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Revision 2316 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Feb 15 14:44:01 2019 UTC (4 hours, 51 minutes ago) by wastl
File length: 100942 byte(s)
Diff to previous 2314
update

Revision 2314 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Feb 15 14:18:27 2019 UTC (5 hours, 17 minutes ago) by wastl
File length: 100822 byte(s)
Diff to previous 2313
remove deprecated enlargeData()

Revision 2313 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Feb 15 14:11:42 2019 UTC (5 hours, 24 minutes ago) by wastl
File length: 100800 byte(s)
Diff to previous 2285
remove deprecated correct53to52()

Revision 2285 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Feb 14 22:05:41 2019 UTC (21 hours, 30 minutes ago) by wastl
File length: 100776 byte(s)
Diff to previous 2284
remove deprecated readData() and associated raw txt files

Revision 2284 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 13 16:11:25 2019 UTC (2 days, 3 hours ago) by wastl
File length: 100707 byte(s)
Diff to previous 2283
remove deprecated compMatrix.writeTable()

Revision 2283 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 13 15:53:34 2019 UTC (2 days, 3 hours ago) by wastl
File length: 100671 byte(s)
Diff to previous 2282
remove deprecated toFileDisProg()

Revision 2282 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 13 15:30:14 2019 UTC (2 days, 4 hours ago) by wastl
File length: 100643 byte(s)
Diff to previous 2281
remove deprecated test()

Revision 2281 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 13 15:05:26 2019 UTC (2 days, 4 hours ago) by wastl
File length: 100628 byte(s)
Diff to previous 2280
remove deprecated makePlot()

Revision 2280 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 13 14:58:56 2019 UTC (2 days, 4 hours ago) by wastl
File length: 100609 byte(s)
Diff to previous 2277
make testSim() an example of sim.pointSource()

Revision 2277 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 12 20:47:00 2019 UTC (2 days, 22 hours ago) by wastl
File length: 100457 byte(s)
Diff to previous 2275
escape percent symbols

Revision 2275 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 12 20:41:49 2019 UTC (2 days, 22 hours ago) by wastl
File length: 100455 byte(s)
Diff to previous 2273
for monthly and daily data, year() should return the calendar year

Revision 2273 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 12 20:29:21 2019 UTC (2 days, 23 hours ago) by wastl
File length: 100209 byte(s)
Diff to previous 2270
need ISO-based year for 'freq' column of weekly data

Revision 2270 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 12 18:55:21 2019 UTC (3 days ago) by wastl
File length: 99957 byte(s)
Diff to previous 2253
use isoWeekYear of first date as start of the sts object

Revision 2253 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Dec 17 14:00:09 2018 UTC (8 weeks, 4 days ago) by wastl
File length: 99886 byte(s)
Diff to previous 2246
multivariate farringtonFlexible(): fill additional control items for _all_ units

Revision 2246 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Nov 22 14:10:21 2018 UTC (2 months, 3 weeks ago) by wastl
File length: 99651 byte(s)
Diff to previous 2238
implement from0-variant for W_np()

Revision 2238 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 13 15:29:24 2018 UTC (3 months ago) by wastl
File length: 99566 byte(s)
Diff to previous 2237
W_np(): rename argument 'to0' to 'truncate' (to avoid confusion with from0)

Revision 2237 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 13 11:07:11 2018 UTC (3 months ago) by wastl
File length: 99388 byte(s)
Diff to previous 2217
mention new 'from0' variant of W_powerlaw()

Revision 2217 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 14 09:07:33 2018 UTC (5 months ago) by wastl
File length: 99102 byte(s)
Diff to previous 2215
avoid creation of sts objects with epoch[1] != 1

Revision 2215 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Sep 13 15:12:58 2018 UTC (5 months ago) by wastl
File length: 98899 byte(s)
Diff to previous 2213
wording

Revision 2213 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Sep 13 14:48:20 2018 UTC (5 months ago) by wastl
File length: 98885 byte(s)
Diff to previous 2207
update

Revision 2207 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 5 13:55:59 2018 UTC (5 months, 1 week ago) by wastl
File length: 98580 byte(s)
Diff to previous 2198
support negative (and 0) indices in the [,sts-method + more argument checks

Revision 2198 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 24 10:32:00 2018 UTC (6 months, 3 weeks ago) by wastl
File length: 98156 byte(s)
Diff to previous 2197
improve default ylim and color key for log="y"

Revision 2197 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Jul 21 20:45:14 2018 UTC (6 months, 3 weeks ago) by wastl
File length: 98065 byte(s)
Diff to previous 2192
update

Revision 2192 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 19 12:07:40 2018 UTC (6 months, 4 weeks ago) by wastl
File length: 97850 byte(s)
Diff to previous 2191
wording

Revision 2191 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 19 11:35:11 2018 UTC (6 months, 4 weeks ago) by wastl
File length: 97830 byte(s)
Diff to previous 2178
update

Revision 2178 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 17 09:04:22 2018 UTC (7 months ago) by wastl
File length: 97688 byte(s)
Diff to previous 2173
use recently accelerated spatstat::bdist.points()

Revision 2173 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 10 14:45:19 2018 UTC (7 months, 1 week ago) by wastl
File length: 97336 byte(s)
Diff to previous 2172
fix createLambda() for epidemic offsets

Revision 2172 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 10 10:21:53 2018 UTC (7 months, 1 week ago) by wastl
File length: 97272 byte(s)
Diff to previous 2164
fix simulate.hhh4() for epidemic offsets

Revision 2164 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon May 28 10:19:10 2018 UTC (8 months, 2 weeks ago) by wastl
File length: 97045 byte(s)
Diff to previous 2145
update release date

Revision 2145 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon May 14 13:48:49 2018 UTC (9 months ago) by wastl
File length: 97045 byte(s)
Diff to previous 2134
update version and date for release

Revision 2134 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon May 14 08:11:35 2018 UTC (9 months ago) by wastl
File length: 97050 byte(s)
Diff to previous 2131
remove unused internal function

Revision 2131 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 11 14:28:14 2018 UTC (9 months ago) by wastl
File length: 97139 byte(s)
Diff to previous 2127
also deprecate correct53to52() and enlargeData()

Revision 2127 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 11 13:07:55 2018 UTC (9 months ago) by wastl
File length: 97093 byte(s)
Diff to previous 2126
missing paranthesis

Revision 2126 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 11 13:01:09 2018 UTC (9 months ago) by wastl
File length: 97138 byte(s)
Diff to previous 2124
deprecate functions related to "testcalls"

Revision 2124 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 11 08:10:31 2018 UTC (9 months ago) by wastl
File length: 96941 byte(s)
Diff to previous 2113
deprecate qlomax()

Revision 2113 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 18 13:10:07 2018 UTC (9 months, 4 weeks ago) by wastl
File length: 96761 byte(s)
Diff to previous 2108
update

Revision 2108 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 18 08:40:07 2018 UTC (9 months, 4 weeks ago) by wastl
File length: 96662 byte(s)
Diff to previous 2104
fix summary.epidata() for SI[R]S epidemics with initially infectious individuals

Revision 2104 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Apr 13 10:11:51 2018 UTC (10 months ago) by wastl
File length: 96538 byte(s)
Diff to previous 2102
clarify

Revision 2102 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 12 15:06:27 2018 UTC (10 months ago) by wastl
File length: 96483 byte(s)
Diff to previous 2093
as.epidataCS() finally allows for prehistory events

Revision 2093 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Feb 15 16:11:33 2018 UTC (12 months ago) by wastl
File length: 96412 byte(s)
Diff to previous 2075
autoplot.sts sets the calling environment

Revision 2075 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 23 08:02:38 2018 UTC (12 months, 3 weeks ago) by wastl
File length: 96187 byte(s)
Diff to previous 2070
set Date

Revision 2070 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 22 16:50:23 2018 UTC (12 months, 3 weeks ago) by wastl
File length: 96181 byte(s)
Diff to previous 2067
plotHHH4_fitted[1]: implement 'total' argument

Revision 2067 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 22 10:48:06 2018 UTC (12 months, 3 weeks ago) by wastl
File length: 96030 byte(s)
Diff to previous 2059
add news item for [.hhh4sims

Revision 2059 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 19 16:20:53 2018 UTC (12 months, 3 weeks ago) by wastl
File length: 95905 byte(s)
Diff to previous 2057
provide autoplot.sts()

Revision 2057 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 19 14:48:44 2018 UTC (12 months, 3 weeks ago) by wastl
File length: 95789 byte(s)
Diff to previous 2053
scores.oneStepAhead: no longer reverses the time points by default

Revision 2053 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 19 09:21:05 2018 UTC (12 months, 3 weeks ago) by wastl
File length: 95468 byte(s)
Diff to previous 2049
document and export fanplot()

Revision 2049 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 16 21:29:08 2018 UTC (12 months, 4 weeks ago) by wastl
File length: 95371 byte(s)
Diff to previous 2048
adjust MGLM code to work with the new version 0.0.9 [Thanks, Maelle]

Revision 2048 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 16 15:14:52 2018 UTC (12 months, 4 weeks ago) by wastl
File length: 95233 byte(s)
Diff to previous 2042
all.equal.hhh4() and all.equal.twinstim() first need to check the class

Revision 2042 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Nov 16 11:17:52 2017 UTC (15 months ago) by wastl
File length: 95098 byte(s)
Diff to previous 2036
as.epidata.data.frame(): add max.time argument

Revision 2036 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 14 12:18:46 2017 UTC (15 months ago) by wastl
File length: 94909 byte(s)
Diff to previous 2035
as.epidata.data.frame(): allow for latent periods (EXPERIMENTAL)

Revision 2035 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 3 21:51:45 2017 UTC (15 months, 1 week ago) by wastl
File length: 94665 byte(s)
Diff to previous 2019
no need to attach polyCub

Revision 2019 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 12 12:43:22 2017 UTC (16 months ago) by wastl
File length: 94525 byte(s)
Diff to previous 2010
fix subset handling in twinSIR()

Revision 2010 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Oct 10 14:49:00 2017 UTC (16 months ago) by wastl
File length: 94144 byte(s)
Diff to previous 2009
document and export tidy.sts()

