Man pages for qPharmetra/qpToolkit
qPharmetra R Tools
| abline.color | abline.color (Autograph) |
| abline.color.box | abline.color.box (Autograph) |
| align.around.decimal.point | Pad Numeric Vector Around Decimal Point |
| amber | amber |
| apple | apple |
| asNumeric | Convert Character to Numeric with NA Substitution |
| as.tornado | Coerce to Tornado |
| as.tornado.data.frame | Coerce to Tornado from data.frame |
| blue | blue |
| bootstrap.ParTab | Create Parameter Table from NONMEM Bootsrap |
| boxcoxf | Apply a Box-Cox Transformation to a Vector |
| box.plot.color | box.plot.color (Autograph) |
| brown | brown |
| catDataFun | Summary: length (%) |
| cfc | Create a Vector, Matrix, or Data Frame from Clipboard object |
| cobalt | cobalt |
| conDataFun1 | Summary: mean (SD) |
| conDataFun2 | Summary: median (min - max) |
| conDataFun3 | Summary: (95%.lower - 95%.upper) |
| convert.omega | Omega Names Conversion |
| convert.sigma | Sigma Names Conversion |
| covInfo | Make a covInfo S3 object |
| crimson | crimson |
| ctc | Copy a data.frame or matrix to clipboard |
| cut3 | Divide numeric variable into bins |
| cyan | cyan |
| doubleStack | Stack a Value Twice by Two Covariates |
| emerald | emerald |
| eval.eqs | Evaluate a list of equations |
| example.CWRES.plot | Examples for qPharmetra style CWRES plot |
| example.NONMEM.dataset | Examples for qPharmetra style NONMEM data set |
| example.pkpdData | Examples for qPharmetra style PKPD data set |
| example.xpose.VPC | qPharmetra examples for plot, VPC and NONMEM dataset |
| expand.data | Multiply data.frames |
| extract.character | Extract character information from a string |
| extract.number | Takes character string and parses the numeric input from it,... |
| extract.varcov | Get the covariance matrix from an already parsed .cov output... |
| formalize | Formalize Something |
| formalize.data.frame | Formalize Data Frame |
| format.demoTable | Format a tabulated summary for LaTeX |
| formatted.signif | Forced length significant digits |
| full.names | swaps shorthand / abbreviated column names in data frame for... |
| fxs | Fixed character length of a String |
| geomean | Geometric Mean |
| get.covmat | Get the covariance matrix |
| get.description | Scan the runrecord tag for 'Description' |
| get.diag.names | Find diagonal OMEGA names |
| get.dOFV | Create brief NONMEM run record |
| get.eigen | NONMEM run Eigen values |
| get.multiple.xpose.tables | Get xpose tables of multiple runs |
| get.nm.version | NONMEM version used |
| get.npar | Calculate Number of Parameters |
| get.ofv | Objective Function Value parser |
| get.omega | Summary: OMEGA estimates |
| get.omega.npar | Calculate Number of Omegas |
| get.shrinkage | NONMEM shrinkage estimates |
| get.sigma | Summary: SIGMA estimates |
| get.sigma.npar | Calculate Number of Sigmas |
| get.theta | Summary: THETA estimates |
| get.theta.npar | Calculate number of Thetas |
| get.xpose.tables | Get NONMEM output tables into one data frame |
| ggvpc_standard | VPC plot using ggplot2 (standard) |
| ggvpc_xpose | VPC plot using ggplot2 (Xpose-alike version) |
| gray | gray |
| green | green |
| histogram.bootstrap | Bootstrap Histograms |
| histogram.color | histogram.color (Autograph) |
| indigo | indigo |
| insert.blank.line | Inserting blank lines in a table (alias) |
| insert.blanks | Inserting blank lines in a table |
| ipred.color | ipred.color (Autograph) |
| isMissing | Check for missing values |
| isNumeric | Check for numeric values |
| ketchup | ketchup |
| latex.update.glosssaries | Update Glossaries |
| LIBRARY | Load a Specific Package Version |
| lime | lime |
| lines.striptext | Count Lines of Striptext |
