Hello all,
I've been using the countreg package to fit a zero-inflated negative binomial model successfully up until yesterday. I'm a newbie to R and so I'm sure I've done something silly to goof this up, I just cannot figure out what.
I've been using the "zeroinfl" function successfully for the model below but now I get the following warning message (and I have not knowingly changed the code in the model, or the data it's based on):
lag.all.zinb = zeroinfl(fox ~ coy_7 + area + factor(site) + month,
data = foxl,
dist = "negbin")
Warning message:In value[[3L]](cond):system is computationally singular:reciprocal condition number = 2.3445e-35FALSE
I tried redownloading countreg and am getting the following series of warnings during the installation that I do not think I got when I first downloaded the package. I'm wondering if these warnings point to the problem that's leading to the "system is computationally singular" message when I tried to run the model. How can I address the installation warnings that say the file links in various packages do not exist and are being treated as topics?
Any help is much appreciated!
install.packages("countreg", repos="http://R-Forge.R-project.org", type="source")
Installing package into ‘C:/Users/lpowe/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'R-Forge.R-project.org/src/contrib/countreg_0.2-1.tar.gz'
Content type 'application/x-gzip' length 685268 bytes (669 KB)
downloaded 669 KB
* installing *source* package 'countreg' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
package 'MASS' was built under R version 4.0.3
** help
*** installing help indices
converting help for package 'countreg'
finding HTML links ... done
CodParasites html
CrabSatellites html
FLXMRnegbin html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/FLXMRnegbin.Rd:34: file link 'glm.fit' in package 'stats' does not exist and so has been treated as a topic
MBnegbin html
OralHealthNL html
SerumPotassium html
TakeoverBids html
VolcanoHeights html
binom html
disptest html
hnbinom html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/hnbinom.Rd:79: file link 'dnbinom' in package 'stats' does not exist and so has been treated as a topic
hpois html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/hpois.Rd:73: file link 'dpois' in package 'stats' does not exist and so has been treated as a topic
hurdle html
Rd warning: /tmp/RtmplRwhXA/Rbuild33b8aa21d3ce7f/countreg/man/hurdle.Rd:80: file link 'glm.fit' in package 'stats' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmplRwhXA/Rbuild33b8aa21d3ce7f/countreg/man/hurdle.Rd:95: file link 'fitted' in package 'stats' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmplRwhXA/Rbuild33b8aa21d3ce7f/countreg/man/hurdle.Rd:160: file link 'glm.fit' in package 'stats' does not exist and so has been treated as a topic
hurdle.control html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/hurdle.control.Rd:40: file link 'glm.fit' in package 'stats' does not exist and so has been treated as a topic
hurdletest html
nbinom html
pit html
pithist html
pois html
predict.hurdle html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/predict.hurdle.Rd:69: file link 'fitted' in package 'stats' does not exist and so has been treated as a topic
predict.zeroinfl html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/predict.zeroinfl.Rd:69: file link 'fitted' in package 'stats' does not exist and so has been treated as a topic
predict.zerotrunc html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/predict.zerotrunc.Rd:54: file link 'fitted' in package 'stats' does not exist and so has been treated as a topic
qqrplot html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/qqrplot.Rd:28: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
qresiduals html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/qresiduals.Rd:39: file link 'qnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/qresiduals.Rd:59: file link 'qnorm' in package 'stats' does not exist and so has been treated as a topic
rootogram html
zeroinfl html
Rd warning: /tmp/RtmplRwhXA/Rbuild33b8aa21d3ce7f/countreg/man/zeroinfl.Rd:79: file link 'glm.fit' in package 'stats' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmplRwhXA/Rbuild33b8aa21d3ce7f/countreg/man/zeroinfl.Rd:92: file link 'fitted' in package 'stats' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmplRwhXA/Rbuild33b8aa21d3ce7f/countreg/man/zeroinfl.Rd:156: file link 'glm.fit' in package 'stats' does not exist and so has been treated as a topic
zeroinfl.control html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/zeroinfl.control.Rd:40: file link 'glm.fit' in package 'stats' does not exist and so has been treated as a topic
zerotrunc html
Rd warning: /tmp/RtmplRwhXA/Rbuild33b8aa21d3ce7f/countreg/man/zerotrunc.Rd:46: file link 'glm.fit' in package 'stats' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmplRwhXA/Rbuild33b8aa21d3ce7f/countreg/man/zerotrunc.Rd:58: file link 'fitted' in package 'stats' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmplRwhXA/Rbuild33b8aa21d3ce7f/countreg/man/zerotrunc.Rd:106: file link 'glm.fit' in package 'stats' does not exist and so has been treated as a topic
zerotrunc.control html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/zerotrunc.control.Rd:30: file link 'glm.fit' in package 'stats' does not exist and so has been treated as a topic
zinbinom html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/zinbinom.Rd:68: file link 'dnbinom' in package 'stats' does not exist and so has been treated as a topic
zipois html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/zipois.Rd:62: file link 'dpois' in package 'stats' does not exist and so has been treated as a topic
zitest html
ztnbinom html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/ztnbinom.Rd:76: file link 'dnbinom' in package 'stats' does not exist and so has been treated as a topic
ztpois html
Rd warning: C:/Users/lpowe/AppData/Local/Temp/RtmpWEiOfh/R.INSTALL53445f093a36/countreg/man/ztpois.Rd:85: file link 'dpois' in package 'stats' does not exist and so has been treated as a topic
ztpoisson html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning: package 'MASS' was built under R version 4.0.3
*** arch - x64
Warning: package 'MASS' was built under R version 4.0.3
** testing if installed package can be loaded from final location
*** arch - i386
Warning: package 'MASS' was built under R version 4.0.3
*** arch - x64
Warning: package 'MASS' was built under R version 4.0.3
** testing if installed package keeps a record of temporary installation path
* DONE (countreg)