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mle and semLme not fully supported yet? #283

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IndrajeetPatil opened this issue Aug 16, 2020 · 1 comment
Open

mle and semLme not fully supported yet? #283

IndrajeetPatil opened this issue Aug 16, 2020 · 1 comment
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Enhancement 💥 Implemented features can be improved or revised

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@IndrajeetPatil
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semLme

# setup
set.seed(123)
library(smicd)

# Load and prepare data
data <- Exam
classes <- c(1, 1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.7, 8.5, Inf)
data$examsc.class <- cut(data$examsc, classes)

# run model with random intercept and default settings
model1 <-
  semLme(
    formula = examsc.class ~ standLRT + schavg + (1 | school),
    data = data,
    classes = classes
  )
#> Warning: 'r.squaredGLMM' now calculates a revised statistic. See the help page.

# summary
summary(model1)
#> Call:
#> semLme(formula = examsc.class ~ standLRT + schavg + (1 | school), 
#>     data = data, classes = classes)
#> 
#> Random effects:
#>     Groups        Name   Variance  Std.Dev.
#> 1   school (Intercept) 0.07661185 0.2767884
#> 2 Residual             0.58815835 0.7669148
#> 
#> Fixed effects:
#>              Estimate
#> (Intercept) 5.0138425
#> standLRT    0.5594550
#> schavg      0.3692529
#> 
#> Marginal R-squared:  0.3534 Conditional R-squared:  0.4279
#> 
#> Variable examsc.class is divided into 9 intervals.

# parameters
parameters::model_parameters(model1)
#> Warning: Model has no standard errors. Please fit model again with bootstrapped
#> standard errors.
#> Warning: Model has no standard errors. Please fit model again with bootstrapped
#> standard errors.
#> Error in `$<-.data.frame`(`*tmp*`, "CI", value = 95): replacement has 1 row, data has 0

mle

# avoid printing to unwarranted accuracy
od <- options(digits = 5)

# simulated EC50 experiment with count data
x <- 0:10
y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8)

# easy one-dimensional MLE:
nLL <- function(lambda) -sum(stats::dpois(y, lambda, log = TRUE))
fit0 <- stats4::mle(nLL, start = list(lambda = 5), nobs = NROW(y))

# parameters
parameters::model_parameters(fit0)
#> Error in do.call(cbind, x@data): no slot of name "data" for this object of class "mle"

Created on 2020-08-16 by the reprex package (v0.3.0)

