix-class | Class "envMatrix" |
| fecObj-class | Class "fecObj" |
| fecObjInteger-class | Class "fecObjInteger" |
| generateData | Generates random data in the form used by IPMpack. |
| growSurv | Combines growth and survival. |
| growth | Estimates growth probabilities. |
| growthCum | Models growth allowing for cumulative bin estimation. |
| growthCum-methods | ~~ Methods for Function 'growthCum' ~~ |
| growth-methods | ~~ Methods for Function 'growth' ~~ |
| growthModelComp | Compares growth and survival objects built from different... |
| growthObj-class | Class "growthObj" |
| growthObjDeclineVar-class | Class "growthObjDeclineVar" |
| growthObjHossfeld-class | Class "growthObjHossfeld" |
| growthObjIncr-class | Class "growthObjIncr" |
| growthObjIncrDeclineVar-class | Class "growthObjIncrDeclineVar" |
| growthObjLogIncr-class | Class '"growthObjLogIncr"' |
| growthObjLogIncrDeclineVar-class | Class '"growthObjLogIncrDeclineVar"' |
| growthObjNegBin-class | Class "growthObjNegBin" |
| growthObjPois | Class "growthObjPois" |
| growthObjTruncIncr-class | Class '"growthObjTruncIncr"' |
| Hossfeld | Creates a Hossfeld function defining growth. |
| IPMmatrix-class | Class '"IPMmatrix"' |
| IPMpack-internal | Internal IPMpack objects. |
| IPMpackNews | Show a text file containing package news and updates. |
| IPMpack-package | Construction and analysis of integral projection models and... |
| largeMatrixCalc | Calculates population growth rate (lambda) and stable stage... |
| logit | Implements a logistic transform. |
| makeClonalObj | Function to build clonal reproduction objects |
| makeCompoundCmatrix | Builds a compound C matrix. |
| makeCompoundFmatrix | Builds a compound F matrix. |
| makeCompoundPmatrix | Builds a compound P matrix. |
| makeDiscreteTrans | Builds matrix for transitions between discrete (e.g.... |
| makeDiscreteTransInteger | Builds matrix for transitions between discrete (e.g.... |
| makeEnvObj | Builds environmental transition objects. |
| makeFecObj | Function to build fecundity objects |
| makeFecObjInteger | Function to build fecundity objects |
| makeGrowthObj | Function to build growth objects |
| makeGrowthObjHossfeld | Function to make a Hossfeld Growth Object |
| makeIntegerFmatrix | Builds P and F matrices built off regressions fitted to... |
| makeIPMCmatrix | Builds C matrices. |
| makeIPMFmatrix | Builds F matrices. |
| makeIPMmatrix | Builds IPM matrices. |
| makeIPMPmatrix | Builds P matrices. |
| makeOffspringObj | Function to build offspring objects |
| makeSurvObj | Functions to build survival objects |
| meanLifeExpect | Calculates the mean life expectancy. |
| passageTime | Defines passage time to a chosen continuous stage. |
| picGrow | Makes pictures of data with growth models |
| picSurv | Makes pictures of survival. |
| plotGrowthModelComp | Plots compared models built with 'growthModelComp' and... |
| predictFutureDistribution | Predicts continuous (e.g. size) stage distribution in the... |
| R0Calc | Calculates net reproductive rate (R0) from an IPM. |
| sampleIPM | Builds list of IPMs or P matrices from list growth, survival,... |
| sampleIPMOutput | Gets IPM output from a list of P matrices (only survival and... |
| sampleSequentialIPMs | Makes a list of IPMs where there is a discrete covariate. |
| sampleVitalRateObj | Calculates growth objects reflecting distribution of... |
| sensParams | Estimates sensitivity and elasticity of lambda (or R0, or... |
| simulateCarlina | Generates random data in the form used by IPMpack based on... |
| sizeToAge | Estimates size/stage to age relationships |
| stochGrowthRateManyCov | Estimates stochastic population growth rates (lambda_s) or... |
| stochGrowthRateSampleList | Estimating the stochastic population growth rate (lambda_s)... |
| stochPassageTime | Estimates passage time in a discretely varying environment. |
| surv | Survival |
| survivorship | Estimates survivorship between two time censuses. |
| surv-methods | ~~ Methods for Function surv ~~ |
| survObj-class | Class "survObj" |
| survObjOverDisp-class | Class '"survObjOverDisp"' |
| timeToSize | Projects how long it takes to get from a starting... |
| varLifeExpect | Calculates variation in life expectancy in a discretely... |
| varPassageTime | Estimates variation in passage time. |
| wrapHossfeld | Fitting Hossfeld growth function. |
