From 082be7baa35d7e8131a70ca8cc061d90e08fa584 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 15 Apr 2020 01:27:02 +0200 Subject: A plot method for nlme.mmkin fits --- check.log | 102 +++++--------------------------------------------------------- 1 file changed, 8 insertions(+), 94 deletions(-) (limited to 'check.log') 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 ’ * 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. + -- cgit v1.2.1