-
Notifications
You must be signed in to change notification settings - Fork 46
Expand file tree
/
Copy pathMakefile
More file actions
183 lines (123 loc) · 5.88 KB
/
Makefile
File metadata and controls
183 lines (123 loc) · 5.88 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
## This is ICI3D/RTutorials
## https://github.com/ICI3D/RTutorials
-include target.mk
-include makestuff/perl.def
vim_session:
bash -cl "vmt"
######################################################################
Ignore += pipelines
alldirs += sampling_JD
Sources += $(wildcard *.R *.md)
particCoding_Rabies2017.Rout: particCoding_Rabies2017.R
$(pipeR)
participatoryDesign2021.Rout: participatoryDesign2021.R
$(pipeR)
participatoryDynamics2025.Rout: participatoryDynamics2025.R
$(pipeR)
######################################################################
Ignore += local.mk
## Your data location
datadir = ../datasets ## Override below
-include local.mk
Ignore += data
data: dir=$(datadir)
data:
$(linkdirname)
######################################################################
## Branching
Ignore += branchdir
branchdir:
git clone https://github.com/ICI3D/RTutorials $@
######################################################################
## Building macpan labs 2025 May 20 (Tue)
## mpLabCompartmental.batch.Rout: mpLabCompartmental.R testing/mpLabCompartmental.answers.R
## mpLabFitting.batch.Rout: mpLabFitting.R testing/mpLabFitting.answers.R
## git log -- mpLabFitting.R
######################################################################
## Processing machinery
## Make an answers file that allows batch.pl to convert the published file into something that runs
## Started with a hard-coded batch, then decided to do a weird, flexible batchdir variable. Don't do that; in cases where you want to batch from elsewhere, make new rules
Sources += $(wildcard testing/*.R)
Sources += batch.md
Ignore += batch
batch:
$(mkdir)
Sources += batch.pl
.PRECIOUS: batch/%.R
batch/%.R: %.R testing/%.answers.R batch.pl
$(MAKE) batch
$(PUSHRO)
%.batch.Rout: batch/%.R
$(pipeR)
## ICI3D_RTutorial_1.batch.Rout: ICI3D_RTutorial_1.R testing/ICI3D_RTutorial_1.answers.R
## ICI3D_RTutorial_2.batch.Rout: ICI3D_RTutorial_2.R testing/ICI3D_RTutorial_2.answers.R
## ICI3D_RTutorial_3.batch.Rout: ICI3D_RTutorial_3.R testing/ICI3D_RTutorial_3.answers.R
## ICI3D_Lab1_ODEmodels.batch.Rout: ICI3D_Lab1_ODEmodels.R testing/ICI3D_Lab1_ODEmodels.answers.R
## ICI3D_Lab1_ODEmodels.batch.Rlog: batch/ICI3D_Lab1_ODEmodels.R
## ICI3D_Lab3_EpiStudyDesign.batch.Rout: ICI3D_Lab3_EpiStudyDesign.R testing/ICI3D_Lab3_EpiStudyDesign.answers.R
## ICI3D_RTutorial_1.batch.Rout: testing/ICI3D_RTutorial_1.answers.R
## ICI3D_RTutorial_2.batch.Rout: ICI3D_RTutorial_2.R testing/ICI3D_RTutorial_2.answers.R
## Two Tutorial 4 files; this one is obsolete, I think
## ICI3D_RTutorial_4_VisualizingData.Rout: ICI3D_RTutorial_4_VisualizingData.R testing/ICI3D_RTutorial_4_VisualizingData.answers.R