| lin.fit.col | lin.fit.col (Autograph) |
| load.data | Loading data of various formats |
| locf | Last Observation Carried Forward (LOCF) |
| logit | Logit transformation |
| logit.inv | Logit Back-transformation |
| logTicks | Define ticks for plots with log10 axes |
| loi.color | loi.color (Autograph) |
| lunique | Number of unique values |
| magenta | magenta |
| makeCovInfo | Make a list of covInfo objects from a data frame |
| make.eqs | Make a list of equations |
| make.map | Meta-analysis data tabulation |
| makeRandom | Create a control stream for simulation |
| make.symmetric | Creat symmetrical matrix |
| match.data.frame | Compare two data frames |
| mauve | mauve |
| meta.map | Draw meta-map |
| micro2macro | Convert Micro Parameters to Macro Parameters |
| miss.col | Detect differences between two data.frames |
| mutate_cond | Conditional Mutate (dplyr) rows that match a specified... |
| myPNG | General PNG grpah creator |
| nlme.diag | Diagnostic plots for nlme |
| nlme.extract | Extract information from nlme object |
| nlme.getFixPars | NLME fixed effects and covariance matrix |
| nlme.getRanPars | NLME random effects and covariance matrix |
| nlme.modeltrail | Model trail / Runrecord for series of nested nlme models |
| nlme.predict | Prediction tool for nlme object |
| nlme.run | Run an nlme object augmented with model trail info |
| nlme.simPars | Simulate from an nlme object |
| nlme.vpc | Create VPC output of an nlme object |
| nlme.vpcplot | Plot a VPC of an nlme object |
| nls.predict | Predict partial residuals from an nls object |
| nls.vcov | NLS variance covariance matrix |
| nm.compare.plot | Create a runrecord like GOF plot of selected runs |
| nm.cormat.extract | Correlation Matrix Extraction |
| nm.covmat.extract | Covariance Matrix Extraction |
| nm.covplot | Create covariate plot and data |
| nm.create.control | Documentation stub Create a control stream for simulation |
| nm.extract.ext | NONMEM output extraction using .lst and .ext files |
| nm.extract.xml | NONMEM output extraction from XML output |
| nm.insert.dose.multiple.compartments | Insert doses in other compartments |
| nm.insert.evid2amt0 | Insert doses in other compartments |
| nm.modeltrail.graph | Graphical Bayesian model trail |
| nm.params.table | Create NONMEM Parameter Estimate Table |
| nm.parse2r.operators | Change NONMEM operators into R operators |
| nm.parse.control.stream | Parse NONMEM control stream |
| nm.process.coveffects | Evaluate equations (as a list of calls) over the covariates... |
| nm.process.scm | Parsing SCM output |
| nm.read.vpc | Read VPC output |
| nm.remove.section | Extract control stream sections |
| nm.runtime | NONMEM run time |
| nm_unzip | Unzip a NONMEM File |
| nm.unzip | Unzip function for zipped PsN output |
| nm.vpcplot | Create covariate plot and data |
| obs.color | obs.color (Autograph) |
| odeSim | ODE simulation with Multiprocessor Computation |
| olive | olive |
| orange | orange |
| orderedNumeric | like as.ordered with extended formatting |
| panel.avg.LP | Lattice panel function for average lines |
| panel.cwres | Lattice panel function for CWRES plots |
| panel.meanspag | Lattice panel function for spagghetti plots with a mean line |
| panel.modelfit | Panel function for Residual Variability Plots |
| panel.nlme.vpc.obs | Lattice function for observed components of an nlme VPCs |
| panel.nlme.vpc.pred | Lattice function for predicted components of an nlme VPCs |
| panel.nonmem.vpc | Lattice function for predicted components of a NONMEM VPC |
| panel.residual | Panel function for Residual Variability Plots |
| panel.superpose.arrows | Panel function for hysteresis plots |