Session info 
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.3 (2020-02-29)
#>  os       macOS Mojave 10.14.6        
#>  system   x86_64, darwin15.6.0        
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       Europe/Berlin               
#>  date     2020-08-16                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package        * version  date       lib source                               
#>  assertthat       0.2.1    2019-03-21 [1] CRAN (R 3.6.0)                       
#>  backports        1.1.8    2020-06-17 [1] CRAN (R 3.6.2)                       
#>  base64enc        0.1-3    2015-07-28 [1] CRAN (R 3.6.0)                       
#>  bayestestR       0.7.2.1  2020-08-15 [1] Github (easystats/bayestestR@1ffb88f)
#>  boot             1.3-25   2020-04-26 [1] CRAN (R 3.6.2)                       
#>  broom            0.7.0    2020-07-09 [1] CRAN (R 3.6.3)                       
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#>  crayon           1.3.4    2017-09-16 [1] CRAN (R 3.6.0)                       
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#>  fs               1.5.0    2020-07-31 [1] CRAN (R 3.6.2)                       
#>  gdata            2.18.0   2017-06-06 [1] CRAN (R 3.6.0)                       
#>  generics         0.0.2    2018-11-29 [1] CRAN (R 3.6.0)                       
#>  ggplot2          3.3.2    2020-06-19 [1] CRAN (R 3.6.2)                       
#>  glue             1.4.1    2020-05-13 [1] CRAN (R 3.6.2)                       
#>  gridExtra        2.3      2017-09-09 [1] CRAN (R 3.6.0)                       
#>  gtable           0.3.0    2019-03-25 [1] CRAN (R 3.6.0)                       
#>  gtools           3.8.2    2020-03-31 [1] CRAN (R 3.6.2)                       
#>  highr            0.8      2019-03-20 [1] CRAN (R 3.6.0)                       
#>  Hmisc            4.4-1    2020-08-10 [1] CRAN (R 3.6.2)                       
#>  htmlTable        2.0.1    2020-07-05 [1] CRAN (R 3.6.2)                       
#>  htmltools        0.5.0    2020-06-16 [1] CRAN (R 3.6.2)                       
#>  htmlwidgets      1.5.1    2019-10-08 [1] CRAN (R 3.6.0)                       
#>  ineq             0.2-13   2014-07-21 [1] CRAN (R 3.6.0)                       
#>  insight          0.9.0.1  2020-08-16 [1] Github (easystats/insight@8088747)   
#>  jpeg             0.1-8.1  2019-10-24 [1] CRAN (R 3.6.0)                       
#>  knitr            1.29     2020-06-23 [1] CRAN (R 3.6.3)                       
#>  laeken           0.5.1    2020-02-05 [1] CRAN (R 3.6.0)                       
#>  lattice          0.20-41  2020-04-02 [1] CRAN (R 3.6.2)                       
#>  latticeExtra     0.6-29   2019-12-19 [1] CRAN (R 3.6.2)                       
#>  lifecycle        0.2.0    2020-03-06 [1] CRAN (R 3.6.0)                       
#>  lme4             1.1-23   2020-04-07 [1] CRAN (R 3.6.2)                       
#>  magrittr         1.5      2014-11-22 [1] CRAN (R 3.6.0)                       
#>  MASS             7.3-51.5 2019-12-20 [2] CRAN (R 3.6.3)                       
#>  Matrix           1.2-18   2019-11-27 [2] CRAN (R 3.6.3)                       
#>  memoise          1.1.0    2017-04-21 [1] CRAN (R 3.6.0)                       
#>  mice             3.11.0   2020-08-05 [1] CRAN (R 3.6.3)                       
#>  minqa            1.2.4    2014-10-09 [1] CRAN (R 3.6.0)                       
#>  MuMIn            1.43.17  2020-04-15 [1] CRAN (R 3.6.2)                       
#>  munsell          0.5.0    2018-06-12 [1] CRAN (R 3.6.0)                       
#>  mvtnorm          1.1-1    2020-06-09 [1] CRAN (R 3.6.2)                       
#>  nlme             3.1-144  2020-02-06 [2] CRAN (R 3.6.3)                       
#>  nloptr           1.2.2.2  2020-07-02 [1] CRAN (R 3.6.2)                       
#>  nnet             7.3-12   2016-02-02 [2] CRAN (R 3.6.3)                       
#>  operator.tools   1.6.3    2017-02-28 [1] CRAN (R 3.6.0)                       
#>  parameters       0.8.2.1  2020-08-16 [1] Github (easystats/parameters@85b91e8)
#>  pillar           1.4.6    2020-07-10 [1] CRAN (R 3.6.3)                       
#>  pkgbuild         1.1.0    2020-07-13 [1] CRAN (R 3.6.3)                       
#>  pkgconfig        2.0.3    2019-09-22 [1] CRAN (R 3.6.0)                       
#>  pkgload          1.1.0    2020-05-29 [1] CRAN (R 3.6.2)                       
#>  png              0.1-7    2013-12-03 [1] CRAN (R 3.6.0)                       
#>  prettyunits      1.1.1    2020-01-24 [1] CRAN (R 3.6.2)                       
#>  processx         3.4.3    2020-07-05 [1] CRAN (R 3.6.2)                       
#>  ps               1.3.4    2020-08-11 [1] CRAN (R 3.6.3)                       
#>  purrr            0.3.4    2020-04-17 [1] CRAN (R 3.6.2)                       
#>  R6               2.4.1    2019-11-12 [1] CRAN (R 3.6.0)                       
#>  RColorBrewer     1.1-2    2014-12-07 [1] CRAN (R 3.6.0)                       
#>  Rcpp             1.0.5    2020-07-06 [1] CRAN (R 3.6.3)                       
#>  remotes          2.2.0    2020-07-21 [1] CRAN (R 3.6.3)                       
#>  rlang            0.4.7    2020-07-09 [1] CRAN (R 3.6.3)                       
#>  rmarkdown        2.3      2020-06-18 [1] CRAN (R 3.6.3)                       
#>  rpart            4.1-15   2019-04-12 [2] CRAN (R 3.6.3)                       
#>  rprojroot        1.3-2    2018-01-03 [1] CRAN (R 3.6.0)                       
#>  rstudioapi       0.11     2020-02-07 [1] CRAN (R 3.6.0)                       
#>  scales           1.1.1    2020-05-11 [1] CRAN (R 3.6.3)                       
#>  sessioninfo      1.1.1    2018-11-05 [1] CRAN (R 3.6.0)                       
#>  smicd          * 1.1.1    2020-07-18 [1] CRAN (R 3.6.2)                       
#>  statmod          1.4.34   2020-02-17 [1] CRAN (R 3.6.0)                       
#>  stringi          1.4.6    2020-02-17 [1] CRAN (R 3.6.2)                       
#>  stringr          1.4.0    2019-02-10 [1] CRAN (R 3.6.0)                       
#>  survival         3.2-3    2020-06-13 [1] CRAN (R 3.6.2)                       
#>  testthat         2.3.2    2020-03-02 [1] CRAN (R 3.6.2)                       
#>  tibble           3.0.3    2020-07-10 [1] CRAN (R 3.6.2)                       
#>  tidyr            1.1.1    2020-07-31 [1] CRAN (R 3.6.3)                       
#>  tidyselect       1.1.0    2020-05-11 [1] CRAN (R 3.6.3)                       
#>  truncnorm        1.0-8    2018-02-27 [1] CRAN (R 3.6.0)                       
#>  usethis          1.6.1    2020-04-29 [1] CRAN (R 3.6.2)                       
#>  vctrs            0.3.2    2020-07-15 [1] CRAN (R 3.6.3)                       
#>  weights          1.0.1    2020-02-12 [1] CRAN (R 3.6.0)                       
#>  withr            2.2.0    2020-04-20 [1] CRAN (R 3.6.2)                       
#>  xfun             0.16     2020-07-24 [1] CRAN (R 3.6.3)                       
#>  yaml             2.2.1    2020-02-01 [1] CRAN (R 3.6.0)                       
#> 
#> [1] /Users/patil/Library/R/3.6/library
#> [2] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
@IndrajeetPatil IndrajeetPatil added the Enhancement 💥 Implemented features can be improved or revised label Aug 16, 2020
strengejacke added a commit that referenced this issue Aug 16, 2020
@strengejacke
#283 (make sem more robust)
fd3e283
@strengejacke
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semLme should now also work for models w/o bootstrapped se. mle is indeed a problem.

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