Implementation of S3 method for lme class

[RomanTsegelskyi]

S3 method for lme class from nlme package.

Basic example

library(nlme)
fm1 <- lme(distance ~ age, data = Orthodont)
pander(fm1, summary = TRUE)
fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
pander(fm2, summary=TRUE)

[tbates]

Hi,
Shouldn’t this work?

devtools::install_github("RomanTsegelskyi/pander")
library(nlme)
fm1 <- lme(distance ~ age, data = Orthodont)
pander(fm1, summary = TRUE)

Error in x[[i]] : subscript out of bounds
In addition: Warning messages:
1: In pander.default(fm1, summary = TRUE) :
No pander method for "lme", reverting to default.
2: In pander.default(x[[i]], indent = indent + 1) :
No pander method for "lmeStructInt", reverting to default.No pander method for "lmeStruct", reverting to default.No pander method for "modelStruct", reverting to default.
3: In pander.default(x[[i]], indent = indent + 1) :
No pander method for "reStruct", reverting to default.
4: In pander.default(x[[i]], indent = indent + 1) :
No pander method for "pdSymm", reverting to default.No pander method for "pdMat", reverting to default.

On 28 May 2014, at 06:19, Roman Tsegelskyi notifications@github.com wrote:

S3 method for lme class from nlme package.

Basic example

library(nlme)
fm1 <- lme(distance ~ age, data = Orthodont)
pander(fm1, summary = TRUE)
fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
pander(fm2, summary=TRUE)
You can merge this Pull Request by running

git pull https://github.com/RomanTsegelskyi/pander lme
Or view, comment on, or merge it at:

#71

Commit Summary

Implementation of S3 method for zoo class
Implementation of S3 method for lme class
File Changes

M NAMESPACE (2)
M R/S3.R (44)
Patch Links:

https://github.com/Rapporter/pander/pull/71.patch
https://github.com/Rapporter/pander/pull/71.diff
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[daroczig]

@tbates it's in the lme branch, thus try instead:

devtools::install_github('pander', 'RomanTsegelskyi', 'lme')

[daroczig]

@RomanTsegelskyi the main caption has a line-break just before the colon:

Table: Linear mixed-effects model fit by REML
 : distance ~ age + Sex

In the other captions you put the formula on the same line, so just checking: did you add the \n on purpose?

[RomanTsegelskyi]

Sorry, that was a typo. Fixed that. Also deleted code from zoo branch (somehow, this branch was based on zoo, not on master)

[daroczig]

Great, thanks @RomanTsegelskyi!
But I am not sure if we do not have the same typo for method="ML":

> fm1 <- lme(distance ~ age, data = Orthodont, method="ML")
> pander(fm1, summary = TRUE)

--------------------------------------------------------------
     &nbsp;        Value   Std.Error   DF   t-value   p-value 
----------------- ------- ----------- ---- --------- ---------
 **(Intercept)**   16.76    0.7679     80    21.83   1.946e-35

     **age**      0.6602    0.07058    80    9.354   1.773e-14
--------------------------------------------------------------

Table: Fixed effects: distance ~ age


------------------------------------
 Min     Q1      Med      Q3    Max 
------ ------- -------- ------ -----
-3.306 -0.4874 0.007598 0.4822 3.923
------------------------------------

Table: Standardized Within-Group Residuals


-----------------------------------------------------------------
   &nbsp;      Observations   Groups   Log-restricted-likelihood 
------------- -------------- -------- ---------------------------
 **Subject**       108          27              -219.6           
-----------------------------------------------------------------

Table: Linear mixed-effects model fit by maximum likelihood
 : distance ~ age

[RomanTsegelskyi]

Sorry, fixed that also.