## Warning! This uses setwd, and thus default plots are made elsewhere
## ICI3D_RtvTutorial_4.batch.pdf: ICI3D_RtvTutorial_4.R testing/ICI3D_RtvTutorial_4.answers.R
Ignore += ICI3D_RtvTutorial_4.batch.pdf
ICI3D_RtvTutorial_4.batch.pdf: ICI3D_RtvTutorial_4.batch.Rout
$(MV) data/visualizingData/Rplots.pdf $@
## ICI3D_RtvTutorial_4.batch.Rout: ICI3D_RtvTutorial_4.R testing/ICI3D_RtvTutorial_4.answers.R
## batch/ICI3D_RtvTutorial_4.R: ICI3D_RtvTutorial_4.R testing/ICI3D_RtvTutorial_4.answers.R
## Not working, something about where is the data!
ICI3D_RTutorial_5_DataCleaning.batch.Rout: batchdir=data/dataCleaning/
## ICI3D_RTutorial_5_DataCleaning.batch.Rout: ICI3D_RTutorial_5_DataCleaning.R testing/ICI3D_RTutorial_5_DataCleaning.answers.R
######################################################################
pipeRdesc += ICI3D_Lab_Heterogeneous_Groups.batch
## ICI3D_Lab_Heterogeneous_Groups.batch.noSpread.pdf:
## ICI3D_Lab_Heterogeneous_Groups.batch.noSpread-0.pdf:
ICI3D_Lab_Heterogeneous_Groups.batch.Rout.pdf: ICI3D_Lab_Heterogeneous_Groups.batch.Rout
$(MV) Rplots.pdf $@
## ICI3D_Lab_Heterogeneous_Groups.batch.Rout: ICI3D_Lab_Heterogeneous_Groups.R testing/ICI3D_Lab_Heterogeneous_Groups.answers.R
ICI3D_Lab_Heterogeneous_Groups.batch.Rout: ICI3D_Heterogeneous_Groups.R ICI3D_Lab_Heterogeneous_Groups.R
## ICI3D_Lab_Heterogeneous_Groups.batch.Rout-0.pdf:
## labNow.homoLess.pdf: labNow.R
pdfDesc += labnow
labNow.Rout: labNow.R ICI3D_Heterogeneous_Groups.R
$(pipeR)
## ICI3D_Ex1_StochasticSpillover.batch.Rout: ICI3D_Ex1_StochasticSpillover.R testing/ICI3D_Ex1_StochasticSpillover.answers.R
ICI3D_Ex1_StochasticSpillover.batch.Rout: ICI3D_Ex1_StochasticSpillover_functions.R
## ICI3D_Lab1_ODEmodels.batch.Rout: ICI3D_Lab1_ODEmodels.R testing/ICI3D_Lab1_ODEmodels.answers.R
## ICI3D_Lab2_Heterogeneity.R
## ICI3D_Lab3_EpiStudyDesign.batch.Rout: ICI3D_Lab3_EpiStudyDesign.R testing/ICI3D_Lab3_EpiStudyDesign.answers.R
## ICI3D_Lab4_RCT.batch.Rout: ICI3D_Lab4_RCT.R testing/ICI3D_Lab4_RCT.answers.R
## ICI3D_Lab5a_introLikelihoodPlusRejectionP.R
## ICI3D_Lab5_introLikelihood.batch.Rout: ICI3D_Lab5_introLikelihood.R testing/ICI3D_Lab5_introLikelihood.answers.R
## ICI3D_Lab6_MLE_SIV_HIV.batch.Rout: ICI3D_Lab6_MLE_SIV_HIV.R testing/ICI3D_Lab6_MLE_SIV_HIV.answers.R
## ICI3D_Lab7_MCMC-Binomial.R
## ICI3D_Lab8_MCMC-SI_HIV.R
## ICI3D_Lab_SampDistrVariability.R
######################################################################
## New sandbox (see also content.mk)
## Follow-up
hetero_play.Rout: HetSIR_functions.Rdata hetero_play.R
$(pipeR)
HetSIR.Rout: HetSIR_functions.Rdata HetSIR.R
## Dev for MMED 2025
seir.w.seasonal.Rout: seir.w.seasonal.R
$(pipeR)
######################################################################
## Look at labnames branch for a sketched-out implementation of the renaming
## Edit in place
Sources += names.txt
######################################################################
### Makestuff
## Makefile gutted 2021 Jun 21 (Mon)
Sources += Makefile content.mk
Ignore += makestuff
msrepo = https://github.com/dushoff
Makefile: makestuff/Makefile
makestuff/Makefile:
git clone $(msrepo)/makestuff
ls makestuff/Makefile
-include makestuff/os.mk
-include makestuff/pipeR.mk
-include makestuff/git.mk
-include makestuff/visual.mk