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add options to set initial mu0 and r0 for optim() in cnbinom.pars() #1

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add options to set initial mu0 and r0 for optim() in cnbinom.pars() #1

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9 changes: 5 additions & 4 deletions R/cnbinom.pars_function.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ library(stringr)
# cnbinom.pars is a function that outputs mu and r from univariate censored table input
# assume negative binomial

cnbinom.pars<-function (censoredtable){
cnbinom.pars<-function (censoredtable, mu0 = 100, r0 = 100, warn = -1, ...){


# make probabilities if not already
Expand Down Expand Up @@ -283,11 +283,12 @@ findtypeofcensoring_univariatetable<-function (univariatefreqtable){

# optimize mu and r in loglikelihood_univariatecase
# hide warnings...
options(warn=-1)
options(warn = warn)

fixdata_univariatecase_output=fixdata_univariatecase(censoredtable)
op<- optim(par=c(100,100),
op<- optim(par=c(mu0, r0),
fn =loglikelihood_univariatecase,
fixdata_univariatecase_output=fixdata_univariatecase_output)
fixdata_univariatecase_output=fixdata_univariatecase_output, ...)
final<-op$par
mu = final[1]
r = final[2]
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7 changes: 5 additions & 2 deletions README.md
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Expand Up @@ -23,13 +23,16 @@ library(revengc)
## Usage
`cnbinom.pars()` has the following format
```
cnbinom.pars(censoredtable)
cnbinom.pars(censoredtable, mu0 = 100, r0 = 100, warn = -1, ...)
```

where a description of the argument directly below

* **censoredtable** - A frequency table (censored and/or uncensored). A data.frame and matrix are acceptable classes. See Table format section below.

* **mu0, r0** starting values for `mu` and `r` used by optim.
* **warn** - Value used for `options(warn)` during `optim()` fitting.
`-1` suppresses warnings
* **...** - Additional arguments to be passed to `optim()`

`rec()` has the following format where a description of each argument is found below

Expand Down