Merge branch 'dev-docs' of github.com:EarthSystemDiagnostics/paleospe…

…c into dev-docs

# Conflicts:
#	README.Rmd

DESCRIPTION

@@ -23,5 +23,8 @@ Suggests:
     covr,
     testthat,
     ggplot2,
-    tibble
+    tibble,
+    knitr,
+    rmarkdown
 URL: https://earthsystemdiagnostics.github.io/paleospec/
+VignetteBuilder: knitr

R/AddConfInterval.R

@@ -1,7 +1,7 @@
 #' Add confidence interval
 #'
 #' Add a confidence interval to a spectral estimate assuming the uncertainty of
-#' the spectral estimates follows a chi-squared distribution with the degress of
+#' the spectral estimates follows a chi-squared distribution with the degrees of
 #' the freedom from the spectral estimates.
 #'
 #' @param spec a spectral object of class \code{"spec"} or a list with the
@@ -16,7 +16,7 @@
 #'   respectively.
 #' @author Thomas Laepple
 #' @examples
-#' 
+#'
 #' N.R <- 1000
 #' N.T <- 100
 #' save.spec <- matrix(NA, N.T / 2, N.R)
@@ -33,7 +33,7 @@
 #' legend("bottomleft", lwd = 2, col = c("black", "red"),
 #'        legend = c("one realization with chisq conf intervals",
 #'                   "MC confidence intervals"))
-#' 
+#'
 #' @export
 AddConfInterval <- function(spec, pval = 0.05, MINVALUE = 1e-10) {
 
@@ -44,6 +44,8 @@ AddConfInterval <- function(spec, pval = 0.05, MINVALUE = 1e-10) {
   spec$lim.1[spec$lim.1 < MINVALUE] <- MINVALUE
   spec$lim.2[spec$lim.2 < MINVALUE] <- MINVALUE
 
+  spec$pval <- pval
+
   return(spec)
 
 }

README.Rmd

@@ -29,18 +29,16 @@ PaleoSpec is an R package to assist in the spectral analysis of timeseries, in p
 
 You can install the development version of PaleoSpec from [GitHub](https://github.com/) with:
 
-``` r
+```{r, eval=FALSE}
 # install.packages("remotes")
 remotes::install_github("EarthSystemDiagnostics/paleospec")
 ```
 
 
 Please refer to function references here:
-
 https://earthsystemdiagnostics.github.io/paleospec/reference/index.html
 
 
-
 ## Usage
 
 ### Estimating power spectra

README.md

@@ -26,7 +26,6 @@ remotes::install_github("EarthSystemDiagnostics/paleospec")
 ```
 
 Please refer to function references here:
-
 <https://earthsystemdiagnostics.github.io/paleospec/reference/index.html>
 
 ## Usage
@@ -46,15 +45,15 @@ sunspot <- datasets::sunspot.month
 plot(sunspot)
 ```
 
-<img src="man/figures/README-unnamed-chunk-2-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" />
 
 ``` r
 library(PaleoSpec)
 sp_sun <- SpecMTM(sunspot)
 LPlot(sp_sun)
 ```
 
-<img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-4-1.png" width="100%" />
 
 Alternatively we can use the gg_spec() function to get a ggplot2
 
@@ -64,7 +63,7 @@ gg_spec(sp_sun)
 #> Adding another scale for colour, which will replace the existing scale.
 ```
 
-<img src="man/figures/README-unnamed-chunk-4-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-5-1.png" width="100%" />
 
 Appproximate confidence intervals can be added with the function
 AddConfInterval()
@@ -76,7 +75,7 @@ gg_spec(sp_sun)
 #> Adding another scale for colour, which will replace the existing scale.
 ```
 
-<img src="man/figures/README-unnamed-chunk-5-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-6-1.png" width="100%" />
 
 ### Simulating timeseries with given spectral properties
 
@@ -99,7 +98,7 @@ ts1 <- SimPLS(N = N, b = beta, a = alpha)
 plot(ts1, type = "l")
 ```
 
-<img src="man/figures/README-unnamed-chunk-6-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-7-1.png" width="100%" />
 
 `SpecMTM` can again be used to estimate the power spectrum using the
 multitaper method. If we convert the vector from SimPLS to a timeseries
@@ -113,7 +112,7 @@ LPlot(sp1)
 abline(log10(alpha), -beta, col = "red")
 ```
 
-<img src="man/figures/README-unnamed-chunk-7-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-8-1.png" width="100%" />
 
 You can add confidence intervals to the spectral estimates with
 `AddConfInterval`
@@ -124,7 +123,7 @@ LPlot(sp1)
 abline(log10(alpha), -beta, col = "red")
 ```
 
-<img src="man/figures/README-unnamed-chunk-8-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-9-1.png" width="100%" />
 
 The `LogSmooth` function can be used to smooth power spectra with
 equally spaced filter in log-space.
@@ -135,4 +134,4 @@ LPlot(sp1)
 LLines(sp1_f, col = "green")
 ```
 
-<img src="man/figures/README-unnamed-chunk-9-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-10-1.png" width="100%" />