Revision 2009 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Oct 10 14:25:17 2017 UTC (16 months ago) by wastl
File length: 94092 byte(s)
Diff to previous 2004
add tidy.sts()

Revision 2004 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Oct 10 09:39:09 2017 UTC (16 months ago) by wastl
File length: 93888 byte(s)
Diff to previous 2001
drop map after aggregation over units

Revision 2001 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Oct 10 09:16:57 2017 UTC (16 months ago) by wastl
File length: 93855 byte(s)
Diff to previous 1995
aggregate(stsObj, by="unit") lost colnames

Revision 1995 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Oct 6 13:44:27 2017 UTC (16 months, 1 week ago) by wastl
File length: 93622 byte(s)
Diff to previous 1961
update

Revision 1961 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 29 09:49:38 2017 UTC (16 months, 2 weeks ago) by wastl
File length: 93053 byte(s)
Diff to previous 1959
scores.oneStepAhead(): warn if the awkward default reverse=TRUE is used

Revision 1959 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 26 09:31:46 2017 UTC (16 months, 2 weeks ago) by wastl
File length: 92793 byte(s)
Diff to previous 1958
add quantile() and plot() methods for "oneStepAhead" predictions

Revision 1958 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 25 15:10:07 2017 UTC (16 months, 3 weeks ago) by wastl
File length: 92737 byte(s)
Diff to previous 1957
add confint() for "oneStepAhead" predictions

Revision 1957 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 25 13:54:45 2017 UTC (16 months, 3 weeks ago) by wastl
File length: 92670 byte(s)
Diff to previous 1948
allow oneStepAhead() beyond fitted subset (but within data range)

Revision 1948 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Aug 10 20:38:10 2017 UTC (18 months ago) by wastl
File length: 92479 byte(s)
Diff to previous 1947
use a smaller initial value for the epidemic intercept

Revision 1947 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 9 21:30:30 2017 UTC (18 months, 1 week ago) by wastl
File length: 92336 byte(s)
Diff to previous 1938
mention change in arguments

Revision 1938 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jul 31 13:39:15 2017 UTC (18 months, 2 weeks ago) by wastl
File length: 92261 byte(s)
Diff to previous 1937
hack to detect siaf.gaussian() for larger initial logsd

Revision 1937 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jul 28 14:21:25 2017 UTC (18 months, 2 weeks ago) by wastl
File length: 92272 byte(s)
Diff to previous 1936
non-default parametrizations of siaf.gaussian() are deprecated

Revision 1936 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jul 28 13:22:27 2017 UTC (18 months, 2 weeks ago) by wastl
File length: 92125 byte(s)
Diff to previous 1930
'validpars' only worked if 'trace' was set (optimArgs is NULL per default)

Revision 1930 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jul 12 07:55:28 2017 UTC (19 months ago) by wastl
File length: 91493 byte(s)
Diff to previous 1926
use larger initial value for siaf.gaussian()'s e.siaf.1 parameter

Revision 1926 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jul 7 21:21:49 2017 UTC (19 months, 1 week ago) by wastl
File length: 91253 byte(s)
Diff to previous 1925
closing brace

Revision 1925 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jul 7 21:12:02 2017 UTC (19 months, 1 week ago) by wastl
File length: 91250 byte(s)
Diff to previous 1915
switch intrfr formulae using a numerical tolerance of 1e-7 (for Solaris)

Revision 1915 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jun 28 21:45:48 2017 UTC (19 months, 2 weeks ago) by wastl
File length: 90838 byte(s)
Diff to previous 1912
update

Revision 1912 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jun 28 19:57:21 2017 UTC (19 months, 2 weeks ago) by wastl
File length: 90824 byte(s)
Diff to previous 1902
new function makeControl(), moved here from hhh4contacts

Revision 1902 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 20 19:32:13 2017 UTC (19 months, 3 weeks ago) by wastl
File length: 90712 byte(s)
Diff to previous 1901
simplified "simEpidataCSlist" was missing 'bbox' and 'control.siaf' elements

Revision 1901 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 20 15:17:41 2017 UTC (19 months, 3 weeks ago) by wastl
File length: 90541 byte(s)
Diff to previous 1898
'nmax' could have been too small because 'gridBlocks' is truncated by 'T'

Revision 1898 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 20 10:30:12 2017 UTC (19 months, 3 weeks ago) by wastl
File length: 90368 byte(s)
Diff to previous 1889
plotHHH4sims_fan: new argument 'key.args' for an automatic color key

Revision 1889 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jun 19 15:09:15 2017 UTC (19 months, 4 weeks ago) by wastl
File length: 90233 byte(s)
Diff to previous 1885
numerical tweak to avoid NaN result (stopping nlminb) from log(Inf)/Inf

Revision 1885 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jun 19 13:51:48 2017 UTC (19 months, 4 weeks ago) by wastl
File length: 89954 byte(s)
Diff to previous 1881
update

Revision 1881 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 13 14:59:42 2017 UTC (20 months ago) by wastl
File length: 89662 byte(s)
Diff to previous 1880
implement C-engine for siaf.powerlawL()

Revision 1880 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 13 13:42:56 2017 UTC (20 months ago) by wastl
File length: 89636 byte(s)
Diff to previous 1878
implement C-engine for siaf.student()

Revision 1878 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 13 10:24:55 2017 UTC (20 months ago) by wastl
File length: 89611 byte(s)
Diff to previous 1863
add new features

Revision 1863 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon May 29 13:35:13 2017 UTC (20 months, 2 weeks ago) by wastl
File length: 89114 byte(s)
Diff to previous 1852
start implementing C-version of siaf.powerlaw() and 

Revision 1852 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Apr 28 14:29:32 2017 UTC (21 months, 2 weeks ago) by wastl
File length: 88481 byte(s)
Diff to previous 1843
mention upcoming JSS publication

Revision 1843 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 28 14:37:16 2017 UTC (22 months, 2 weeks ago) by wastl
File length: 87956 byte(s)
Diff to previous 1842
fix createLambda() bug reported by Johannes + add suitable tests

Revision 1842 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 15 16:06:45 2017 UTC (23 months ago) by wastl
File length: 87713 byte(s)
Diff to previous 1836
add plotHHH4sims_fan()

Revision 1836 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 15 14:02:47 2017 UTC (23 months ago) by wastl
File length: 87563 byte(s)
Diff to previous 1834
make scores.default() work with vectors and matrices without dimnames

Revision 1834 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 15 12:38:33 2017 UTC (23 months ago) by wastl
File length: 87424 byte(s)
Diff to previous 1829
scores.hhh4(): set rownames on result (as for oneStepAhead)

Revision 1829 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 23 13:00:47 2017 UTC (2 years ago) by wastl
File length: 87335 byte(s)
Diff to previous 1827
add units-argument to calibrationTest()- and pit()-methods for "oneStepAhead"

Revision 1827 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Dec 21 14:20:18 2016 UTC (2 years, 1 month ago) by wastl
File length: 87166 byte(s)
Diff to previous 1821
1.13.0 is on CRAN now; bump version

Revision 1821 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Dec 20 10:37:55 2016 UTC (2 years, 1 month ago) by wastl
File length: 86929 byte(s)
Diff to previous 1817
this new version is a minor update rather than a patch only

Revision 1817 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Dec 20 08:57:19 2016 UTC (2 years, 1 month ago) by wastl
File length: 86929 byte(s)
Diff to previous 1813
plot.hhh4simslist() no longer ignores its par.settings argument if groups=NULL

Revision 1813 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Dec 13 13:22:41 2016 UTC (2 years, 2 months ago) by wastl
File length: 86813 byte(s)
Diff to previous 1810
catch unsupported use of 'tp' beyond the originally fitted time range

Revision 1810 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Dec 12 11:31:07 2016 UTC (2 years, 2 months ago) by wastl
File length: 86421 byte(s)
Diff to previous 1807
fix endemic-only simulation with unit-specific overdispersion

Revision 1807 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Dec 8 11:03:29 2016 UTC (2 years, 2 months ago) by wastl
File length: 86247 byte(s)
Diff to previous 1802
fix shared overdispersion parameters in simulate.hhh4()

Revision 1802 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Dec 1 14:11:02 2016 UTC (2 years, 2 months ago) by wastl
File length: 85975 byte(s)
Diff to previous 1800
support use of population(x) in stsplot_space() + timy-varying population in animation

Revision 1800 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 30 18:41:39 2016 UTC (2 years, 2 months ago) by wastl
File length: 85708 byte(s)
Diff to previous 1793
tweak pretty color breaks for incidence maps (no automatic use of quantiles)

Revision 1793 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 29 15:03:56 2016 UTC (2 years, 2 months ago) by wastl
File length: 85593 byte(s)
Diff to previous 1792
animate.sts: add support for date labels in timeplot

Revision 1792 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 29 12:09:45 2016 UTC (2 years, 2 months ago) by wastl
File length: 85475 byte(s)
Diff to previous 1791
back to LF line endings

Revision 1791 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 29 12:03:30 2016 UTC (2 years, 2 months ago) by salmonm
File length: 87455 byte(s)
Diff to previous 1789
adds the NEWS entry about the new parameters in earsC

Revision 1789 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 29 11:46:06 2016 UTC (2 years, 2 months ago) by wastl
File length: 85091 byte(s)
Diff to previous 1782
update

Revision 1782 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Nov 28 15:27:38 2016 UTC (2 years, 2 months ago) by wastl
File length: 84659 byte(s)
Diff to previous 1779
animate.sts() now supports objects with missing values

Revision 1779 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 22 10:07:41 2016 UTC (2 years, 2 months ago) by wastl
File length: 84576 byte(s)
Diff to previous 1773
guard hhh4() against the misuse of family=factor('Poisson')

Revision 1773 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Nov 14 13:28:54 2016 UTC (2 years, 3 months ago) by wastl
File length: 84079 byte(s)
Diff to previous 1767
update

Revision 1767 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 4 15:56:08 2016 UTC (2 years, 3 months ago) by wastl
File length: 83813 byte(s)
Diff to previous 1762
update e-mail address

