A plot method for nlme.mmkin fits

1 files changed, 8 insertions, 94 deletions

diff --git a/check.log b/check.log
index fc06bc0d..43cc5f64 100644
--- a/check.log
+++ b/check.log
@@ -41,14 +41,7 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... NOTE
-nlme.mmkin: no visible binding for global variable ‘na.fail’
-nlme.mmkin: no visible binding for global variable ‘f’
-Undefined global functions or variables:
-  f na.fail
-Consider adding
-  importFrom("stats", "na.fail")
-to your NAMESPACE file.
+* checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -63,91 +56,11 @@ to your NAMESPACE file.
 * checking data for ASCII and uncompressed saves ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... ERROR
-Running examples in ‘mkin-Ex.R’ failed
-The error most likely occurred in:
-
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
-> ### Name: nlme_function
-> ### Title: Estimation of parameter distributions from mmkin row objects
-> ### Aliases: nlme_function mean_degparms nlme_data
-> 
-> ### ** Examples
-> 
-> sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-> m_SFO <- mkinmod(parent = mkinsub("SFO"))
-> d_SFO_1 <- mkinpredict(m_SFO,
-+   c(k_parent_sink = 0.1),
-+   c(parent = 98), sampling_times)
-> d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
-> d_SFO_2 <- mkinpredict(m_SFO,
-+   c(k_parent_sink = 0.05),
-+   c(parent = 102), sampling_times)
-> d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
-> d_SFO_3 <- mkinpredict(m_SFO,
-+   c(k_parent_sink = 0.02),
-+   c(parent = 103), sampling_times)
-> d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
-> 
-> d1 <- add_err(d_SFO_1, function(value) 3, n = 1)
-> d2 <- add_err(d_SFO_2, function(value) 2, n = 1)
-> d3 <- add_err(d_SFO_3, function(value) 4, n = 1)
-> ds <- c(d1 = d1, d2 = d2, d3 = d3)
-> 
-> f <- mmkin("SFO", ds, cores = 1, quiet = TRUE)
-> mean_dp <- mean_degparms(f)
-> grouped_data <- nlme_data(f)
-> nlme_f <- nlme_function(f)
-> # These assignments are necessary for these objects to be
-> # visible to nlme and augPred when evaluation is done by
-> # pkgdown to generated the html docs.
-> assign("nlme_f", nlme_f, globalenv())
-> assign("grouped_data", grouped_data, globalenv())
-> 
-> library(nlme)
-> m_nlme <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink),
-+   data = grouped_data,
-+   fixed = parent_0 + log_k_parent_sink ~ 1,
-+   random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
-+   start = mean_dp)
-> summary(m_nlme)
-Nonlinear mixed-effects model fit by maximum likelihood
-  Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) 
- Data: grouped_data 
-       AIC      BIC    logLik
-  253.6377 262.9937 -121.8188
-
-Random effects:
- Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
- Level: ds
- Structure: Diagonal
-        parent_0 log_k_parent_sink Residual
-StdDev: 2.486822         0.6481355 2.368137
-
-Fixed effects: parent_0 + log_k_parent_sink ~ 1 
-                      Value Std.Error DF  t-value p-value
-parent_0          101.43096 1.5960157 44 63.55261       0
-log_k_parent_sink  -3.07614 0.3827294 44 -8.03737       0
- Correlation: 
-                  prnt_0
-log_k_parent_sink 0.011 
-
-Standardized Within-Group Residuals:
-       Min         Q1        Med         Q3        Max 
--1.9643731 -0.5430765  0.1659516  0.6160408  1.8082871 
-
-Number of Observations: 48
-Number of Groups: 3 
-> plot(augPred(m_nlme, level = 0:1), layout = c(3, 1))
-> 
-> m_nlme <- nlme(nlme_formula,
-+   data = grouped_data,
-+   fixed = parent_0 + log_k_parent_sink ~ 1,
-+   random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
-+   start = mean_dp)
-Error in nlme(nlme_formula, data = grouped_data, fixed = parent_0 + log_k_parent_sink ~  : 
-  object 'nlme_formula' not found
-Execution halted
+* checking examples ... NOTE
+Examples with CPU or elapsed time > 5s
+                 user system elapsed
+nlme.mmkin      4.801  1.040   4.497
+plot.nlme.mmkin 4.751  0.285   4.680
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
@@ -157,8 +70,9 @@ Execution halted
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 1 ERROR, 1 NOTE
+Status: 1 NOTE
 See
   ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
 for details.
 
+