1.0.2

resp.Rcheck/00check.log

@@ -0,0 +1,148 @@
+* using log directory ‘/disk2/Documentos/ProjectesR/resp/resp.Rcheck’
+* using R version 3.4.1 (2017-06-30)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* checking for file ‘resp/DESCRIPTION’ ... OK
+* this is package ‘resp’ version ‘1.0.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... NOTE
+Found the following hidden files and directories:
+  man/.Rhistory
+These were most likely included in error. See section ‘Package
+structure’ in the ‘Writing R Extensions’ manual.
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘resp’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... NOTE
+Authors@R field gives no person with maintainer role, valid email
+address and non-empty name.
+Checking should be performed on sources prepared by ‘R CMD build’.
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... WARNING
+'library' or 'require' call not declared from: ‘lme4’
+'library' or 'require' calls in package code:
+  ‘lme4’ ‘stats’
+  Please use :: or requireNamespace() instead.
+  See section 'Suggested packages' in the 'Writing R Extensions' manual.
+Namespaces in Imports field not imported from:
+  ‘lme4’ ‘stats’
+  All declared Imports should be used.
+* checking S3 generic/method consistency ... WARNING
+log:
+  function(x, base)
+log.dataset:
+  function(data, columns)
+
+See section ‘Generic functions and methods’ in the ‘Writing R
+Extensions’ manual.
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... NOTE
+formula_from_vec: no visible global function definition for
+  ‘as.formula’
+mod.check: no visible global function definition for ‘anova’
+mod.check: no visible global function definition for ‘shapiro.test’
+mod.check: no visible global function definition for ‘residuals’
+mod.check: no visible global function definition for ‘cor.test’
+mod.check: no visible global function definition for ‘na.omit’
+mod.check: no visible global function definition for ‘fitted’
+mod.check: no visible global function definition for ‘AIC’
+mod.check: no visible global function definition for ‘BIC’
+mod.check: no visible global function definition for ‘logLik’
+mod.choose: no visible global function definition for ‘named_range’
+mod.choose: no visible binding for global variable ‘n’
+mod.resp : mod.form: no visible global function definition for ‘lmer’
+mod.resp: no visible global function definition for ‘na.omit’
+mod.resp: no visible global function definition for ‘as.formula’
+name_range.default: possible error in which(mid = i): unused argument
+  (mid = i)
+Undefined global functions or variables:
+  AIC BIC anova as.formula cor.test fitted lmer logLik n na.omit
+  named_range residuals shapiro.test
+Consider adding
+  importFrom("stats", "AIC", "BIC", "anova", "as.formula", "cor.test",
+             "fitted", "logLik", "na.omit", "residuals", "shapiro.test")
+to your NAMESPACE file.
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... WARNING
+Unknown package ‘<pkg>’ in Rd xrefs
+* checking for missing documentation entries ... WARNING
+Undocumented code objects:
+  ‘mod.choose’ ‘name_range.data.frame’ ‘name_range.default’
+  ‘name_range.numeric’
+All user-level objects in a package should have documentation entries.
+See chapter ‘Writing R documentation files’ in the ‘Writing R
+Extensions’ manual.
+* checking for code/documentation mismatches ... WARNING
+Codoc mismatches from documentation object 'mod.resp':
+mod.resp
+  Code: function(data, fixed, random, r_group, exclude, omit_NA = TRUE,
+                 fixed_interaction = TRUE, check_models = TRUE,
+                 choose_models = TRUE, lmer_warnings = FALSE)
+  Docs: function(data, fixed, random, r_group, exclude, omit_NA = TRUE,
+                 fixed_interaction = TRUE, check_models = TRUE)
+  Argument names in code not in docs:
+    choose_models lmer_warnings
+
+* checking Rd \usage sections ... WARNING
+Documented arguments not in \usage in documentation object 'mod.resp':
+  ‘lmer_warnings’
+
+Functions with \usage entries need to have the appropriate \alias
+entries, and all their arguments documented.
+The \usage entries must correspond to syntactically valid R code.
+See chapter ‘Writing R documentation files’ in the ‘Writing R
+Extensions’ manual.
+S3 methods shown with full name in documentation object 'log.dataset':
+  ‘log.dataset’
+
+The \usage entries for S3 methods should use the \method markup and not
+their full name.
+See chapter ‘Writing R documentation files’ in the ‘Writing R
+Extensions’ manual.
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... WARNING
+Warning: parse error in file 'resp-Ex.R':
+11: unexpected symbol
+65: 
+66: ~~ simple examples
+              ^
+* checking examples ... ERROR
+Running examples in ‘resp-Ex.R’ failed
+The error most likely occurred in:
+
+> ### Name: resp-package
+> ### Title: Creates response models for whole datasets
+> ### Aliases: resp-package resp
+> ### Keywords: package
+> 
+> ### ** Examples
+> 
+> ~~ simple examples of the most important functions ~~
+Error: unexpected symbol in "~~ simple examples"
+Execution halted
+* checking PDF version of manual ... WARNING
+LaTeX errors when creating PDF version.
+This typically indicates Rd problems.
+* checking PDF version of manual without hyperrefs or index ... OK
+* DONE
+Status: 1 ERROR, 8 WARNINGs, 3 NOTEs