Revision 1762 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Aug 5 21:34:58 2016 UTC (2 years, 6 months ago) by hoehle
File length: 83813 byte(s)
Diff to previous 1761
added info about nowcast func

Revision 1761 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jul 27 02:16:06 2016 UTC (2 years, 6 months ago) by wastl
File length: 83614 byte(s)
Diff to previous 1760
only disable the top padding by default

Revision 1760 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jul 27 01:39:40 2016 UTC (2 years, 6 months ago) by wastl
File length: 83593 byte(s)
Diff to previous 1752
animate.sts(): no padding in timeplot and new option to use aspect="fill"

Revision 1752 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jun 23 13:12:40 2016 UTC (2 years, 7 months ago) by wastl
File length: 83237 byte(s)
Diff to previous 1751
give more specific advice upon non-convergence with low overdispersion

Revision 1751 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 7 11:27:06 2016 UTC (2 years, 8 months ago) by wastl
File length: 82912 byte(s)
Diff to previous 1750
acceleration only relevant for large epidataCS

Revision 1750 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jun 6 18:29:40 2016 UTC (2 years, 8 months ago) by wastl
File length: 82834 byte(s)
Diff to previous 1744
employ new C++ implementation of determinceSources()

Revision 1744 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue May 17 22:29:30 2016 UTC (2 years, 9 months ago) by wastl
File length: 82426 byte(s)
Diff to previous 1739
not() is deprecated since testthat 1.0.0

Revision 1739 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue May 17 15:57:36 2016 UTC (2 years, 9 months ago) by wastl
File length: 82426 byte(s)
Diff to previous 1717
add news item for new vignette

Revision 1717 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue May 17 08:05:40 2016 UTC (2 years, 9 months ago) by wastl
File length: 81970 byte(s)
Diff to previous 1702
update

Revision 1702 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Apr 26 09:16:28 2016 UTC (2 years, 9 months ago) by wastl
File length: 81354 byte(s)
Diff to previous 1699
knox() warns about symmetric input matrices

Revision 1699 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 6 13:50:15 2016 UTC (2 years, 10 months ago) by wastl
File length: 81291 byte(s)
Diff to previous 1698
W_powerlaw() functions use zetaweights() and should thus have the surveillance namespace as their environment

Revision 1698 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 6 12:25:51 2016 UTC (2 years, 10 months ago) by wastl
File length: 81117 byte(s)
Diff to previous 1697
closing brace

Revision 1697 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 6 12:21:54 2016 UTC (2 years, 10 months ago) by wastl
File length: 81114 byte(s)
Diff to previous 1696
let non-convergent hhh4() fits be valid "hhh4" objects -> update.hhh4() works

Revision 1696 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Apr 2 21:06:09 2016 UTC (2 years, 10 months ago) by wastl
File length: 80636 byte(s)
Diff to previous 1687
update

Revision 1687 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Apr 1 19:40:25 2016 UTC (2 years, 10 months ago) by wastl
File length: 80144 byte(s)
Diff to previous 1684
remove legacy methods for old hhh4() fits of class "ah4"

Revision 1684 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Apr 1 18:33:29 2016 UTC (2 years, 10 months ago) by wastl
File length: 79939 byte(s)
Diff to previous 1676
initialization of 'stsBP' and 'stsNC' with new callNextMethod() implementation requires R >= 3.2.0 (due to bugs in older versions of R)

Revision 1676 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Apr 1 09:42:40 2016 UTC (2 years, 10 months ago) by wastl
File length: 79909 byte(s)
Diff to previous 1674
add simple matplot() implementation of stsplot_time(..., as.one=TRUE)

Revision 1674 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 31 14:43:24 2016 UTC (2 years, 10 months ago) by wastl
File length: 79777 byte(s)
Diff to previous 1667
plotHHH4_season() draws a reference line for component seasonality if intercept=FALSE

Revision 1667 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 29 22:46:43 2016 UTC (2 years, 10 months ago) by wastl
File length: 79531 byte(s)
Diff to previous 1664
add vignette("hhh4_spacetime")

Revision 1664 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 24 13:33:25 2016 UTC (2 years, 10 months ago) by wastl
File length: 79407 byte(s)
Diff to previous 1657
add vignette("twinSIR")

Revision 1657 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 17 14:57:58 2016 UTC (2 years, 11 months ago) by wastl
File length: 78992 byte(s)
Diff to previous 1643
move data("fluBYBW") analysis of Paul and Held (2011) to a separate demo script

Revision 1643 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 16 16:34:46 2016 UTC (2 years, 11 months ago) by wastl
File length: 78668 byte(s)
Diff to previous 1635
document the new sts() constructor

Revision 1635 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 16 11:11:48 2016 UTC (2 years, 11 months ago) by wastl
File length: 78653 byte(s)
Diff to previous 1632
overhaul the "sts" implementation

* the user-level constructor sts() now has some explicit arguments for clarity;
  the simple generator function now is .sts() but kept internal

* with the new sts() constructor, "observed" does not need to be named,
  i.e., sts(observed, start = c(2016, 3), frequency = 12) works,
  just like for the classical ts()

* adjust storage.mode() of default matrices: "upperbound" now defaults to
  numeric instead of logical NA's and "state" defaults to FALSE values
  (instead of 0's)

* "stsBP" and "stsNC" objects can now be initialized from an "sts" object,
  e.g., new("stsBP", stsObj, ci=ci, lambda=lambda), due to the new internal
  callNextMethod() approach (which also greatly simplifies the code).
  The array slots are filled with numeric instead of logical NA's by default.
  The default dimnames of the extra "stsBP" arrays now use dimnames(observed).

* the validity function for the "sts" class is now really used

* added tests for "sts" construction and for conversion from "ts" to "sts"

* updated "fluBYBW" and "measlesWeserEms" datasets to reflect change in default
  storage modes of the "upperbound" and "state" slots (because reconstruction
  is checked in vignette("hhh4") and help("sts-class"), respectively)

Revision 1632 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 15 19:26:07 2016 UTC (2 years, 11 months ago) by wastl
File length: 78100 byte(s)
Diff to previous 1628
undo r1624 -> stick to the old r193 behaviour of ignoring disProgObj

Revision 1628 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 15 12:31:41 2016 UTC (2 years, 11 months ago) by wastl
File length: 78230 byte(s)
Diff to previous 1624
fix 'start' calculation in as(ts, "sts")

Revision 1624 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 14 14:53:11 2016 UTC (2 years, 11 months ago) by wastl
File length: 78007 byte(s)
Diff to previous 1609
fix bug sitting in disProg2sts() since renaming in r193: week was always ignored

Revision 1609 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Mar 4 23:43:27 2016 UTC (2 years, 11 months ago) by wastl
File length: 77873 byte(s)
Diff to previous 1606
add vignette("twinstim")

Revision 1606 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Mar 4 12:58:47 2016 UTC (2 years, 11 months ago) by wastl
File length: 77835 byte(s)
Diff to previous 1601
update

Revision 1601 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 2 11:59:38 2016 UTC (2 years, 11 months ago) by wastl
File length: 77592 byte(s)
Diff to previous 1588
stsplot_spacetime() ignored its opts.col argument

Revision 1588 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 8 17:34:40 2016 UTC (3 years ago) by wastl
File length: 77394 byte(s)
Diff to previous 1576
update

Revision 1576 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 8 01:29:26 2016 UTC (3 years ago) by wastl
File length: 77361 byte(s)
Diff to previous 1563
updated cache of vignette("surveillance") to account for corrected algo.bayes (since 1.10-0) and smaller set of cached objects

Revision 1563 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Feb 6 21:50:15 2016 UTC (3 years ago) by wastl
File length: 77166 byte(s)
Diff to previous 1560
thorough revision of vignette("hhh4")

Revision 1560 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Feb 6 11:59:32 2016 UTC (3 years ago) by wastl
File length: 77020 byte(s)
Diff to previous 1548
this version is really a minor bump not only a patch

Revision 1548 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 2 09:45:50 2016 UTC (3 years ago) by wastl
File length: 77020 byte(s)
Diff to previous 1542
add Maƫlle's NEWS item

Revision 1542 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 1 14:10:18 2016 UTC (3 years ago) by wastl
File length: 76557 byte(s)
Diff to previous 1538
parallel epitest() now catches NULL replications caused by forking in low memory

Revision 1538 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Jan 17 16:19:02 2016 UTC (3 years ago) by hoehle
File length: 76255 byte(s)
Diff to previous 1537
added experimental return of cases for the full glr based on the negative binomial distribution

Revision 1537 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Jan 16 18:07:14 2016 UTC (3 years, 1 month ago) by hoehle
File length: 76014 byte(s)
Diff to previous 1536
more on the glrnb function, also added the algo.quality function so it handles sts objects

Revision 1536 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Jan 16 13:53:06 2016 UTC (3 years, 1 month ago) by hoehle
File length: 75815 byte(s)
Diff to previous 1528
fixed bugged in estimateGLRNb function reported by the EpiConcept ppl

Revision 1528 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Jan 3 22:12:03 2016 UTC (3 years, 1 month ago) by hoehle
File length: 75517 byte(s)
Diff to previous 1520
fixed bug in the categorical CUSUM function

Revision 1520 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 24 14:12:29 2015 UTC (3 years, 2 months ago) by wastl
File length: 75251 byte(s)
Diff to previous 1518
fix intensity.twinstim() for non-endemic models

Revision 1518 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 13 12:22:31 2015 UTC (3 years, 3 months ago) by wastl
File length: 75132 byte(s)
Diff to previous 1508
update.epidata(): allow 'D' to be a "Matrix"

Revision 1508 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 4 14:44:19 2015 UTC (3 years, 3 months ago) by wastl
File length: 74865 byte(s)
Diff to previous 1502
oneStepAhead() allows for explicit start values through the 'which.start' argument

Revision 1502 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Oct 20 15:56:31 2015 UTC (3 years, 3 months ago) by wastl
File length: 74602 byte(s)
Diff to previous 1497
add new plot type for hhh4 fits: plotHHH4_maps()

