predictnl.default method is not exported/used

Question

predictnl.default method is not exported/used

Closed this issue 6 years ago · 2 comments

Hello!
I was replicating one of the examples from the vignette on predictnl that you sent me, and I couldn't reproduce the example with the linear regression model:

library(rstpm2)
#> Loading required package: survival
#> Loading required package: splines
#> 
#> Attaching package: 'rstpm2'
#> The following object is masked from 'package:survival':
#> 
#>     colon
set.seed(123456)
x1 <- rnorm(1000)
y <- rnorm(1000, x1)
fit <- lm(y ~ x1)
invert <- function(object, newdata) {
  thetahat <- coef(object)
  (newdata$y - thetahat[1])/thetahat[2]
}
predictnl(fit, invert, newdata = data.frame(y = seq(0, 2, by = 0.5)))
#> Error in UseMethod("predictnl"): no applicable method for 'predictnl' applied 
#>  to an object of class "lm"

I was expecting the predictnl.default method to be dispatched by default, but that did not happen. However, if I call it directly (and via the ::: operator - is it not exported on purpose?) if works fine:

rstpm2:::predictnl.default(fit, invert, newdata = data.frame(y = seq(0, 2, by = 0.5)))
#>      Estimate         SE
#> 1 0.007973223 0.03208338
#> 2 0.505825537 0.03585955
#> 3 1.003677852 0.04540490
#> 4 1.501530166 0.05793476
#> 5 1.999382481 0.07190551

Should this be useful, my R session info follows:

devtools::session_info()
#> Session info -------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.5.0 (2018-04-23)
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language (EN)                        
#>  collate  English_United Kingdom.1252 
#>  tz       Europe/London               
#>  date     2018-05-29
#> Packages -----------------------------------------------------------------
#>  package   * version  date       source        
#>  backports   1.1.2    2017-12-13 CRAN (R 3.5.0)
#>  base      * 3.5.0    2018-04-23 local         
#>  bbmle       1.0.20   2017-10-30 CRAN (R 3.5.0)
#>  compiler    3.5.0    2018-04-23 local         
#>  datasets  * 3.5.0    2018-04-23 local         
#>  devtools    1.13.5   2018-02-18 CRAN (R 3.5.0)
#>  digest      0.6.15   2018-01-28 CRAN (R 3.5.0)
#>  evaluate    0.10.1   2017-06-24 CRAN (R 3.5.0)
#>  formatR     1.5      2017-04-25 CRAN (R 3.5.0)
#>  graphics  * 3.5.0    2018-04-23 local         
#>  grDevices * 3.5.0    2018-04-23 local         
#>  grid        3.5.0    2018-04-23 local         
#>  htmltools   0.3.6    2017-04-28 CRAN (R 3.5.0)
#>  knitr       1.20     2018-02-20 CRAN (R 3.5.0)
#>  lattice     0.20-35  2017-03-25 CRAN (R 3.5.0)
#>  magrittr    1.5      2014-11-22 CRAN (R 3.5.0)
#>  Matrix      1.2-14   2018-04-13 CRAN (R 3.5.0)
#>  memoise     1.1.0    2017-04-21 CRAN (R 3.5.0)
#>  methods   * 3.5.0    2018-04-23 local         
#>  mgcv        1.8-23   2018-01-21 CRAN (R 3.5.0)
#>  nlme        3.1-137  2018-04-07 CRAN (R 3.5.0)
#>  numDeriv    2016.8-1 2016-08-27 CRAN (R 3.5.0)
#>  Rcpp        0.12.17  2018-05-18 CRAN (R 3.5.0)
#>  rmarkdown   1.9      2018-03-01 CRAN (R 3.5.0)
#>  rprojroot   1.3-2    2018-01-03 CRAN (R 3.5.0)
#>  rstpm2    * 1.4.1    2017-09-20 CRAN (R 3.5.0)
#>  splines   * 3.5.0    2018-04-23 local         
#>  stats     * 3.5.0    2018-04-23 local         
#>  stats4      3.5.0    2018-04-23 local         
#>  stringi     1.2.2    2018-05-02 CRAN (R 3.5.0)
#>  stringr     1.3.1    2018-05-10 CRAN (R 3.5.0)
#>  survival  * 2.42-3   2018-04-16 CRAN (R 3.5.0)
#>  tools       3.5.0    2018-04-23 local         
#>  utils     * 3.5.0    2018-04-23 local         
#>  withr       2.1.2    2018-03-15 CRAN (R 3.5.0)
#>  yaml        2.1.19   2018-05-01 CRAN (R 3.5.0)

Answer 1 · 2018-05-29T11:52:26.000Z

Alessandro, Does this work with the version on GitHub? I need to push a new version to CRAN...

