Update README, increase version number.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hklmirs
 Title: Reproducible Research Compendium for "Improving Models to Predict Holocellulose and Klason Lignin Contents for Peat Soil Organic Matter with Mid Infrared Spectra" and "Predicting Absolute Holocellulose and Klason Lignin Contents for Peat Remains Challenging". 
-Version: 0.1.2
+Version: 0.1.3
 Authors@R:
     c(
     person(given = "Henning",

README.Rmd

@@ -59,7 +59,7 @@ manuscript2$year <-
 
 manuscript2$title <-
   manuscript2_yaml$title %>%
-  paste0(".")
+  paste0("_", ., "._")
 
 manuscript2$journal <-
   eval(parse(text = manuscript2_yaml$journal %>% stringr::str_remove("^`r ") %>% stringr::str_remove("`$"))) %>%
@@ -96,11 +96,11 @@ The **analysis** directory contains:
     - [003-paper-m-gaussian-beta.Rmd](analysis/paper/003-paper-m-gaussian-beta.Rmd): Computes models assuming a Beta distribution for holocellulose and Klason lignin contents and compares them to the original models.
     - [004-paper-m-reduce-underfitting.Rmd](analysis/paper/004-paper-m-reduce-underfitting.Rmd): Extents the Beta regression models by including additional variables (additional peaks) or using a different approach (using measured spectral intensities of binned spectra instead of extracted peaks), and validates these models using LOO-CV.
     - [005-paper-m-minerals.Rmd](analysis/paper/005-paper-m-minerals.Rmd): Uses the models from `003-paper-m-gaussian-beta.Rmd` to test how accurate a model for holocellulose content is which is also calibrated on training samples with higher mineral contents.
-    - [006-paper-m-prediction-domain.Rmd](analysis/paper/006-paper-m-prediction-domain.Rmd): Analyzes the prediction domain [@Wadoux.2021] of the original models and the modified models and identifie under which conditions models extrapolate for peat and vegetation smaples from @Hodgkins.2018.
+    - [006-paper-m-prediction-domain.Rmd](analysis/paper/006-paper-m-prediction-domain.Rmd): Analyzes the prediction domain [@Wadoux.2021] of the original models and the modified models and identifies under which conditions models extrapolate for peat and vegetation samples from @Hodgkins.2018.
     - [007-paper-m-prediction-differences.Rmd](analysis/paper/007-paper-m-prediction-differences.Rmd): Compares predictions for the training data and the peat and vegetation data from @Hodgkins.2018 for the original models from @Hodgkins.2018 and the modified models from `004-paper-m-reduce-underfitting.Rmd`.
     - [008-paper-supplementary.Rmd](analysis/paper/008-paper-supplementary.Rmd): Computes supplementary analyses and figures for the first manuscript.
-    - [001-reply-main.Rmd](analysis/paper/001-reply-main.Rmd): This is the main script for manuscript 2. It is run from within `001-paper-main.Rmd` and produces the supplementary information for manuscript 2.
-    - [002-reply-main.Rmd](analysis/paper/002-reply-main.Rmd): This script produces the document for manuscript 2. It is run from within `001-reply-main.Rmd`.
+    - [001-reply-main.Rmd](analysis/paper/001-reply-main.Rmd): This is the main script for manuscript 2. It is compiled from within `001-paper-main.Rmd` and produces the supplementary information for manuscript 2.
+    - [002-reply-main.Rmd](analysis/paper/002-reply-main.Rmd): This script produces the document for manuscript 2. It is compiled from within `001-reply-main.Rmd`.
 
 - [:file\_folder: data](/analysis/data): Data used in the analysis. Note that raw data is not stored in [:file\_folder: raw_data](/analysis/data/raw_data) (empty folder), but in [:file\_folder: /inst/extdata](/inst/extdata). [:file\_folder: derived_data](/analysis/data/derived_data) contains derived data computed from the scripts. The raw data are derived from @Hodgkins.2018.
 
@@ -136,7 +136,7 @@ remotes::install_github("henningte/hklmirs")
 
 #### Reproduce the analyses
 
-To reproduce the analyses for the paper, open the Rstudio project included in this research compendium and run the Rmarkdown script in `analysis/paper/001-paper-main.rmd`.
+To reproduce the analyses for the paper, open the RStudio project included in this research compendium and run the Rmarkdown script in `analysis/paper/001-paper-main.rmd`.
 