resp.Rcheck/00install.out

@@ -0,0 +1,8 @@
+* installing *source* package ‘resp’ ...
+** R
+** preparing package for lazy loading
+** help
+*** installing help indices
+** building package indices
+** testing if installed package can be loaded
+* DONE (resp)

resp.Rcheck/Rdlatex.log

@@ -0,0 +1,130 @@
+Hmm ... looks like a package
+This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
+ restricted \write18 enabled.
+entering extended mode
+(./Rd2.tex
+LaTeX2e <2017/01/01> patch level 3
+Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
+Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
+(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
+(/usr/share/R/share/texmf/tex/latex/Rd.sty
+(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
+(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
+(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
+(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty))
+(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
+(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
+(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
+(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
+(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu)))
+No file Rd2.aux.
+(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
+No file Rd2.toc.
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
+Underfull \hbox (badness 10000) in paragraph at lines 37--39
+
+[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd)
+Overfull \hbox (12.78088pt too wide) in paragraph at lines 73--73
+ []\T1/pcr/m/n/10 formula_from_vec(x, start=\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ~ \
+TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , mid=\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 + \TS1/pc
+r/m/n/10 '\T1/pcr/m/n/10 , end=\TS1/pcr/m/n/10 ''\T1/pcr/m/n/10 , as_formula=FA
+LSE)[] 
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
+Overfull \hbox (12.00732pt too wide) in paragraph at lines 132--134
+[]\T1/ptm/m/n/10 After a \T1/pcr/m/n/10 mresp \T1/ptm/m/n/10 ob-ject is cre-ate
+d, check for fixed fac-tors sig-nif-i-cance and un-val-i-dated re-sults, mod.ch
+eck
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [3] [4]
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6] (./Rd2.aux) )
+(see the transcript file for additional information){/usr/share/texlive/texmf-d
+ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/urw/
+courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
+8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
+are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
+mf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/t
+ype1/urw/times/utmri8a.pfb>
+Output written on Rd2.pdf (6 pages, 75167 bytes).
+Transcript written on Rd2.log.
+This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
+ restricted \write18 enabled.
+entering extended mode
+(./Rd2.tex
+LaTeX2e <2017/01/01> patch level 3
+Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
+
+(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
+Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
+(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
+(/usr/share/R/share/texmf/tex/latex/Rd.sty
+(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
+(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
+(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
+(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
+(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty))
+(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
+(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
+(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
+(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
+(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (./Rd2.aux)
+(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
+Underfull \hbox (badness 10000) in paragraph at lines 37--39
+
+[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
+(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd)
+Overfull \hbox (12.78088pt too wide) in paragraph at lines 73--73
+ []\T1/pcr/m/n/10 formula_from_vec(x, start=\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ~ \
+TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , mid=\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 + \TS1/pc
+r/m/n/10 '\T1/pcr/m/n/10 , end=\TS1/pcr/m/n/10 ''\T1/pcr/m/n/10 , as_formula=FA
+LSE)[] 
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
+Overfull \hbox (12.00732pt too wide) in paragraph at lines 132--134
+[]\T1/ptm/m/n/10 After a \T1/pcr/m/n/10 mresp \T1/ptm/m/n/10 ob-ject is cre-ate
+d, check for fixed fac-tors sig-nif-i-cance and un-val-i-dated re-sults, mod.ch
+eck
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [3] [4]
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
+(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6] (./Rd2.aux) )
+(see the transcript file for additional information){/usr/share/texlive/texmf-d
+ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/urw/
+courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
+8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
+are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
+mf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/t
+ype1/urw/times/utmri8a.pfb>
+Output written on Rd2.pdf (6 pages, 75354 bytes).
+Transcript written on Rd2.log.
+Saving output to ‘resp-manual.pdf’ ...
+Done
+You may want to clean up by 'rm -rf /tmp/RtmpyYqho2/Rd2pdf7fab2e28e890'

