random fixes and notes

Makefile

@@ -3,7 +3,7 @@ BASENAME=scientificcomputing-script
 SUBDIRS=programming debugging plotting codestyle statistics bootstrap regression likelihood pointprocesses designpattern 
 SUBTEXS=$(foreach subd, $(SUBDIRS), $(subd)/lecture/$(subd).tex)
 
-all : script chapters
+all : plots chapters index script
 
 chapters :
 	for sd in $(SUBDIRS); do $(MAKE) -C $$sd/lecture chapter; done

chapter.mk

@@ -10,6 +10,8 @@ pythonplots : $(PYPDFFILES)
 
 $(PYPDFFILES) : %.pdf: %.py ../../plotstyle.py
 	PYTHONPATH="../../" python3 $<
+	#ps2pdf $@ $(@:.pdf=-temp.pdf)  # strip fonts, saves only about 1.5MB
+	#mv $(@:.pdf=-temp.pdf) $@
 
 cleanpythonplots :
 	rm -f $(PYPDFFILES)

codestyle/lecture/codestyle.tex

@@ -4,6 +4,7 @@
   more months might as well have been written by someone
   else.}{Eagleson's law}
 
+\noindent
 Cultivating a good code style is not just a matter of good taste but
 rather is a key ingredient for readability and maintainability of code
 and, in the end, facilitates reproducibility of scientific

header.tex

@@ -319,7 +319,7 @@
 %
 \newboolean{showexercisesolutions}
 \setboolean{showexercisesolutions}{true}
-\newcommand{\exercisesolutions}{chapter}  % 0: here, 1: chapter, 2: end
+\newcommand{\exercisesolutions}{end}  % 0: here, 1: chapter, 2: end
 % we need this also as numbers:
 \ifthenelse{\equal{\exercisesolutions}{end}}{\newcommand{\exercisesolutionsnum}{2}}{%
   \ifthenelse{\equal{\exercisesolutions}{chapter}}{\newcommand{\exercisesolutionsnum}{1}}{%

plotting/lecture/plotting.tex

@@ -74,20 +74,20 @@ the data was changed or the same kind of plot has to be created for a
 number of datasets.
 
 \begin{important}[Why manual editing should be avoided.]
-  On first glance the manual editing of a figure using tools such as
+  On first glance manual editing of a figure using tools such as
-  Corel draw, Illustrator, etc.\,appears much more convenient and less
+  inkscape, Corel draw, Illustrator, etc.\,appears much more
-  complex than coding everything into the analysis scripts. This,
+  convenient and less complex than coding everything into the analysis
-  however, is not entirely true. What if the figure has to be re-drawn
+  scripts. This, however, is not entirely true. What if the figure has
-  or updated? Then the editing work starts all over again. Rather,
+  to be re-drawn or updated, because, for example, you got more data?
-  there is a great risk associated with the manual editing
+  Then the editing work starts all over again. In addition, there is a
-  approach. Axes may be shifted, fonts have not been embedded into the
+  great risk associated with the manual editing approach. Axes may be
-  final document, annotations have been copy pasted between figures
+  shifted, fonts have not been embedded into the final document,
-  and are not valid. All of these mistakes can be found in
+  annotations have been copy-pasted between figures and are not
-  publications and then require an erratum, which is not
+  valid. All of these mistakes can be found in publications and then
-  desirable. Even if it appears more cumbersome in the beginning one
+  require an erratum, which is not desirable. Even if it appears more
-  should always try to create publication-ready figures directly from
+  cumbersome in the beginning, one should always try to generate
-  the data analysis tool using scripts or functions to properly layout
+  publication-ready figures directly from the data analysis tool using
-  the plot.
+  scripts or functions to properly layout and annotate the plot.
 \end{important}
 
 \subsection{Simple plotting}

pointprocesses/lecture/pointprocessscetchA.eps

@@ -1,7 +1,7 @@
 %!PS-Adobe-2.0 EPSF-2.0
 %%Title: pointprocessscetchA.tex
 %%Creator: gnuplot 4.6 patchlevel 4
-%%CreationDate: Fri Dec 11 21:08:22 2020
+%%CreationDate: Sun Dec 13 09:18:35 2020
 %%DocumentFonts: 
 %%BoundingBox: 50 50 373 135
 %%EndComments
@@ -433,7 +433,7 @@ SDict begin [
   /Author (jan)
 %  /Producer (gnuplot)
 %  /Keywords ()
-  /CreationDate (Fri Dec 11 21:08:22 2020)
+  /CreationDate (Sun Dec 13 09:18:35 2020)
   /DOCINFO pdfmark
 end
 } ifelse

pointprocesses/lecture/pointprocessscetchB.eps

@@ -1,7 +1,7 @@
 %!PS-Adobe-2.0 EPSF-2.0
 %%Title: pointprocessscetchB.tex
 %%Creator: gnuplot 4.6 patchlevel 4
-%%CreationDate: Fri Dec 11 21:08:22 2020
+%%CreationDate: Sun Dec 13 09:18:35 2020
 %%DocumentFonts: 
 %%BoundingBox: 50 50 373 237
 %%EndComments
@@ -433,7 +433,7 @@ SDict begin [
   /Author (jan)
 %  /Producer (gnuplot)
 %  /Keywords ()
-  /CreationDate (Fri Dec 11 21:08:22 2020)
+  /CreationDate (Sun Dec 13 09:18:35 2020)
   /DOCINFO pdfmark
 end
 } ifelse

scientificcomputing-script.tex

@@ -71,19 +71,18 @@
 
 \includechapter{regression}
 
+\includechapter{likelihood}
+
 % add chapter on generalized linear models (versus ANOVA)
 
-% add chapter on nonlinear fitting (methods, initial values, local minima)
+% add chapter on nonlinear fitting (methods, initial values, local minima, power law fits on log-log data)
-
-\includechapter{likelihood}
 
 \includechapter{pointprocesses}
 
 % add chapter on time series (amplitude distribution, autocorrelation, crosscorrelation)
-
 %\includechapter{spectral}
 
-% add chapter on digital filtering
+% add chapter on filtering and envelopes
 
 % add chapter on event detection, signal detection, ROC
 
@@ -97,11 +96,11 @@
 
 %\part{Tools}
 % Latex
-% markdown
+% markdown, html
 % Makefile
 % version control (git and github) only put source files into repository!
 % distributed computing (ssh and grid engines)
-% data handling (structure, data bases, storage (rsync), backup)
+% data handling (structure, storage (rsync), backup, data bases)
 % data annotation, meta data
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -111,7 +110,7 @@
 %\chapter{Cheat-Sheet}
 
 %%%% solutions: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% \printallsolutions
+\printallsolutions
 
 %%%% indices: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%