Revision 1497 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Oct 20 09:38:05 2015 UTC (3 years, 3 months ago) by wastl
File length: 74457 byte(s)
Diff to previous 1495
plotHHH4_fitted1() gains an argument 'xaxis' to enable a formatted time axis as in stsplot_time1()

Revision 1495 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Oct 16 14:31:03 2015 UTC (3 years, 4 months ago) by wastl
File length: 74326 byte(s)
Diff to previous 1488
add pit() methods for oneStepAhead predictions and hhh4 fits

Revision 1488 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Oct 6 12:43:47 2015 UTC (3 years, 4 months ago) by wastl
File length: 74357 byte(s)
Diff to previous 1487
new argument 'D' in update.epidata() to allow for a pre-computed distance matrix

Revision 1487 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 29 19:10:40 2015 UTC (3 years, 4 months ago) by wastl
File length: 74061 byte(s)
Diff to previous 1486
add convenient all.equal.hhh4() method

Revision 1486 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 29 12:20:15 2015 UTC (3 years, 4 months ago) by wastl
File length: 73895 byte(s)
Diff to previous 1483
bugfix: a consistency check in as.epidata.default() failed for SI-type data (spotted by George Wood)

Revision 1483 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Sep 26 12:22:30 2015 UTC (3 years, 4 months ago) by wastl
File length: 73689 byte(s)
Diff to previous 1481
stsplot_time(): only apply the internal par() call if 'par.list' is a list

Revision 1481 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 25 21:24:57 2015 UTC (3 years, 4 months ago) by wastl
File length: 73574 byte(s)
Diff to previous 1479
make addFormattedXAxis() work for classical sts objects with integer epochs

Revision 1479 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 23 09:12:21 2015 UTC (3 years, 4 months ago) by hoehle
File length: 73323 byte(s)
Diff to previous 1476
fixed algo bayes and updated documentation of salmNewport

Revision 1476 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 14 22:08:30 2015 UTC (3 years, 5 months ago) by wastl
File length: 73004 byte(s)
Diff to previous 1475
add scores-method for "hhh4sims"

Revision 1475 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 14 20:38:55 2015 UTC (3 years, 5 months ago) by wastl
File length: 72896 byte(s)
Diff to previous 1472
make default time variable in hhh4() work with sts objects that use epochAsDate

Revision 1472 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 14 15:34:45 2015 UTC (3 years, 5 months ago) by wastl
File length: 72706 byte(s)
Diff to previous 1468
add time series plot for simulations from hhh4 fits, improve hhh4simslist handling, add indexing methods

Revision 1468 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Sep 10 17:14:40 2015 UTC (3 years, 5 months ago) by wastl
File length: 72680 byte(s)
Diff to previous 1466
new argument 'draw' (=TRUE) for animate.sts(), which now invisibly returns a list of the sequential plot objects (for post-processing)

Revision 1466 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 9 17:37:28 2015 UTC (3 years, 5 months ago) by wastl
File length: 72395 byte(s)
Diff to previous 1464
add a plot-method for "hhh4sims" (not documented yet)

Revision 1464 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 7 21:32:57 2015 UTC (3 years, 5 months ago) by wastl
File length: 72119 byte(s)
Diff to previous 1463
add coeflist-method for "hhh4" fits

Revision 1463 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 7 19:06:12 2015 UTC (3 years, 5 months ago) by wastl
File length: 72048 byte(s)
Diff to previous 1462
allow additional style arguments in layout.scalebar()

Revision 1462 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 1 15:17:42 2015 UTC (3 years, 5 months ago) by wastl
File length: 71939 byte(s)
Diff to previous 1461
add convenient option idx2Exp = TRUE

Revision 1461 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 1 11:57:15 2015 UTC (3 years, 5 months ago) by wastl
File length: 71796 byte(s)
Diff to previous 1459
add generator function sts()

Revision 1459 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Aug 21 14:35:39 2015 UTC (3 years, 5 months ago) by wastl
File length: 71636 byte(s)
Diff to previous 1458
summary.twinstim(): new 'runtime' argument (no longer included by default)

Revision 1458 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 19 18:55:00 2015 UTC (3 years, 5 months ago) by wastl
File length: 71276 byte(s)
Diff to previous 1448
document shared overdispersion

Revision 1448 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Aug 17 13:40:28 2015 UTC (3 years, 6 months ago) by wastl
File length: 71103 byte(s)
Diff to previous 1444
update

Revision 1444 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 30 22:47:56 2015 UTC (3 years, 6 months ago) by hoehle
File length: 70919 byte(s)
Diff to previous 1438
fixed two bugs when calling algo.outbreakP using wrap.univariate

Revision 1438 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 21 12:14:02 2015 UTC (3 years, 6 months ago) by wastl
File length: 70630 byte(s)
Diff to previous 1435
stsplot_time1(): if 'missing(legend.opts)', the default legend is only produced if there really are any alarms, outbreaks or upperbounds in the "sts" object

Revision 1435 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 21 09:41:22 2015 UTC (3 years, 6 months ago) by wastl
File length: 70426 byte(s)
Diff to previous 1434
stsplot_time(): the 'units' argument was ignored when determining the default 'mfrow' setting

Revision 1434 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 21 08:46:41 2015 UTC (3 years, 6 months ago) by wastl
File length: 70194 byte(s)
Diff to previous 1433
init.sts(): renamed formal argument 'freq' to 'frequency' (backward compatible)

Revision 1433 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 21 07:32:56 2015 UTC (3 years, 6 months ago) by wastl
File length: 69911 byte(s)
Diff to previous 1432
initialize epoch to 1:nrow(observed) by default

Revision 1432 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jul 20 16:02:39 2015 UTC (3 years, 6 months ago) by wastl
File length: 69678 byte(s)
Diff to previous 1431
plotHHH4_fitted[1](): new option 'decompose' to plot the fully decomposed mean

Revision 1431 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jul 20 13:25:59 2015 UTC (3 years, 6 months ago) by wastl
File length: 69429 byte(s)
Diff to previous 1428
plotHHH4_fitted[1](): separate argument for 'pt.col' and reversed 'col' order

Revision 1428 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 16 10:14:52 2015 UTC (3 years, 7 months ago) by wastl
File length: 69082 byte(s)
Diff to previous 1427
add calibrationTest.oneStepAhead() + outsourcing psi2size.oneStepAhead()

Revision 1427 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jul 15 23:46:27 2015 UTC (3 years, 7 months ago) by wastl
File length: 68889 byte(s)
Diff to previous 1402
make scores() generic with a new method for "hhh4" and the original identified via the new dedicated class "oneStepAhead" (with argument 'object' renamed to 'x')

Revision 1402 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jul 8 16:01:03 2015 UTC (3 years, 7 months ago) by wastl
File length: 68374 byte(s)
Diff to previous 1385
add calibration tests (changed version number to 1.10-0)

Revision 1385 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 12 10:07:30 2015 UTC (3 years, 8 months ago) by wastl
File length: 68110 byte(s)
Diff to previous 1384
forgot itemize

Revision 1384 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 12 10:03:53 2015 UTC (3 years, 8 months ago) by wastl
File length: 68082 byte(s)
Diff to previous 1370
NEWS for the quick patch release

Revision 1370 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 9 15:54:26 2015 UTC (3 years, 8 months ago) by wastl
File length: 67725 byte(s)
Diff to previous 1368
today's bug fix still goes into 1.9-0

Revision 1368 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 9 13:08:08 2015 UTC (3 years, 8 months ago) by wastl
File length: 67883 byte(s)
Diff to previous 1358
update.hhh4(, use.estimates = TRUE) no longer ignores the coefW part

Revision 1358 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Jun 7 20:18:34 2015 UTC (3 years, 8 months ago) by wastl
File length: 67492 byte(s)
Diff to previous 1352
tidy NEWS

Revision 1352 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jun 3 19:46:10 2015 UTC (3 years, 8 months ago) by wastl
File length: 67329 byte(s)
Diff to previous 1349
new options for scaling and normalization in hhh4() models

Revision 1349 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 2 21:17:20 2015 UTC (3 years, 8 months ago) by wastl
File length: 67218 byte(s)
Diff to previous 1346
update NEWS

Revision 1346 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 29 09:38:01 2015 UTC (3 years, 8 months ago) by wastl
File length: 66980 byte(s)
Diff to previous 1342
smarter plot option for permutationTest()

Revision 1342 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed May 27 07:46:52 2015 UTC (3 years, 8 months ago) by wastl
File length: 66774 byte(s)
Diff to previous 1325
update

Revision 1325 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 30 11:56:23 2015 UTC (3 years, 9 months ago) by wastl
File length: 66560 byte(s)
Diff to previous 1324
iafplot(): new option scaled="standardized"

Revision 1324 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 29 16:06:20 2015 UTC (3 years, 9 months ago) by wastl
File length: 66421 byte(s)
Diff to previous 1323
update

Revision 1323 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 29 10:00:30 2015 UTC (3 years, 9 months ago) by wastl
File length: 66014 byte(s)
Diff to previous 1294
layout.labels() and layout.scalebar() can optionally plot in the traditional graphics system

Revision 1294 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 26 14:33:24 2015 UTC (3 years, 10 months ago) by wastl
File length: 65972 byte(s)
Diff to previous 1281
fe(): specifying unit-specific fixed effects has always been a pain with this awkward 'which' argument; now just set unitSpecific = TRUE

Revision 1281 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 24 09:17:20 2015 UTC (3 years, 10 months ago) by wastl
File length: 65766 byte(s)
Diff to previous 1275
intensity.twinstim()(tp) returns NA if tp<t0 (previously this was an error)

Revision 1275 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Mar 22 23:15:35 2015 UTC (3 years, 10 months ago) by wastl
File length: 65578 byte(s)
Diff to previous 1267
new function stKtest(): wraps functions in package "splancs" for use with "epidataCS"

Revision 1267 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Mar 21 10:44:51 2015 UTC (3 years, 10 months ago) by wastl
File length: 65492 byte(s)
Diff to previous 1266
tune package description and increase minor version number (many new features)

