I am keen to promote the use of generalised mixed models for the analysis of proportions to psychologists Have straight fowl code in SPSS [costly] and would like to supply equivalent R Code without ?tears? Design is a follows raw frequencies are: FreqPos for ?success? and FreqNeg for ?failure? Predictors are Rab with 4 levels, repeated over participants and Between with 2 separate groups of participants Model is binomial with logit link Require following output to correspond to SPSS output from code below Descriptive: Means, se and 95% CIs by Rab, by Between and by Rab*Between Inferential: fo Rab, Between and Rab*Between: F value, MSE, numerator df, denominator df [this enables p-values] Have tried logit1 <- glmer(cbind(FreqPos,FreqNeg) ~ Rab + Between + Rab*Between + (1| Participant), family=binomial(link="logit")) gives F and MSE no denominator df or MSE. Different results to SPSS nb F=MSE - that can?t be right F is supposed to be ratio of chi-squares summary (logit1) gives coefficients and SEs. Different results to SPSS also tried predicted and fitted but still no means have spent days searching internet for examples - but none of them seem to show how to get the output I need All help greatly appreciated ____ Spss syntax *Generalized Linear Mixed Models. GENLINMIXED /DATA_STRUCTURE SUBJECTS=Participant REPEATED_MEASURES=Rab COVARIANCE_TYPE=UNSTRUCTURED /FIELDS TARGET=FreqPos TRIALS=FIELD(Nmax) OFFSET=NONE /TARGET_OPTIONS DISTRIBUTION=BINOMIAL LINK=LOGIT /FIXED EFFECTS=Rab Between Rab*Between USE_INTERCEPT=TRUE /BUILD_OPTIONS TARGET_CATEGORY_ORDER=DESCENDING INPUTS_CATEGORY_ORDER=DESCENDING MAX_ITERATIONS=100 CONFIDENCE_LEVEL=95 DF_METHOD=SATTERTHWAITE COVB=MODEL PCONVERGE=0.000001(ABSOLUTE) SCORING=0 SINGULAR=0.000000000001 /EMMEANS TABLES=Rab COMPARE=Rab CONTRAST=DEVIATION /EMMEANS TABLES=Between CONTRAST=NONE /EMMEANS TABLES=Rab*Between CONTRAST=NONE /EMMEANS_OPTIONS SCALE=ORIGINAL PADJUST=LSD. best Diana _____________________________________ Professor Diana Kornbrot Mobile +44 (0) 7403 18 16 12 Work University of Hertfordshire College Lane, Hatfield, Hertfordshire AL10 9AB, UK +44 (0) 170 728 4626 d.e.kornbrot at herts.ac.uk<mailto:d.e.kornbrot at herts.ac.uk> http://dianakornbrot.wordpress.com/ http://go.herts.ac.uk/Diana_Kornbrot skype: kornbrotme Home 19 Elmhurst Avenue London N2 0LT, UK +44 (0) 208 444 2081 ------------------------------------------------------------
means , CIs from lmer, glmer
4 messages · Kornbrot, Diana, Ben Bolker, Rune Haubo
Hi Diana, A reproducible example is always helpful/increases your chances of getting a useful answer ... It might help if you included the SPSS output (or posted it somewhere -- note that this list doesn't take HTML-formatted messages nor most attachments), as many of us don't have access to it. Look into the (very well-documented) emmeans package: https://CRAN.R-project.org/package=emmeans and the lmerTest package (for Satterthwaite df approximations) On Mon, Feb 26, 2018 at 12:11 PM, Kornbrot, Diana
<d.e.kornbrot at herts.ac.uk> wrote:
I am keen to promote the use of generalised mixed models for the analysis of proportions to psychologists Have straight fowl code in SPSS [costly] and would like to supply equivalent R Code without ?tears? Design is a follows raw frequencies are: FreqPos for ?success? and FreqNeg for ?failure? Predictors are Rab with 4 levels, repeated over participants and Between with 2 separate groups of participants Model is binomial with logit link Require following output to correspond to SPSS output from code below Descriptive: Means, se and 95% CIs by Rab, by Between and by Rab*Between Inferential: fo Rab, Between and Rab*Between: F value, MSE, numerator df, denominator df [this enables p-values] Have tried logit1 <- glmer(cbind(FreqPos,FreqNeg) ~ Rab + Between + Rab*Between + (1| Participant), family=binomial(link="logit")) gives F and MSE no denominator df or MSE. Different results to SPSS nb F=MSE - that can?t be right F is supposed to be ratio of chi-squares summary (logit1) gives coefficients and SEs. Different results to SPSS also tried predicted and fitted but still no means have spent days searching internet for examples - but none of them seem to show how to get the output I need All help greatly appreciated ____ Spss syntax *Generalized Linear Mixed Models. GENLINMIXED /DATA_STRUCTURE SUBJECTS=Participant REPEATED_MEASURES=Rab COVARIANCE_TYPE=UNSTRUCTURED /FIELDS TARGET=FreqPos TRIALS=FIELD(Nmax) OFFSET=NONE /TARGET_OPTIONS DISTRIBUTION=BINOMIAL LINK=LOGIT /FIXED EFFECTS=Rab Between Rab*Between USE_INTERCEPT=TRUE /BUILD_OPTIONS TARGET_CATEGORY_ORDER=DESCENDING INPUTS_CATEGORY_ORDER=DESCENDING MAX_ITERATIONS=100 CONFIDENCE_LEVEL=95 DF_METHOD=SATTERTHWAITE COVB=MODEL PCONVERGE=0.000001(ABSOLUTE) SCORING=0 SINGULAR=0.000000000001 /EMMEANS TABLES=Rab COMPARE=Rab CONTRAST=DEVIATION /EMMEANS TABLES=Between CONTRAST=NONE /EMMEANS TABLES=Rab*Between CONTRAST=NONE /EMMEANS_OPTIONS SCALE=ORIGINAL PADJUST=LSD. best Diana