resp.Rcheck/resp-Ex.R

@@ -0,0 +1,80 @@
+pkgname <- "resp"
+source(file.path(R.home("share"), "R", "examples-header.R"))
+options(warn = 1)
+library('resp')
+
+base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
+cleanEx()
+nameEx("mod.resp")
+### * mod.resp
+
+flush(stderr()); flush(stdout())
+
+### Name: mod.resp
+### Title: Create response lmer models for a whole data.frame
+### Aliases: mod.resp
+
+### ** Examples
+
+n <- 500L
+tr <- c('T1','T2','T3')
+sp <- c('S1','S2','S3')
+gr <- c('A','B')
+F1 <- c();F2 <- c();F3 <- c()
+R1 <- c();R2 <- c();R3 <- c()
+for (i in 1:n) {
+ F1[i] <- tr[round(i/n*3,0)]
+ F2[i] <- sp[round(runif(1L,1L,3L),0)]
+ F3[i] <- gr[round(runif(1L,1L,2L),0)]
+ R1[i] <- rnorm(1,10,2)+runif(1L)+(which(tr==F1[i])*3)
+ R2[i] <- rnorm(1,10,2)+runif(1L)+(which(sp==F2[i])*10)
+ R3[i] <- rnorm(1,600,20)+runif(1L)+(which(tr==F1[i])*20)
+}
+table(F1,F2)
+
+x <- data.frame(
+    Treatment=F1,
+    Specie=F2,
+    Group=F3,
+    Rand=runif(n),
+    Heigth=R1,
+    Diameter=R2,
+    Number_leaves=R3,
+    other=runif(n)
+)
+# rm(n,tr,sp,gr,F1,F2,F3)
+a <- mod.resp(data = x, fixed = c('Treatment','Specie'), random='Rand',
+              r_group = c('Group'),exclude='other',lmer_warnings=TRUE,
+              choose_models=FALSE,check_models=FALSE)
+print(a)
+
+
+
+cleanEx()
+nameEx("resp-package")
+### * resp-package
+
+flush(stderr()); flush(stdout())
+
+### Name: resp-package
+### Title: Creates response models for whole datasets
+### Aliases: resp-package resp
+### Keywords: package
+
+### ** Examples
+
+~~ simple examples of the most important functions ~~
+
+
+
+### * <FOOTER>
+###
+options(digits = 7L)
+base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
+grDevices::dev.off()
+###
+### Local variables: ***
+### mode: outline-minor ***
+### outline-regexp: "\\(> \\)?### [*]+" ***
+### End: ***
+quit('no')