| panel.superpose.bubble | Panel function for bubble plots |
| panel.thalf | Panel function for elimination half life |
| PI.ci.down.arcol | PI.ci.down.arcol (Autograph) |
| PI.ci.med.arcol | PI.ci.med.arcol (Autograph) |
| PI.ci.up.arcol | PI.ci.up.arcol (Autograph) |
| pink | pink |
| PI.real.down.col | PI.real.down.col (Autograph) |
| PI.real.med.col | PI.real.med.col (Autograph) |
| PI.real.up.col | PI.real.up.col (Autograph) |
| plot.covEffects | Plot a covariate effects object |
| plot.fit | Plotting function for nls.predict and nlme.predict |
| plot.tornado | Tornado plots |
| png.report | PNG graph for reports generation |
| png.slide.full | PNG graph for PowerPoint generation (full size) |
| png.slide.semi | PNG graph for PowerPoint generation (semi-full size) |
| pred.color | pred.color (Autograph) |
| print.covInfo | Print a covInfo S3 object |
| process.parTable | Format parameter estimate table |
| process.runrec | Format runrecord for reports |
| purple | purple |
| qp.blue | qp.blue |
| qp.colors | qPharmetra Colors |
| qp.colors.sorted | qP Colors Sorted |
| qp.green | qp.green |
| qpToolkit | qpToolkit: Tools for population PK/PD modeling,... |
| qP.welcome | Print a welcome message |
| qqGamma | Plot QQ Gamma distribution |
| read.bootstrap | Documentation stub |
| read.ext | Parse the information from the .ext file |
| read.mod | Scan NONMEM output file |
| read.out | Scan NONMEM output file |
| read.runrec | Read the runrecord |
| read.vpc | Create covariate plot and data |
| red | red |
| remove.tex.files | Remove intermediate LaTeX Files |
| removeTrailing | Remove trailing items from vector |
| reorder.data.frame | Reorder names in a data.frame |
| repeat.nth | Hide repetition of character strings |
| rgenpois | Sample from Generalized Poisson distribution |
| R.installation.validation | R Installation Validation |
| rnorm.by.id | Group-wise sampling from normal distribution |
| runrec | Construct a Run Record |
| sample.by.id | Group-wise sampling from prespecified distribution |
| set.trellis.colors | Set Trellis/Lattice colors |
| sgeomean.cl.normal | Summary of geometric mean and 95% CI |
| shuffle.list | Shuffle/reorder lists |
| smooth.ci.color | smooth.ci.color (Autograph) |
| smooth.color | smooth.color (Autograph) |
| steel | steel |
| striptext | Extract Striptext |
| striptext.ggplot | Extract Striptext from ggplot |
| sunique | Unique values sorted |
| superPosition | Superposition of concentration-time profiles |
| swap | Exchange Existing set of Values for another set of Values |
| table.meta.analysis.summary | Summarize meta-analysis dataset |
| tabStats | Table Statistics |
| tabSummarize | Tabulate a summary |
| tabulate.samples | Summarize endpoints for numeric/non-numeric |
| taupe | taupe |
| teal | teal |
| transform_log10 | Log10 transformation |
| transform_micro | Transform Micro Parameters |
| trellis.strip.color | Set strip colors to gray scales |
| trimSpace | Trimming spaces |
| uncertainParams | Sample parameters across uncertainty |
| unitDensity | Density plot normalized to unity |
| unitHistogram | Histogram normalized to unity |
| vec2df | Turn vector into data.frame |
| violet | violet |
| whichNumeric | Which entries are numeric? |
| xml.Extract.NM.Matrix | XML parser for matrices |
| xml.Extract.NM.Value | XML parser for vectors |
| xscale.components.log10 | Labels 10-logged x axes appropriately in lattice |
| xscale.components.log10.3 | Labels 10-logged x axes appropriately in lattice (ticks at... |
| yellow | yellow |
| yscale.components.log10 | Labels 10-logged y axes appropriately in lattice |
| yscale.components.log10.3 | Labels 10-logged y axes appropriately in lattice (ticks at... |