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Modified Fri Mar 20 22:33:00 2015 UTC (3 years, 10 months ago) by wastl
File length: 65492 byte(s)
Diff to previous 1264
new spplot() functionality of epidataCSplot_space()

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Modified Fri Mar 20 22:25:12 2015 UTC (3 years, 10 months ago) by wastl
File length: 65337 byte(s)
Diff to previous 1263
new auxiliary function layout.scalebar()

Revision 1263 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Mar 20 13:06:34 2015 UTC (3 years, 10 months ago) by wastl
File length: 65220 byte(s)
Diff to previous 1251
new argument 'tiles' for the spatial plot of "epidataCS"

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Modified Wed Mar 11 13:44:35 2015 UTC (3 years, 11 months ago) by wastl
File length: 65131 byte(s)
Diff to previous 1250
drop=FALSE error in simEpidataCS() for the case when 'stgrid' had no covariates

Revision 1250 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 11 12:53:57 2015 UTC (3 years, 11 months ago) by wastl
File length: 65014 byte(s)
Diff to previous 1246
bugfix in simEpidataCS(): did not work for a single-cell 'stgrid'

Revision 1246 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 10 14:23:11 2015 UTC (3 years, 11 months ago) by wastl
File length: 64866 byte(s)
Diff to previous 1241
plot.hhh4() checks for convergence of the supplied model (required)

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Modified Tue Mar 10 10:22:05 2015 UTC (3 years, 11 months ago) by wastl
File length: 64750 byte(s)
Diff to previous 1238
fix URLs as detected by R-devel CMD check on win-builder.r-project.org

Revision 1238 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 9 21:50:01 2015 UTC (3 years, 11 months ago) by wastl
File length: 64758 byte(s)
Diff to previous 1228
add argument 'newcoef' for simulate.twinstim()

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Modified Mon Mar 9 13:51:27 2015 UTC (3 years, 11 months ago) by wastl
File length: 64625 byte(s)
Diff to previous 1227
specifying step iaf via a vector of knots finally works in twinstim()

Revision 1227 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 9 13:49:53 2015 UTC (3 years, 11 months ago) by wastl
File length: 64503 byte(s)
Diff to previous 1226
add Maelle's news item

Revision 1226 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 9 13:45:45 2015 UTC (3 years, 11 months ago) by wastl
File length: 64295 byte(s)
Diff to previous 1225
back to r1223 (character encoding issues)

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Modified Mon Mar 9 12:05:19 2015 UTC (3 years, 11 months ago) by salmonm
File length: 66071 byte(s)
Diff to previous 1220
Solves various issues with the algo for delay correction.

Revision 1220 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Mar 8 17:20:47 2015 UTC (3 years, 11 months ago) by wastl
File length: 64295 byte(s)
Diff to previous 1215
document and export simpleR0

Revision 1215 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Mar 6 23:16:22 2015 UTC (3 years, 11 months ago) by wastl
File length: 64229 byte(s)
Diff to previous 1211
export new coeflist generic and methods

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Modified Fri Mar 6 15:44:56 2015 UTC (3 years, 11 months ago) by wastl
File length: 64045 byte(s)
Diff to previous 1210
epidataCSplot_time(): new default breaks="stgrid" + bugfix: use same breaks for all strata

Revision 1210 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 5 21:05:07 2015 UTC (3 years, 11 months ago) by wastl
File length: 63780 byte(s)
Diff to previous 1197
bugfix in twinstim(): finetune and optim methods only worked if optim.args was supplied

Revision 1197 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 23 17:01:45 2015 UTC (3 years, 11 months ago) by wastl
File length: 63560 byte(s)
Diff to previous 1192
new function plapply(): a parallel and verbose version of lapply()

Revision 1192 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 18 18:05:40 2015 UTC (3 years, 11 months ago) by hoehle
File length: 63371 byte(s)
Diff to previous 1188
added maelles code for proper sampling from the posterior in the boda algorithm

Revision 1188 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 18 13:24:13 2015 UTC (3 years, 11 months ago) by wastl
File length: 63062 byte(s)
Diff to previous 1178
document new function epitest()

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Modified Wed Feb 4 16:58:40 2015 UTC (4 years ago) by wastl
File length: 62934 byte(s)
Diff to previous 1173
new function 'knox' implementing Knox test for space-time interaction

Revision 1173 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 26 23:13:51 2015 UTC (4 years ago) by wastl
File length: 62723 byte(s)
Diff to previous 1172
formatPval() disables scientific notation by default

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Modified Mon Jan 19 17:34:45 2015 UTC (4 years ago) by wastl
File length: 62640 byte(s)
Diff to previous 1169
new function permute.epidataCS()

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Modified Tue Jan 13 15:05:56 2015 UTC (4 years, 1 month ago) by wastl
File length: 62497 byte(s)
Diff to previous 1168
ensure polygonal type for the result of intersectPolyCircle.owin

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Modified Tue Jan 13 13:22:22 2015 UTC (4 years, 1 month ago) by wastl
File length: 62354 byte(s)
Diff to previous 1167
replaced new argument 'bytype' by a more general argument 'by', which can also specify other variables for stratification

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Modified Tue Jan 13 11:02:50 2015 UTC (4 years, 1 month ago) by wastl
File length: 62262 byte(s)
Diff to previous 1164
'bytype' argument now also for epidataCSplot_space()

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Modified Mon Jan 12 17:02:47 2015 UTC (4 years, 1 month ago) by wastl
File length: 62055 byte(s)
Diff to previous 1162
'constantsiaf' is only defined if there is an epidemic component

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Modified Mon Jan 12 12:15:46 2015 UTC (4 years, 1 month ago) by wastl
File length: 61946 byte(s)
Diff to previous 1160
only re-determine .sources in twinstim if effectively needed

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Modified Thu Jan 8 22:12:37 2015 UTC (4 years, 1 month ago) by wastl
File length: 61691 byte(s)
Diff to previous 1150
fix epidataCS area checks

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Modified Mon Jan 5 09:11:05 2015 UTC (4 years, 1 month ago) by hoehle
File length: 61241 byte(s)
Diff to previous 1149
fixed NEWS file and made linelist2sts work for quarters by adding extra %q formatting in formatDate

Revision 1149 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Jan 4 23:24:06 2015 UTC (4 years, 1 month ago) by hoehle
File length: 61215 byte(s)
Diff to previous 1143
updated news file also

Revision 1143 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Dec 16 13:05:03 2014 UTC (4 years, 2 months ago) by wastl
File length: 61022 byte(s)
Diff to previous 1142
name random intercepts in coefficient vector

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Modified Tue Dec 16 12:30:50 2014 UTC (4 years, 2 months ago) by wastl
File length: 60910 byte(s)
Diff to previous 1139
random effects currently do not have names

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Modified Tue Dec 16 11:04:07 2014 UTC (4 years, 2 months ago) by wastl
File length: 60751 byte(s)
Diff to previous 1136
update.hhh4() now does 'use.estimates' by default and also respects an extra start argument

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Modified Mon Dec 15 23:35:25 2014 UTC (4 years, 2 months ago) by wastl
File length: 60522 byte(s)
Diff to previous 1116
hhh4() now matches start values by name (if available); start vectors no longer need to be complete

Revision 1116 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 14 12:33:40 2014 UTC (4 years, 3 months ago) by wastl
File length: 60289 byte(s)
Diff to previous 1114
stsplot_space() now shows extra (unobserved) regions of the map by default

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Modified Fri Nov 14 09:33:35 2014 UTC (4 years, 3 months ago) by wastl
File length: 60133 byte(s)
Diff to previous 1110
move check of map completeness from unused validity function to init.sts

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Modified Wed Nov 12 10:24:56 2014 UTC (4 years, 3 months ago) by wastl
File length: 59889 byte(s)
Diff to previous 1109
sts-methods: dimnames instead of colnames, dropped redundant nrow and ncol

Revision 1109 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 12 09:21:26 2014 UTC (4 years, 3 months ago) by wastl
File length: 59653 byte(s)
Diff to previous 1094
for univariate sts objects, do not show meaningless head(object@neighbourhood)

Revision 1094 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Oct 29 20:32:04 2014 UTC (4 years, 3 months ago) by wastl
File length: 59409 byte(s)
Diff to previous 1090
checkResidualProcess(): changed default mfrow argument to side by side plots

Revision 1090 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Oct 24 08:34:23 2014 UTC (4 years, 3 months ago) by wastl
File length: 59238 byte(s)
Diff to previous 1081
profile.twinSIR() gained a class and an associated plot-method

Revision 1081 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Oct 18 22:20:15 2014 UTC (4 years, 3 months ago) by wastl
File length: 59131 byte(s)
Diff to previous 1079
we effectively depend on R >= 3.0.2 since surveillance 1.7-0

Revision 1079 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Oct 17 23:26:00 2014 UTC (4 years, 4 months ago) by wastl
File length: 58934 byte(s)
Diff to previous 1078
twinSIR updates:
- account for new 'w' covariates in simulation
- for f-covariates, distance to oneself is no longer assumed Inf
- accordingly dropped redundant is.finite restrictions in example f's
- updated hagelloch, fooepidata and foofit to reflect changes

Revision 1078 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Oct 17 14:48:43 2014 UTC (4 years, 4 months ago) by wastl
File length: 58447 byte(s)
Diff to previous 1076
plot.epidata(): use colored lines by default

Revision 1076 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 16 23:58:38 2014 UTC (4 years, 4 months ago) by wastl
File length: 58352 byte(s)
Diff to previous 1074
integrated new hagelloch data into the package (changes are documented at the beginning of dataio-hagelloch.R)

Revision 1074 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 16 22:49:29 2014 UTC (4 years, 4 months ago) by wastl
File length: 58570 byte(s)
Diff to previous 1071
new argument 'w' in as.epidata.default() for epidemic weights as function of time-constant covariates

Revision 1071 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Oct 15 23:28:00 2014 UTC (4 years, 4 months ago) by wastl
File length: 58363 byte(s)
Diff to previous 1058
new as.epidata.data.frame method to convert from a simple individual-based data.frame to the start/stop event history format