_____________________________________ Professor Diana Kornbrot Mobile +44 (0) 7403 18 16 12 Work University of Hertfordshire College Lane, Hatfield, Hertfordshire AL10 9AB, UK +44 (0) 170 728 4626 d.e.kornbrot at herts.ac.uk<mailto:d.e.kornbrot at herts.ac.uk> http://dianakornbrot.wordpress.com/ http://go.herts.ac.uk/Diana_Kornbrot skype: kornbrotme Home 19 Elmhurst Avenue London N2 0LT, UK +44 (0) 208 444 2081 ------------------------------------------------------------ [[alternative HTML version deleted]] _______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
Just a small note that lmerTest (and the Satterthwaite method for degrees of freedom) is only meaningful for _linear_ mixed models - not for the generalized variants such as the one considered here for proportions. Best, Rune
On 27 February 2018 at 02:02, Ben Bolker <bbolker at gmail.com> wrote:
Hi Diana, A reproducible example is always helpful/increases your chances of getting a useful answer ... It might help if you included the SPSS output (or posted it somewhere -- note that this list doesn't take HTML-formatted messages nor most attachments), as many of us don't have access to it. Look into the (very well-documented) emmeans package: https://CRAN.R-project.org/package=emmeans and the lmerTest package (for Satterthwaite df approximations) On Mon, Feb 26, 2018 at 12:11 PM, Kornbrot, Diana <d.e.kornbrot at herts.ac.uk> wrote:
I am keen to promote the use of generalised mixed models for the analysis of proportions to psychologists Have straight fowl code in SPSS [costly] and would like to supply equivalent R Code without ?tears? Design is a follows raw frequencies are: FreqPos for ?success? and FreqNeg for ?failure? Predictors are Rab with 4 levels, repeated over participants and Between with 2 separate groups of participants Model is binomial with logit link Require following output to correspond to SPSS output from code below Descriptive: Means, se and 95% CIs by Rab, by Between and by Rab*Between Inferential: fo Rab, Between and Rab*Between: F value, MSE, numerator df, denominator df [this enables p-values] Have tried logit1 <- glmer(cbind(FreqPos,FreqNeg) ~ Rab + Between + Rab*Between + (1| Participant), family=binomial(link="logit")) gives F and MSE no denominator df or MSE. Different results to SPSS nb F=MSE - that can?t be right F is supposed to be ratio of chi-squares summary (logit1) gives coefficients and SEs. Different results to SPSS also tried predicted and fitted but still no means have spent days searching internet for examples - but none of them seem to show how to get the output I need All help greatly appreciated ____ Spss syntax *Generalized Linear Mixed Models. GENLINMIXED /DATA_STRUCTURE SUBJECTS=Participant REPEATED_MEASURES=Rab COVARIANCE_TYPE=UNSTRUCTURED /FIELDS TARGET=FreqPos TRIALS=FIELD(Nmax) OFFSET=NONE /TARGET_OPTIONS DISTRIBUTION=BINOMIAL LINK=LOGIT /FIXED EFFECTS=Rab Between Rab*Between USE_INTERCEPT=TRUE /BUILD_OPTIONS TARGET_CATEGORY_ORDER=DESCENDING INPUTS_CATEGORY_ORDER=DESCENDING MAX_ITERATIONS=100 CONFIDENCE_LEVEL=95 DF_METHOD=SATTERTHWAITE COVB=MODEL PCONVERGE=0.000001(ABSOLUTE) SCORING=0 SINGULAR=0.000000000001 /EMMEANS TABLES=Rab COMPARE=Rab CONTRAST=DEVIATION /EMMEANS TABLES=Between CONTRAST=NONE /EMMEANS TABLES=Rab*Between CONTRAST=NONE /EMMEANS_OPTIONS SCALE=ORIGINAL PADJUST=LSD. best Diana
_____________________________________ Professor Diana Kornbrot Mobile +44 (0) 7403 18 16 12 Work University of Hertfordshire College Lane, Hatfield, Hertfordshire AL10 9AB, UK +44 (0) 170 728 4626 d.e.kornbrot at herts.ac.uk<mailto:d.e.kornbrot at herts.ac.uk> http://dianakornbrot.wordpress.com/ http://go.herts.ac.uk/Diana_Kornbrot skype: kornbrotme Home 19 Elmhurst Avenue London N2 0LT, UK +44 (0) 208 444 2081 ------------------------------------------------------------ [[alternative HTML version deleted]] _______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
Yes, that was a thinko on my part. Thanks.
