R Under development (unstable) (2023-10-04 r85267 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(matrixTests)
> source("utils/capture.r")
> 
> #--- removing na timepoints ----------------------------------------------------
> 
> wrn <- '2 columns dropped due to missing time information'
> 
> # 2 NAs
> x <- 1:10
> t <- c(1,2,3,4,NA,NA,7,8,9,10)
> res <- capture(row_cosinor(x, t))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all.equal(res$value$obs, 8))
> 
> 
> #--- less than 3 observations --------------------------------------------------
> 
> wrn <- 'row_cosinor: 1 of the rows had less than 3 complete observations: no p-values produced, amplitude and acrophase will be unreliable.\nFirst occurrence at row 1'
> nacolumns <- c("df.model", "df.residual", "statistic", "pvalue")
> 
> # 1 observations
> res <- capture(row_cosinor(1, 1))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all(is.na(res$value[,nacolumns])))
> stopifnot(all.equal(res$value$obs, 1))
> 
> # 2 observations
> res <- capture(row_cosinor(1:2, 1:2))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all(is.na(res$value[,nacolumns])))
> stopifnot(all.equal(res$value$obs, 2))
> 
> # 2 observations with NAs
> res <- capture(row_cosinor(c(1:2,NA,NA), 1:4))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all(is.na(res$value[,nacolumns])))
> stopifnot(all.equal(res$value$obs, 2))
> 
> 
> #--- exactly 3 observations ----------------------------------------------------
> 
> wrn <- 'row_cosinor: 1 of the rows had exactly 3 complete observations: no p-values produced.\nFirst occurrence at row 1'
> nacolumns <- c("df.model", "df.residual", "statistic", "pvalue")
> 
> # 3 observations
> res <- capture(row_cosinor(1:3, 1:3))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all(is.na(res$value[,nacolumns])))
> stopifnot(all.equal(res$value$obs, 3))
> 
> # with NAs present
> res <- capture(row_cosinor(c(1:3,NA), 1:4))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all(is.na(res$value[,nacolumns])))
> stopifnot(all.equal(res$value$obs, 3))
> 
> 
> #--- 1 unique timepoint --------------------------------------------------------
> 
> wrn <- 'row_cosinor: 1 of the rows had only 1 unique timepoint within the specified period: no p-values produced, amplitude and acrophase will be unreliable.\nFirst occurrence at row 1'
> nacolumns <- c("df.model", "df.residual", "statistic", "pvalue")
> 
> # one distinct point, duplicated multiple times
> res <- capture(row_cosinor(1:4, rep(1,4)))
> stopifnot(all(is.na(res$value[,nacolumns])))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all.equal(res$value$obs, 4))
> 
> 
> #--- 2 unique timepoints -------------------------------------------------------
> 
> wrn <- 'row_cosinor: 1 of the rows had only 2 unique timepoints within the specified period: amplitude and acrophase will be unreliable.\nFirst occurrence at row 1'
> 
> # two distinct points, duplicated multiple times
> res <- capture(row_cosinor(1:4, c(1,2,1,2)))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all.equal(res$value$obs, 4))
> 
> # with NAs present
> res <- capture(res <- row_cosinor(c(1,2,3,4,NA,NA), c(1,2,1,2,3,4)))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all.equal(res$value$obs, 4))
> 
> # four points, but period is such that they are not unique
> res <- capture(row_cosinor(1:4, c(1,2,3,4), 2))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all.equal(res$value$obs, 4))
> 
> 
> #--- constant values -----------------------------------------------------------
> 
> wrn <- 'row_cosinor: 1 of the rows had essentially constant values.\nFirst occurrence at row 1'
> nacolumns <- c("df.model", "df.residual", "statistic", "pvalue")
> 
> # all the values are 0
> res <- capture(row_cosinor(c(0,0,0,0), c(1,2,3,4)))
> stopifnot(all(is.na(res$value[,nacolumns])))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all.equal(res$value$obs, 4))
> 
> # all the values are constant
> res <- capture(row_cosinor(c(1,1,1,1), c(1,2,3,4)))
> stopifnot(all(is.na(res$value[,nacolumns])))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all.equal(res$value$obs, 4))
> 
> # all the vallues are constant with NAs
> res <- capture(row_cosinor(c(1,1,1,1,4), c(2,2,2,2,NA)))
> stopifnot(all(is.na(res$value[,nacolumns])))
> stopifnot(all.equal(res$warning[2], wrn))
> stopifnot(all.equal(res$value$obs, 4))
> 
> 
> #--- perfect fit ---------------------------------------------------------------
> 
> wrn <- 'row_cosinor: 1 of the rows had essentially perfect fit.\nFirst occurrence at row 1'
> 
> # perfect sine
> res <- capture(row_cosinor(sin(2*pi*1:24/24), 1:24))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all.equal(res$value$statistic, Inf))
> 
> # only three distinct points present
> res <- capture(row_cosinor(c(1:3,3), c(1:3,3), 24))
> stopifnot(all.equal(res$warning, wrn))
> stopifnot(all.equal(res$value$statistic, Inf))
> 
> 
> proc.time()
   user  system elapsed 
   0.18    0.03    0.20