Revision 1058 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 9 09:54:01 2014 UTC (4 years, 4 months ago) by wastl
File length: 58173 byte(s)
Diff to previous 1056
the trivial (identity) call aggregate(stsObj, nfreq=stsObj@freq) did not work

Revision 1056 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Oct 7 10:10:13 2014 UTC (4 years, 4 months ago) by wastl
File length: 58072 byte(s)
Diff to previous 1051
pitPxPxm1(): use ... with mapply(pdistr, x, ...) such that it can be x-specific; use match.fun() for a single pdistr

Revision 1051 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Oct 6 20:40:52 2014 UTC (4 years, 4 months ago) by wastl
File length: 57749 byte(s)
Diff to previous 1049
new auxiliary function layout.labels(), extracted from stsplot_space() code, now also used for plotHHH4_ri()

Revision 1049 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Oct 6 12:33:20 2014 UTC (4 years, 4 months ago) by wastl
File length: 57604 byte(s)
Diff to previous 1043
plotHHH4_season(): intercept=FALSE

Revision 1043 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Oct 3 07:46:12 2014 UTC (4 years, 4 months ago) by wastl
File length: 57343 byte(s)
Diff to previous 1041
scores(): new argument 'which', excluding the improper nses by default; tidy code of score functions

Revision 1041 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Oct 1 21:39:46 2014 UTC (4 years, 4 months ago) by wastl
File length: 57102 byte(s)
Diff to previous 1038
update.hhh4(): gained arguments 'S' and 'evaluate' and is now documented

Revision 1038 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 30 19:14:10 2014 UTC (4 years, 4 months ago) by wastl
File length: 56909 byte(s)
Diff to previous 1036
added formula.hhh4()

Revision 1036 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 30 09:17:30 2014 UTC (4 years, 4 months ago) by wastl
File length: 56747 byte(s)
Diff to previous 1033
measlesWeserEms: added vaccdoc.2004 and vacc1.2004 variables in the @map@data slot

Revision 1033 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 26 15:06:42 2014 UTC (4 years, 4 months ago) by wastl
File length: 56583 byte(s)
Diff to previous 1029
epidataCSplot_space(): did not draw the point for single-event epidataCS

Revision 1029 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 26 09:10:19 2014 UTC (4 years, 4 months ago) by wastl
File length: 56471 byte(s)
Diff to previous 1028
simulate.twinstim(): use data as default for W

Revision 1028 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 24 07:52:59 2014 UTC (4 years, 4 months ago) by wastl
File length: 56359 byte(s)
Diff to previous 1027
permutationTest(): added 'verbose' argument with default FALSE

Revision 1027 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 23 21:59:04 2014 UTC (4 years, 4 months ago) by wastl
File length: 56188 byte(s)
Diff to previous 1025
re-implementation of scores() fixing several bugs, adding a feature, and changing the dimensions of the result for multivariate individual predictions (see the NEWS for details)

Revision 1025 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 22 15:58:48 2014 UTC (4 years, 4 months ago) by wastl
File length: 55496 byte(s)
Diff to previous 1024
checkWeights() unintentionally blocked the use of W_np(maxlag=2) in hhh4-models

Revision 1024 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 22 14:02:37 2014 UTC (4 years, 4 months ago) by wastl
File length: 55364 byte(s)
Diff to previous 1019
W_np(): new default to0=TRUE for consistency with the meaning of "maxlag" and W_powerlaw

Revision 1019 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Sep 20 21:42:53 2014 UTC (4 years, 4 months ago) by wastl
File length: 55132 byte(s)
Diff to previous 1017
hhh4(): argument control now defaults to 'neighbourhood(stsObj) == 1'

Revision 1017 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 19 13:12:28 2014 UTC (4 years, 4 months ago) by wastl
File length: 54760 byte(s)
Diff to previous 1011
new plot type="neweights" for hhh4-fits

Revision 1011 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 17 20:49:45 2014 UTC (4 years, 4 months ago) by wastl
File length: 54692 byte(s)
Diff to previous 1005
plotHHH4_fitted(): argument 'legend.observed' now defaults to FALSE

Revision 1005 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 10 21:55:11 2014 UTC (4 years, 5 months ago) by wastl
File length: 54582 byte(s)
Diff to previous 1003
untie.epidataCS(): added 'verbose' argument, reuse original 'clipper'

Revision 1003 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Sep 7 09:28:42 2014 UTC (4 years, 5 months ago) by wastl
File length: 54303 byte(s)
Diff to previous 1002
added 'units' argument to stsplot_time()

Revision 1002 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Sep 7 08:50:25 2014 UTC (4 years, 5 months ago) by wastl
File length: 54167 byte(s)
Diff to previous 1000
animate.sts(): automatic choice of color breaks ('at') now also works for incidence maps (i.e. with a 'population' argument)

Revision 1000 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 3 20:52:27 2014 UTC (4 years, 5 months ago) by wastl
File length: 53986 byte(s)
Diff to previous 994
simEpidataCS(): fixed lambda.h values stored with simulated events

Revision 994 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 3 08:06:14 2014 UTC (4 years, 5 months ago) by wastl
File length: 53803 byte(s)
Diff to previous 991
'simulate.twinstim(..., rmarks=NULL)' can now handle the case where 'data' does not have events within the simulation period

Revision 991 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 1 21:13:26 2014 UTC (4 years, 5 months ago) by wastl
File length: 53604 byte(s)
Diff to previous 985
simulation-based computation of osAIC weights for twinSIR fits is more robust now by rescaling the objective function for quadprog::solve.QP() in Ztilde.chibarsq(); this fixes the "constraints are inconsistent, no solution!" error for the hagelloch fit; related code has also been cleaned and tuned such that the runtime is more than halved

Revision 985 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 27 20:35:55 2014 UTC (4 years, 5 months ago) by wastl
File length: 53332 byte(s)
Diff to previous 982
fixed buggy confint.hhh4 for models with random effects

Revision 982 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Aug 26 09:39:53 2014 UTC (4 years, 5 months ago) by wastl
File length: 53205 byte(s)
Diff to previous 980
ani.options("outdir") is no longer supported by the "animation" package

Revision 980 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Aug 25 14:41:47 2014 UTC (4 years, 5 months ago) by wastl
File length: 53056 byte(s)
Diff to previous 972
updated NEWS

Revision 972 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Aug 25 09:30:05 2014 UTC (4 years, 5 months ago) by wastl
File length: 52784 byte(s)
Diff to previous 963
updated NEWS

Revision 963 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Aug 22 20:20:15 2014 UTC (4 years, 5 months ago) by wastl
File length: 52564 byte(s)
Diff to previous 960
argument newcoef for R0.twinstim

Revision 960 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Aug 22 14:18:13 2014 UTC (4 years, 5 months ago) by wastl
File length: 52378 byte(s)
Diff to previous 958
tidy

Revision 958 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Aug 14 08:23:36 2014 UTC (4 years, 6 months ago) by salmonm
File length: 52362 byte(s)
Diff to previous 957
explains change in farringtonFlexible

Revision 957 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 13 20:59:35 2014 UTC (4 years, 6 months ago) by hoehle
File length: 52219 byte(s)
Diff to previous 954
added a nowcast specific plot method to the stsNC class

Revision 954 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Aug 12 14:07:04 2014 UTC (4 years, 6 months ago) by hoehle
File length: 51949 byte(s)
Diff to previous 940
updated the hagelloch data to fix the local and global columns

Revision 940 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 17 07:51:45 2014 UTC (4 years, 8 months ago) by hoehle
File length: 51454 byte(s)
Diff to previous 936
added add repos field to description

Revision 936 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 23 13:41:55 2014 UTC (4 years, 8 months ago) by wastl
File length: 51454 byte(s)
Diff to previous 934
updated imdepi (=> imdepifit) using new polyclip 1.3-0

Revision 934 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 23 13:07:37 2014 UTC (4 years, 8 months ago) by wastl
File length: 51331 byte(s)
Diff to previous 930
tidy NEWS

Revision 930 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu May 22 15:16:59 2014 UTC (4 years, 8 months ago) by wastl
File length: 50631 byte(s)
Diff to previous 919
documented pit() and changed default plot-argument -> do the plot

Revision 919 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue May 13 12:50:58 2014 UTC (4 years, 9 months ago) by wastl
File length: 50564 byte(s)
Diff to previous 911
control.siaf=NULL in update.twinstim()

Revision 911 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Apr 22 14:37:38 2014 UTC (4 years, 9 months ago) by hoehle
File length: 50508 byte(s)
Diff to previous 905
fixed a bug in LRCUSUM.runlength which always lead to the computation of the in-control ARL (i.e. mu0) instead of using mu as specified

Revision 905 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Apr 13 09:22:22 2014 UTC (4 years, 10 months ago) by hoehle
File length: 50337 byte(s)
Diff to previous 892
started to add truncated nowcasting to the surveillance package. Documentation only partially complete

Revision 892 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 7 22:03:56 2014 UTC (4 years, 10 months ago) by wastl
File length: 49924 byte(s)
Diff to previous 891
finally provide glm_epidataCS()

Revision 891 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 7 19:32:27 2014 UTC (4 years, 10 months ago) by wastl
File length: 49682 byte(s)
Diff to previous 890
twinstim() minor changes:
- cumCIF argument defaults to FALSE
- optional result components "fisherinfo", "fisherinfo.observed", "tau",
  and "functions" are included as NULL if not applicable (previously missing)
  such that all twinstim objects have the same list structure

Revision 890 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 7 07:56:54 2014 UTC (4 years, 10 months ago) by wastl
File length: 49277 byte(s)
Diff to previous 888
animate.sts() -- not documented yet

Revision 888 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Apr 5 21:27:58 2014 UTC (4 years, 10 months ago) by wastl
File length: 49025 byte(s)
Diff to previous 883
stsplot_space(): support for labels; match.ID=FALSE; no need to require(grid)