On 18-02-27 05:22 AM, Rune Haubo wrote:
Just a small note that lmerTest (and the Satterthwaite method for degrees of freedom) is only meaningful for _linear_ mixed models - not for the generalized variants such as the one considered here for proportions. Best, Rune On 27 February 2018 at 02:02, Ben Bolker <bbolker at gmail.com> wrote:
Hi Diana, A reproducible example is always helpful/increases your chances of getting a useful answer ... It might help if you included the SPSS output (or posted it somewhere -- note that this list doesn't take HTML-formatted messages nor most attachments), as many of us don't have access to it. Look into the (very well-documented) emmeans package: https://CRAN.R-project.org/package=emmeans and the lmerTest package (for Satterthwaite df approximations) On Mon, Feb 26, 2018 at 12:11 PM, Kornbrot, Diana <d.e.kornbrot at herts.ac.uk> wrote:
I am keen to promote the use of generalised mixed models for the analysis of proportions to psychologists Have straight fowl code in SPSS [costly] and would like to supply equivalent R Code without ?tears? Design is a follows raw frequencies are: FreqPos for ?success? and FreqNeg for ?failure? Predictors are Rab with 4 levels, repeated over participants and Between with 2 separate groups of participants Model is binomial with logit link Require following output to correspond to SPSS output from code below Descriptive: Means, se and 95% CIs by Rab, by Between and by Rab*Between Inferential: fo Rab, Between and Rab*Between: F value, MSE, numerator df, denominator df [this enables p-values] Have tried logit1 <- glmer(cbind(FreqPos,FreqNeg) ~ Rab + Between + Rab*Between + (1| Participant), family=binomial(link="logit")) gives F and MSE no denominator df or MSE. Different results to SPSS nb F=MSE - that can?t be right F is supposed to be ratio of chi-squares summary (logit1) gives coefficients and SEs. Different results to SPSS also tried predicted and fitted but still no means have spent days searching internet for examples - but none of them seem to show how to get the output I need All help greatly appreciated ____ Spss syntax *Generalized Linear Mixed Models. GENLINMIXED /DATA_STRUCTURE SUBJECTS=Participant REPEATED_MEASURES=Rab COVARIANCE_TYPE=UNSTRUCTURED /FIELDS TARGET=FreqPos TRIALS=FIELD(Nmax) OFFSET=NONE /TARGET_OPTIONS DISTRIBUTION=BINOMIAL LINK=LOGIT /FIXED EFFECTS=Rab Between Rab*Between USE_INTERCEPT=TRUE /BUILD_OPTIONS TARGET_CATEGORY_ORDER=DESCENDING INPUTS_CATEGORY_ORDER=DESCENDING MAX_ITERATIONS=100 CONFIDENCE_LEVEL=95 DF_METHOD=SATTERTHWAITE COVB=MODEL PCONVERGE=0.000001(ABSOLUTE) SCORING=0 SINGULAR=0.000000000001 /EMMEANS TABLES=Rab COMPARE=Rab CONTRAST=DEVIATION /EMMEANS TABLES=Between CONTRAST=NONE /EMMEANS TABLES=Rab*Between CONTRAST=NONE /EMMEANS_OPTIONS SCALE=ORIGINAL PADJUST=LSD. best Diana
_____________________________________ Professor Diana Kornbrot Mobile +44 (0) 7403 18 16 12 Work University of Hertfordshire College Lane, Hatfield, Hertfordshire AL10 9AB, UK +44 (0) 170 728 4626 d.e.kornbrot at herts.ac.uk<mailto:d.e.kornbrot at herts.ac.uk> http://dianakornbrot.wordpress.com/ http://go.herts.ac.uk/Diana_Kornbrot skype: kornbrotme Home 19 Elmhurst Avenue London N2 0LT, UK +44 (0) 208 444 2081 ------------------------------------------------------------ [[alternative HTML version deleted]] _______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models