…

-- Mark On 05/29/2018 01:41 PM, Alessandro Gasparini wrote: Hello! I was replicating one of the examples from the vignette on predictnl that you sent me, and I couldn't reproduce the example with the linear regression model: library(rstpm2) #> Loading required package: survival #> Loading required package: splines #> #> Attaching package: 'rstpm2' #> The following object is masked from 'package:survival': #> #> colon set.seed(123456) x1 <- rnorm(1000) y <- rnorm(1000, x1) fit <- lm(y ~ x1) invert <- function(object, newdata) { thetahat <- coef(object) (newdata$y - thetahat[1])/thetahat[2] } predictnl(fit, invert, newdata = data.frame(y = seq(0, 2, by = 0.5))) #> Error in UseMethod("predictnl"): no applicable method for 'predictnl' applied #> to an object of class "lm" I was expecting the predictnl.default method to be dispatched by default, but that did not happen. However, if I call it directly (and via the ::: operator - is it not exported on purpose?) if works fine: rstpm2:::predictnl.default(fit, invert, newdata = data.frame(y = seq(0, 2, by = 0.5))) #> Estimate SE #> 1 0.007973223 0.03208338 #> 2 0.505825537 0.03585955 #> 3 1.003677852 0.04540490 #> 4 1.501530166 0.05793476 #> 5 1.999382481 0.07190551 Should this be useful, my R session info follows: devtools::session_info() #> Session info ------------------------------------------------------------- #> setting value #> version R version 3.5.0 (2018-04-23) #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate English_United Kingdom.1252 #> tz Europe/London #> date 2018-05-29 #> Packages ----------------------------------------------------------------- #> package * version date source #> backports 1.1.2 2017-12-13 CRAN (R 3.5.0) #> base * 3.5.0 2018-04-23 local #> bbmle 1.0.20 2017-10-30 CRAN (R 3.5.0) #> compiler 3.5.0 2018-04-23 local #> datasets * 3.5.0 2018-04-23 local #> devtools 1.13.5 2018-02-18 CRAN (R 3.5.0) #> digest 0.6.15 2018-01-28 CRAN (R 3.5.0) #> evaluate 0.10.1 2017-06-24 CRAN (R 3.5.0) #> formatR 1.5 2017-04-25 CRAN (R 3.5.0) #> graphics * 3.5.0 2018-04-23 local #> grDevices * 3.5.0 2018-04-23 local #> grid 3.5.0 2018-04-23 local #> htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0) #> knitr 1.20 2018-02-20 CRAN (R 3.5.0) #> lattice 0.20-35 2017-03-25 CRAN (R 3.5.0) #> magrittr 1.5 2014-11-22 CRAN (R 3.5.0) #> Matrix 1.2-14 2018-04-13 CRAN (R 3.5.0) #> memoise 1.1.0 2017-04-21 CRAN (R 3.5.0) #> methods * 3.5.0 2018-04-23 local #> mgcv 1.8-23 2018-01-21 CRAN (R 3.5.0) #> nlme 3.1-137 2018-04-07 CRAN (R 3.5.0) #> numDeriv 2016.8-1 2016-08-27 CRAN (R 3.5.0) #> Rcpp 0.12.17 2018-05-18 CRAN (R 3.5.0) #> rmarkdown 1.9 2018-03-01 CRAN (R 3.5.0) #> rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0) #> rstpm2 * 1.4.1 2017-09-20 CRAN (R 3.5.0) #> splines * 3.5.0 2018-04-23 local #> stats * 3.5.0 2018-04-23 local #> stats4 3.5.0 2018-04-23 local #> stringi 1.2.2 2018-05-02 CRAN (R 3.5.0) #> stringr 1.3.1 2018-05-10 CRAN (R 3.5.0) #> survival * 2.42-3 2018-04-16 CRAN (R 3.5.0) #> tools 3.5.0 2018-04-23 local #> utils * 3.5.0 2018-04-23 local #> withr 2.1.2 2018-03-15 CRAN (R 3.5.0) #> yaml 2.1.19 2018-05-01 CRAN (R 3.5.0) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#8>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AAiBCW19xRqogs_NnAG79tA8wtBimoM1ks5t3TPIgaJpZM4URVEt>.

Answer 2 · 2018-05-29T12:05:29.000Z

My bad, it works flawlessly using the version from the develop branch. Thanks!