Diagnostics: R [Study Assessment]
❝ 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!
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Helmut Schütz
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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
- Phoenix 64 Warning AngusMcLean 2016-05-15 20:11
- Setup in Phoenix/WinNonlin ElMaestro 2016-05-15 20:54
- Setup in Phoenix/WinNonlin AngusMcLean 2016-05-15 22:30
- Phoenix 64 Warning Helmut 2016-05-15 15:56
- Setup in Phoenix/WinNonlin AngusMcLean 2016-05-15 15:17
- Setup in Phoenix/WinNonlin Helmut 2016-05-15 14:47
- 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
- doubts about NCSS Helmut 2016-05-26 19:13
- 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
- 90% confidence interval for R_dnm Shuanghe 2019-01-07 17:11
- 90% confidence interval for R_dnm d_labes 2019-01-07 15:17
- Visualizing lmer and limits mittyri 2019-01-06 17:00
- 90% confidence interval for R_dnm d_labes 2019-01-05 14:01
- REML or not d_labes 2016-05-24 16:33
- Compilation Helmut 2016-05-24 14:27
- SASian potpourri d_labes 2016-05-24 12:02
- Diagnostics: RHelmut 2016-05-23 01:22
- Diagnostics: R zizou 2016-05-22 19:07
- Diagnostics: R and Phoenix Helmut 2016-05-18 15:14
- Smith’s paper Helmut 2016-05-18 14:44
- Smith’s paper d_labes 2019-01-05 15:00
- Diagnostics ElMaestro 2016-05-18 09:20
- NCSS vs. PHX/WNL vs. SAS - Validation? mittyri 2016-05-18 08:23
- NCSS vs. PHX/WNL vs. SAS Helmut 2016-05-17 01:50
- Setup in Phoenix/WinNonlin AngusMcLean 2016-05-14 18:54
- Setup in Phoenix/WinNonlin Helmut 2016-05-14 02:26
- More information, please AngusMcLean 2016-05-13 16:40
- More information, please Helmut 2016-05-12 14:34