 Running the whole script takes about 12 hours and occupies additional disk space of ~2 Gb.  
 

README.md

@@ -2,7 +2,7 @@
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 [![DOI](https://zenodo.org/badge/465653387.svg)](https://zenodo.org/badge/latestdoi/465653387)
-![Last-changedate](https://img.shields.io/badge/last%20change-2022--06--01-brightgreen.svg)
+![Last-changedate](https://img.shields.io/badge/last%20change-2022--07--29-brightgreen.svg)
 
 # hklmirs
 
@@ -15,9 +15,9 @@ preparation):
 > methods, June 1, 2022. DOI:
 > [10.5194/soil-2022-27](https://doi.org/10.5194/soil-2022-27).
 
-> Henning Teickner and Klaus-Holger Knorr (in preparation): Predicting
-> Absolute Holocellulose and Klason Lignin Contents for Peat Remains
-> Challenging.
+> Henning Teickner and Klaus-Holger Knorr (in preparation): *Comment on
+> Hodgkins et al. (2018): Predicting Absolute Holocellulose and Klason
+> Lignin Contents for Peat Remains Challenging.*
 
 ### How to cite
 
@@ -26,9 +26,10 @@ Please cite this compendium as:
 > Henning Teickner and Klaus-Holger Knorr, (2022). *Compendium of R code
 > and data for “Improving Models to Predict Holocellulose and Klason
 > Lignin Contents for Peat Soil Organic Matter with Mid Infrared
-> Spectra” and “Predicting Absolute Holocellulose and Klason Lignin
-> Contents for Peat Remains Challenging”*. Accessed 01 Jun 2022. Online
-> at <https://doi.org/10.5281/zenodo.6325760>
+> Spectra” and “Comment on Hodgkins et al. (2018): Predicting Absolute
+> Holocellulose and Klason Lignin Contents for Peat Remains
+> Challenging”*. Accessed 29 Jul 2022. Online at
+> <https://doi.org/10.5281/zenodo.6325760>
 
 ## Contents
 
@@ -59,9 +60,9 @@ The **analysis** directory contains:
         calibrated on training samples with higher mineral contents.
       - [006-paper-m-prediction-domain.Rmd](analysis/paper/006-paper-m-prediction-domain.Rmd):
         Analyzes the prediction domain (Wadoux et al. 2021) of the
-        original models and the modified models and identifie under
+        original models and the modified models and identifies under
         which conditions models extrapolate for peat and vegetation
-        smaples from Hodgkins et al. (2018).
+        samples from Hodgkins et al. (2018).
       - [007-paper-m-prediction-differences.Rmd](analysis/paper/007-paper-m-prediction-differences.Rmd):
         Compares predictions for the training data and the peat and
         vegetation data from Hodgkins et al. (2018) for the original
@@ -71,12 +72,12 @@ The **analysis** directory contains:
         Computes supplementary analyses and figures for the first
         manuscript.
       - [001-reply-main.Rmd](analysis/paper/001-reply-main.Rmd): This is
-        the main script for manuscript 2. It is run from within
+        the main script for manuscript 2. It is compiled from within
         `001-paper-main.Rmd` and produces the supplementary information
         for manuscript 2.
       - [002-reply-main.Rmd](analysis/paper/002-reply-main.Rmd): This
-        script produces the document for manuscript 2. It is run from
-        within `001-reply-main.Rmd`.
+        script produces the document for manuscript 2. It is compiled
+        from within `001-reply-main.Rmd`.
 
   - [:file\_folder: data](/analysis/data): Data used in the analysis.
     Note that raw data is not stored in [:file\_folder:
@@ -134,7 +135,7 @@ remotes::install_github("henningte/hklmirs")
 
 #### Reproduce the analyses
 
-To reproduce the analyses for the paper, open the Rstudio project
+To reproduce the analyses for the paper, open the RStudio project
 included in this research compendium and run the Rmarkdown script in
 `analysis/paper/001-paper-main.rmd`.