Revision 883 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Apr 5 15:26:48 2014 UTC (4 years, 10 months ago) by wastl
File length: 48921 byte(s)
Diff to previous 881
- stsplot_space(): new implementation of spatial plot for sts-objects
- cleaned up and largely improved documentation of sts plots
- renamed internal plot.sts.* to stsplot_*,
  which are now exported and partially documented (TODO @ Michael)
- moved sts plot-variants to own source files

Revision 881 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Apr 4 11:32:06 2014 UTC (4 years, 10 months ago) by wastl
File length: 48448 byte(s)
Diff to previous 878
changed defaults for animate.epidataCS and sleep only if interactive

Revision 878 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 3 12:33:38 2014 UTC (4 years, 10 months ago) by wastl
File length: 48226 byte(s)
Diff to previous 872
twinstim() stopped with error if is.null(optim.args) && is.null(offsetGrid)

Revision 872 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 2 14:53:55 2014 UTC (4 years, 10 months ago) by wastl
File length: 48121 byte(s)
Diff to previous 868
as.epidataCS(): gained a 'verbose' argument

Revision 868 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Apr 1 22:14:36 2014 UTC (4 years, 10 months ago) by wastl
File length: 48054 byte(s)
Diff to previous 867
renamed parametric neighbourhood weight functions from W.* to W_*

Revision 867 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Apr 1 21:46:01 2014 UTC (4 years, 10 months ago) by wastl
File length: 48054 byte(s)
Diff to previous 866
plot.epidataCS_time: type-specific sub-histograms, cumulative number, legend

Revision 866 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Apr 1 14:51:38 2014 UTC (4 years, 10 months ago) by wastl
File length: 47890 byte(s)
Diff to previous 865
plot.epidataCS(,aggregate="space") gained arguments for automatic legends

Revision 865 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 31 16:36:49 2014 UTC (4 years, 10 months ago) by wastl
File length: 47504 byte(s)
Diff to previous 857
more rigorous checking of 'tiles'

Revision 857 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 25 11:25:46 2014 UTC (4 years, 10 months ago) by wastl
File length: 46929 byte(s)
Diff to previous 856
iafplot(): optionally 'truncated' at 'eps', new default scaled=TRUE

Revision 856 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 25 10:14:58 2014 UTC (4 years, 10 months ago) by wastl
File length: 46755 byte(s)
Diff to previous 852
- twinstim() appends unique eps as attribute to siaf and tiaf, respectively
- twinstim() allows vector of knots as tiaf specification

Revision 852 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 24 14:39:34 2014 UTC (4 years, 10 months ago) by wastl
File length: 46697 byte(s)
Diff to previous 851
as.stepfun.epidataCS()

Revision 851 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Mar 21 16:01:29 2014 UTC (4 years, 10 months ago) by wastl
File length: 46623 byte(s)
Diff to previous 834
epidataCS: the ID column is no longer reserved nor automatically added for events

Revision 834 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 11 23:47:28 2014 UTC (4 years, 11 months ago) by hoehle
File length: 46521 byte(s)
Diff to previous 832
added to NEWS and slimmed the description

Revision 832 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 11 21:48:54 2014 UTC (4 years, 11 months ago) by wastl
File length: 45989 byte(s)
Diff to previous 803
export and document new maxEV type of hhh4 plots

Revision 803 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Feb 27 08:54:43 2014 UTC (4 years, 11 months ago) by wastl
File length: 45930 byte(s)
Diff to previous 802
the multiplicity-generic and its default method have been integrated into
spatstat 1.36-0 (we now depend on this or later versions)

Revision 802 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 26 20:01:45 2014 UTC (4 years, 11 months ago) by wastl
File length: 45698 byte(s)
Diff to previous 798
support for parallel computation of one-step-ahead predictions

Revision 798 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 26 11:33:21 2014 UTC (4 years, 11 months ago) by wastl
File length: 45573 byte(s)
Diff to previous 796
hhh4(): 
- support for lag != 1 (+ report non-default lag in summary)
- started support for parallelization of oneStepAhead()
- less hhh4-method dispatch by calling .hhh4-methods directly

Revision 796 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 25 16:34:54 2014 UTC (4 years, 11 months ago) by wastl
File length: 45268 byte(s)
Diff to previous 795
hhh4:
- corrected isNA vector leading to wrong score function result in
  endemic-only models for 'subset's including the first time point
- improved output of optimizer messages

Revision 795 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 25 15:36:12 2014 UTC (4 years, 11 months ago) by wastl
File length: 45079 byte(s)
Diff to previous 793
removed redundant AIC/BIC-methods for hhh4 (which hindered the use of multiple objects at a time)

Revision 793 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 25 10:07:12 2014 UTC (4 years, 11 months ago) by wastl
File length: 44953 byte(s)
Diff to previous 791
reimplemented coef.hhh4() making use of vcov.hhh4() and common getCoefIdxRenamed()

Revision 791 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 24 11:59:18 2014 UTC (4 years, 11 months ago) by wastl
File length: 44938 byte(s)
Diff to previous 789
changes in hhh4():
- $se, $cov and $Sigma have names
- neOffsetFUN uses small environment (parent=empty) if weights are fixed
- some code tuning

Revision 789 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Feb 21 17:07:08 2014 UTC (4 years, 11 months ago) by wastl
File length: 44817 byte(s)
Diff to previous 786
hhh4(): allow for offsets in epidemic components

Revision 786 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Feb 20 14:53:10 2014 UTC (4 years, 11 months ago) by wastl
File length: 44676 byte(s)
Diff to previous 784
removed obsolete "lag" component (always=1) from hhh4-result; updated NEWS

Revision 784 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Feb 20 12:52:56 2014 UTC (4 years, 11 months ago) by wastl
File length: 44503 byte(s)
Diff to previous 775
updated NEWS

Revision 775 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 17 11:35:45 2014 UTC (4 years, 11 months ago) by wastl
File length: 44252 byte(s)
Diff to previous 758
added tests for tiaf.step(); updated NEWS

Revision 758 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Feb 13 10:52:40 2014 UTC (5 years ago) by wastl
File length: 44055 byte(s)
Diff to previous 751
re-organized tests to use Hadley's testthat package; RUnit is no longer used.

Revision 751 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 10 11:21:59 2014 UTC (5 years ago) by wastl
File length: 43951 byte(s)
Diff to previous 749
- iafplot(): automatic 'types' argument, changed default of 'verticals', 'do.points' to FALSE
- added Juliane and Dirk to the list of contributors

Revision 749 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Feb 7 22:29:51 2014 UTC (5 years ago) by hoehle
File length: 43760 byte(s)
Diff to previous 745
small changes in campy data set to include o104period

Revision 745 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 5 22:04:58 2014 UTC (5 years ago) by hoehle
File length: 43640 byte(s)
Diff to previous 738
started integrating the boda algo into the package

Revision 738 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 3 20:36:56 2014 UTC (5 years ago) by wastl
File length: 43068 byte(s)
Diff to previous 737
iafplot(): support for logarithmic axes

Revision 737 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 3 14:14:09 2014 UTC (5 years ago) by wastl
File length: 42960 byte(s)
Diff to previous 735
iafplot() treats step kernels in a special fashion

Revision 735 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 31 21:52:57 2014 UTC (5 years ago) by wastl
File length: 42876 byte(s)
Diff to previous 709
new temporal interaction function for twinstim(): tiaf.step()

Revision 709 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 20 15:25:51 2014 UTC (5 years ago) by wastl
File length: 42636 byte(s)
Diff to previous 705
use polyCub.iso() in siaf.powerlaw()

Revision 705 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jan 15 20:32:50 2014 UTC (5 years, 1 month ago) by wastl
File length: 42363 byte(s)
Diff to previous 704
hhh4() stores the runtime just like twinstim()

Revision 704 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jan 15 12:36:50 2014 UTC (5 years, 1 month ago) by wastl
File length: 42286 byte(s)
Diff to previous 703
renamed powerlaw() -> W.powerlaw(), re-organized source code for hhh4() weights

Revision 703 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 14 21:32:16 2014 UTC (5 years, 1 month ago) by hoehle
File length: 41951 byte(s)
Diff to previous 697
fixed bug in glrnb function which used a wrong alpha if fitted automatically using glm.nb

Revision 697 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 13 20:09:50 2014 UTC (5 years, 1 month ago) by wastl
File length: 41465 byte(s)
Diff to previous 696
update.twinstim() no longer uses recursive modifyList() on control.siaf

Revision 696 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 13 20:04:50 2014 UTC (5 years, 1 month ago) by wastl
File length: 41166 byte(s)
Diff to previous 693
- new spatial interaction function for twinstim: siaf.step()
- added residuals.hhh4 (deviance)
- dropped alternative code using numericDeriv() from checksiaf.deriv()

Revision 693 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 7 14:21:33 2014 UTC (5 years, 1 month ago) by wastl
File length: 41039 byte(s)
Diff to previous 691
hhh4() now returns a "hhh4" object (renamed from "ah4")

Revision 691 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Dec 18 13:09:41 2013 UTC (5 years, 1 month ago) by wastl
File length: 40672 byte(s)
Diff to previous 681
- removed siaf.lomax(), added siaf.student()
- removed unsupported options (logpars=FALSE, effRangeProb) from siaf.powerlaw
- moved (unused) qlomax() to own source file
- internal checksiaf() also checks $F and $Deriv and returns check results

Revision 681 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Nov 30 20:28:51 2013 UTC (5 years, 2 months ago) by wastl
File length: 40076 byte(s)
Diff to previous 680
new plot-type for fitted hhh4-objects: seasonality plots

Revision 680 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Nov 28 21:27:45 2013 UTC (5 years, 2 months ago) by wastl
File length: 40029 byte(s)
Diff to previous 678
- got rid of extra map-weserems.{pdf,eps} files, now via data(measlesWeserEms)
- partial update of hhh4-vignette

Revision 678 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 27 16:49:21 2013 UTC (5 years, 2 months ago) by wastl
File length: 39756 byte(s)
Diff to previous 676
- terms-method for hhh4-objects to extract the model, i.e.,
  the result of interpretControl()
- new plot-method for hhh4-fits (moved to seperate file), added doc
- simple coerce-method from sts to ts

