Bioequivalence and Bioavailability Forum

Diagnostics: R [Study As­sess­ment]

posted by Helmut  – Vienna, Austria, 2016-05-23 03:22 (3286 d 17:45 ago) – Posting: # 16349
Views: 32,780

Hi zizou,

❝ DF, p-values, CIs not reported in lmer for the reasons stated there.

Yep, we know.

❝ library lmerTest can be used,

THX; I forgot!

❝ I think there is a little bug in df visualization - rounded on 3 decimal places, visible on 5 (actually I have not the latest version of R).

Same in R 3.2.5 and lmerTest 2.0-30.

❝ summary(muddle)$coefficients["(Intercept)","df"]


❝  # [1] 9.195607

Or easier:
summary(muddle)$coefficients[, "df"]
(Intercept)   log(Dose)
   9.195607    5.896110

summary(muddle, digits=8) doesn’t help. Or as Carl Witthoft wrote: IMHO the proper use of summary is indicated by its name: a way to get a quick-look at your data.

❝ For calculation of 90% CIs: (below is only example for Intercept lower and upper limit)

❝ alpha=0.05


❝ summary(muddle)$coefficients["(Intercept)","Estimate"] - qt(1-alpha,summary(muddle)$coefficients["(Intercept)","df"]) * summary(muddle)$coefficients["(Intercept)","Std. Error"]

Perfect! Little bit shorter:
summary(muddle)$coefficients[1, 1] +c(-1,+1)*qt(1-0.05, summary(muddle)$coefficients[1, 3]) * summary(muddle)$coefficients[1, 2]
[1] 1.496758 2.386013
summary(muddle)$coefficients[2, 1] +c(-1,+1)*qt(1-0.05, summary(muddle)$coefficients[2, 3]) * summary(muddle)$coefficients[2, 2]
[1] 0.6695768 0.8539044

So what do we have? A fair agreement across software – except SAS…

Software               Estimate       90% CI       width
NCSS               B0 1.9414    1.4849    2.3978    0.9129
                   B1 0.7617    0.6659    0.8576    0.1917
Phoenix/WinNonlin  B0 1.9413858 1.4967592 2.3860125 0.8893
                   B1 0.7617406 0.6695783 0.8539029 0.1843
R lmerTest         B0 1.9413858 1.4967584 2.3860132 0.8893
                   B1 0.7617406 0.6695768 0.8539044 0.1843
SAS (code?)        B0 1.94      1.54      2.35      0.8100
                   B1 0.7615    0.679     0.844     0.1650
Since I trust most in Phoenix and R; given the width of the CI: Is NCSS too conservative and SAS liberal? Unfortunately we don’t have Smith’s code. Would be great if one of our SASians could jump in.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна! 
Helmut Schütz


The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

Complete thread:

• Dose Proportionality and Variance AngusMcLean 2016-05-11 16:55 [Study As­sess­ment] 
  • More information, please Helmut 2016-05-12 14:34
    • More information, please AngusMcLean 2016-05-13 16:40
      • Setup in Phoenix/WinNonlin Helmut 2016-05-14 02:26
        • Setup in Phoenix/WinNonlin AngusMcLean 2016-05-14 18:54
          • Setup in Phoenix/WinNonlin Helmut 2016-05-15 14:47
            • Setup in Phoenix/WinNonlin AngusMcLean 2016-05-15 15:17
              • Phoenix 64 Warning Helmut 2016-05-15 15:56
                • Phoenix 64 Warning AngusMcLean 2016-05-15 20:11
                  • OT: imperial vs. metric units Helmut 2016-05-16 16:26
              • Setup in Phoenix/WinNonlin ElMaestro 2016-05-15 20:54
                • Setup in Phoenix/WinNonlin AngusMcLean 2016-05-15 22:30
        • Setup in Phoenix/WinNonlin AngusMcLean 2016-05-16 21:00
          • NCSS vs. PHX/WNL vs. SAS Helmut 2016-05-17 01:50
            • NCSS vs. PHX/WNL vs. SAS - Validation? mittyri 2016-05-18 08:23
              • Diagnostics ElMaestro 2016-05-18 09:20
                • Diagnostics: R and Phoenix Helmut 2016-05-18 15:14
                  • Diagnostics: R zizou 2016-05-22 19:07
                    • Diagnostics: RHelmut 2016-05-23 01:22
                      • SASian potpourri d_labes 2016-05-24 12:02
                        • Compilation Helmut 2016-05-24 14:27
                          • REML or not d_labes 2016-05-24 16:33
                            • complete or not Helmut 2016-05-24 16:57
                          • Compilation AngusMcLean 2016-05-26 16:46
                            • doubts about NCSS Helmut 2016-05-26 19:13
                              • Doubts about NCSS zizou 2016-05-26 23:38
                          • Compilation AngusMcLean 2016-05-28 00:51
                            • Kenward-Roger? Helmut 2016-05-28 15:59
                          • 90% confidence interval for R_dnm Shuanghe 2019-01-04 17:45
                            • 90% confidence interval for R_dnm d_labes 2019-01-05 14:01
                              • Visualizing lmer and limits mittyri 2019-01-06 17:00
                                • Visualizing lmer and limits Shuanghe 2019-01-07 11:05
                                • Visualizing lmer and limits d_labes 2019-01-07 15:08
                                  • Visualizing lmer and limits mittyri 2019-01-13 23:53
                              • 90% confidence interval for R_dnm Shuanghe 2019-01-07 10:53
                                • 90% confidence interval for R_dnm d_labes 2019-01-07 15:17
                                  • 90% confidence interval for R_dnm Shuanghe 2019-01-07 17:11
                                    • 90% confidence interval for R_dnm d_labes 2019-01-07 18:24
                                    • offtop: greek letters and tables mittyri 2019-01-08 00:19
                                      • OT: greek letters and symbols Helmut 2019-02-02 16:04
              • Smith’s paper Helmut 2016-05-18 14:44
                • Smith’s paper d_labes 2019-01-05 15:00