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DoseResponse / drc

Fitting dose-response models in R
https://doseresponse.github.io/drc/
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`predict` not returning confidence intervals for `NEC.3()` model #23

Open dbarneche opened 2 years ago

dbarneche commented 2 years ago

Is this potentially a bug or is it intended behaviour?

I noticed that the spinach.model1 example in ?predict.drc returns a matrix with the credible intervals

> library(drc)
> spinach_model1_ll4 <- drm(SLOPE~DOSE, CURVE, data = spinach, fct = LL.4())
> predict(spinach_model1_ll4, data.frame(dose=2, CURVE=c("1", "2", "3")),
          interval = "confidence")
     Prediction     Lower     Upper
[1,]  0.9048476 0.8552178 0.9544775
[2,]  0.4208307 0.3626741 0.4789873
[3,]  0.5581673 0.4971838 0.6191509
Warning messages:
1: In (tquan * sqrt(varVal + sumObjRV)) * c(-1, 1) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

2: In (tquan * sqrt(varVal + sumObjRV)) * c(-1, 1) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

3: In (tquan * sqrt(varVal + sumObjRV)) * c(-1, 1) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

But as soon as I use NEC.3() for the model, it only returns what I think is the mean?

> spinach_model1_nec3 <- drm(SLOPE~DOSE, CURVE, data = spinach, fct = NEC.3())
> predict(spinach_model1_nec3)
  [1] 1.534025e+00 1.534025e+00 1.534025e+00 1.396653e+00 1.396653e+00
  [6] 1.396653e+00 1.159464e+00 1.159464e+00 1.159464e+00 6.613781e-01
 [11] 6.613781e-01 6.613781e-01 1.231237e-01 1.231237e-01 1.231237e-01
 [16] 7.943600e-04 7.943600e-04 7.943600e-04 2.130037e-10 2.130037e-10
 [21] 2.130037e-10 8.254612e-01 8.254612e-01 8.254612e-01 7.073317e-01
 [26] 7.073317e-01 7.073317e-01 5.206644e-01 5.206644e-01 5.206644e-01
 [31] 2.066325e-01 2.066325e-01 2.066325e-01 1.298029e-02 1.298029e-02
 [36] 1.298029e-02 3.217671e-06 3.217671e-06 3.217671e-06 4.889130e-17
 [41] 4.889130e-17 4.889130e-17 9.281359e-01 9.281359e-01 9.281359e-01
 [46] 9.088835e-01 9.088835e-01 9.088835e-01 8.546830e-01 8.546830e-01
 [51] 8.546830e-01 6.692668e-01 6.692668e-01 6.692668e-01 2.502354e-01
 [56] 2.502354e-01 2.502354e-01 4.917835e-03 4.917835e-03 4.917835e-03
 [61] 7.315787e-10 7.315787e-10 7.315787e-10 2.124491e+00 2.124491e+00
 [66] 2.124491e+00 2.124491e+00 2.124491e+00 2.124491e+00 2.124491e+00
 [71] 2.124491e+00 2.124491e+00 1.703807e+00 1.703807e+00 1.703807e+00
 [76] 7.583491e-01 7.583491e-01 7.583491e-01 4.461082e-02 4.461082e-02
 [81] 4.461082e-02 1.361222e-05 1.361222e-05 1.361222e-05 1.773046e+00
 [86] 1.773046e+00 1.773046e+00 1.773046e+00 1.773046e+00 1.773046e+00
 [91] 1.773046e+00 1.773046e+00 1.773046e+00 1.413257e+00 1.413257e+00
 [96] 1.413257e+00 6.522470e-01 6.522470e-01 6.522470e-01 4.355921e-02
[101] 4.355921e-02 4.355921e-02 1.909801e-05 1.909801e-05 1.909801e-05
Warning message:
In sqrt(diag(varMat)) : NaNs produced

My specs are:

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] drc_3.0-1   MASS_7.3-54

loaded via a namespace (and not attached):
 [1] zip_2.1.1         Rcpp_1.0.7        cellranger_1.1.0  pillar_1.6.2     
 [5] compiler_4.1.1    forcats_0.5.1     tools_4.1.1       lifecycle_1.0.0  
 [9] tibble_3.1.4      lattice_0.20-44   pkgconfig_2.0.3   rlang_0.4.11     
[13] Matrix_1.3-4      openxlsx_4.2.3    curl_4.3.2        mvtnorm_1.1-2    
[17] haven_2.4.3       rio_0.5.26        vctrs_0.3.8       gtools_3.9.2     
[21] hms_1.1.0         grid_4.1.1        data.table_1.14.0 R6_2.5.1         
[25] plotrix_3.8-2     fansi_0.5.0       readxl_1.3.1      survival_3.2-11  
[29] foreign_0.8-81    multcomp_1.4-17   TH.data_1.0-10    carData_3.0-4    
[33] car_3.0-10        magrittr_2.0.1    scales_1.1.1      codetools_0.2-18 
[37] ellipsis_0.3.2    splines_4.1.1     abind_1.4-5       colorspace_2.0-2 
[41] sandwich_3.0-1    utf8_1.2.2        stringi_1.7.4     munsell_0.5.0    
[45] crayon_1.4.1      zoo_1.8-9