Revision 676 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 22 16:00:23 2013 UTC (5 years, 2 months ago) by wastl
File length: 39462 byte(s)
Diff to previous 675
new data(measlesWeserEms)

Revision 675 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 20 16:59:03 2013 UTC (5 years, 2 months ago) by wastl
File length: 39359 byte(s)
Diff to previous 673
- published version 1.7-0 on CRAN -> bump to version 1.7-1
- take verbose=FALSE in hhh4() more seriously
- hhh4() issues a warning() if non-convergent
- changes in oneStepAhead():
  + new argument "type", new type "first"
  + changed default tp[2]: nTime-1 -> max(model$subset)-1
  + +1 on rownames of $pred (now the same as for $observed)
  + nicer interpretation of verbose levels and txtProgressBar()

Revision 673 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 19 10:18:23 2013 UTC (5 years, 2 months ago) by wastl
File length: 38468 byte(s)
Diff to previous 667
updated NEWS

Revision 667 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 8 15:04:44 2013 UTC (5 years, 3 months ago) by wastl
File length: 38371 byte(s)
Diff to previous 666
typo and TODO-list update

Revision 666 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 8 14:45:36 2013 UTC (5 years, 3 months ago) by wastl
File length: 38371 byte(s)
Diff to previous 663
- for major user-visible changes: see NEWS.Rd
- changed version number to 1.7-0 (new software requirements & polygon clipping)
- updated imdepi and imdepifit (due to !identical polygon clipping)
- dropped gpclib-related startup message
- epidataCS internally no longer works with Wgpc, but with Wowin instead
- use mapply() instead of for-loop in .influenceRegions()
- completely import stats into NAMESPACE (list of dependendies too long)
- added missing imports from utils in NAMESPACE
- removed some redundant "::" calls
- moved nbOrder() and poly2adjmat() to dedicated source file graphs.R,
- moved intersectPolyCircle()-methods (previously: intersectCircle) to own file
- moved gpc.poly-methods to own file (no longer used)
- renamed internal maxExtent.gpc.poly to diameter.gpc.poly (but no longer used)

Revision 663 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Oct 22 22:33:01 2013 UTC (5 years, 3 months ago) by wastl
File length: 36165 byte(s)
Diff to previous 662
changed default arguments for plot.epidata (lwd, rug.opts)

Revision 662 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Oct 21 16:12:15 2013 UTC (5 years, 3 months ago) by wastl
File length: 36002 byte(s)
Diff to previous 647
twinstim: changed default tracing from 5 to 1 (i.e. each iteration)

Revision 647 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 10 11:44:54 2013 UTC (5 years, 5 months ago) by wastl
File length: 35751 byte(s)
Diff to previous 640
- 1.6-0 on CRAN now -> bumped version to 1.6-1
- nicer default axis labels for iafplot()

Revision 640 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 4 16:00:17 2013 UTC (5 years, 5 months ago) by wastl
File length: 35628 byte(s)
Diff to previous 633
updated NEWS

Revision 633 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 28 20:32:19 2013 UTC (5 years, 5 months ago) by wastl
File length: 35295 byte(s)
Diff to previous 624
use sapply instead of for-loop in .eEvents()

Revision 624 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Aug 13 11:40:21 2013 UTC (5 years, 6 months ago) by wastl
File length: 35054 byte(s)
Diff to previous 618
checkWeightsArray now works with time-varying weights

Revision 618 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Aug 9 09:27:42 2013 UTC (5 years, 6 months ago) by wastl
File length: 34899 byte(s)
Diff to previous 617
corrected returned optim.args in case of fixed parameters

Revision 617 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Aug 8 15:34:45 2013 UTC (5 years, 6 months ago) by wastl
File length: 34787 byte(s)
Diff to previous 613
documented and exported polyAtBorder()

Revision 613 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Aug 5 12:01:03 2013 UTC (5 years, 6 months ago) by wastl
File length: 34640 byte(s)
Diff to previous 609
removed export of glrnbFarrington (in develop)

Revision 609 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jul 31 11:18:28 2013 UTC (5 years, 6 months ago) by hoehle
File length: 34631 byte(s)
Diff to previous 603
fixed Date bug for reference values in algo.farrington

Revision 603 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 18 09:54:49 2013 UTC (5 years, 7 months ago) by wastl
File length: 33185 byte(s)
Diff to previous 602
tidy

Revision 602 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 18 08:46:02 2013 UTC (5 years, 7 months ago) by wastl
File length: 33182 byte(s)
Diff to previous 584
updated NEWS

Revision 584 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Jul 6 10:03:51 2013 UTC (5 years, 7 months ago) by wastl
File length: 31495 byte(s)
Diff to previous 582
removed redundant and wrong last week from data(fluBYBW)

Revision 582 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 4 15:32:23 2013 UTC (5 years, 7 months ago) by wastl
File length: 31306 byte(s)
Diff to previous 575
simulate.ah4: gained simplify and component arguments

Revision 575 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jul 3 14:57:59 2013 UTC (5 years, 7 months ago) by wastl
File length: 31080 byte(s)
Diff to previous 565
re-implemented simHHH4/simulate.ah4 to make it compatible with parametric W

Revision 565 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jun 10 09:54:24 2013 UTC (5 years, 8 months ago) by wastl
File length: 30353 byte(s)
Diff to previous 564
bugfixes in update.twinstim

Revision 564 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 7 14:58:11 2013 UTC (5 years, 8 months ago) by wastl
File length: 30091 byte(s)
Diff to previous 563
if there are no random intercepts, don't do redundant updateVariance swinging

Revision 563 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 7 12:39:42 2013 UTC (5 years, 8 months ago) by wastl
File length: 29961 byte(s)
Diff to previous 559
implemented conversion from epidataCS to sts

Revision 559 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jun 3 15:31:24 2013 UTC (5 years, 8 months ago) by wastl
File length: 29730 byte(s)
Diff to previous 557
- updated NEWS
- moved untie-methods into own file
- untie-methods (ex post log message):
  + bugfix: res <- x + shift instead of res <- res + shift
    which could have led to jittering greater than 'amount'
  + new feature: 'minsep' of jittered points

Revision 557 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed May 22 11:10:54 2013 UTC (5 years, 8 months ago) by wastl
File length: 29489 byte(s)
Diff to previous 553
- update.twinstim now uses modifyList for control.siaf
- twinstim(...)$converged is either TRUE or contains the failure message

Revision 553 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue May 14 13:59:34 2013 UTC (5 years, 9 months ago) by wastl
File length: 29330 byte(s)
Diff to previous 549
implemented log-parametrization of the power law decay parameter

Revision 549 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat May 11 23:20:26 2013 UTC (5 years, 9 months ago) by wastl
File length: 28546 byte(s)
Diff to previous 548
- added rgeos-support as a substitute for polygon intersection (gpclib) if
  surveillance.options(gpclib=FALSE)
- replaced deprecated overlay-methods by over-method (sp package)
- use identicalCRS-function (-> depend on sp >= 1.0-6)

Revision 548 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat May 11 15:55:18 2013 UTC (5 years, 9 months ago) by wastl
File length: 28273 byte(s)
Diff to previous 542
removed polyCub-methods (now imported from new dedicated package polyCub)

Revision 542 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Apr 28 15:03:50 2013 UTC (5 years, 9 months ago) by wastl
File length: 27907 byte(s)
Diff to previous 539
- tiaf.exponential(1) now works with multi-type data in twinstim()
- support for automatic legend in iafplot()
- added some examples code

Revision 539 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 25 13:33:22 2013 UTC (5 years, 9 months ago) by hoehle
File length: 27609 byte(s)
Diff to previous 538
modifications to get 1.5-4 on CRAN

Revision 538 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Apr 19 13:20:16 2013 UTC (5 years, 9 months ago) by wastl
File length: 27610 byte(s)
Diff to previous 532
- siaf.powerlawL() is now exported and documented
- updated NEWS etc.
- removed THANKS file since it is not part of the built package;
  the acknowledgments are part of surveillance-package.Rd

Revision 532 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 17 15:33:10 2013 UTC (5 years, 10 months ago) by wastl
File length: 27476 byte(s)
Diff to previous 530
- now developing on version 1.5-3
- new siaf for lagged powerlaw

Revision 530 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Mar 15 09:52:26 2013 UTC (5 years, 11 months ago) by wastl
File length: 27095 byte(s)
Diff to previous 518
updated NEWS

Revision 518 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 26 10:49:38 2013 UTC (5 years, 11 months ago) by wastl
File length: 26883 byte(s)
Diff to previous 514
updated NEWS

Revision 514 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 19 12:32:20 2013 UTC (5 years, 11 months ago) by wastl
File length: 26635 byte(s)
Diff to previous 507
bugfix: only calculate initial value for beta0 if it is actually part of the model

Revision 507 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 5 20:55:22 2013 UTC (6 years ago) by wastl
File length: 26499 byte(s)
Diff to previous 506
xtable-method for summary.twinstim; formatPval()

Revision 506 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Feb 4 21:51:00 2013 UTC (6 years ago) by wastl
File length: 26283 byte(s)
Diff to previous 503
toLatex.summary.twinstim: changed defaults and new eps.Pvalue argument

Revision 503 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Feb 1 10:38:34 2013 UTC (6 years ago) by wastl
File length: 26152 byte(s)
Diff to previous 491
warn about 'amount'>minsep in untie.default; updated NEWS

Revision 491 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Jan 27 14:45:47 2013 UTC (6 years ago) by wastl
File length: 25673 byte(s)
Diff to previous 487
- The update.twinstim() method now by default uses the
  parameter estimates from the previous model as initial values for
  the new fit (new argument use.estimates=TRUE)
- Implemented terms() and extractAIC() methods for 
  class "twinstim", which enable the use of step() for the
  endemic component.

Revision 487 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 25 11:17:17 2013 UTC (6 years ago) by wastl
File length: 24839 byte(s)
Diff to previous 485
new argument verbose for twinstim()

Revision 485 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jan 24 22:30:43 2013 UTC (6 years ago) by wastl
File length: 24676 byte(s)
Diff to previous 482
nobs-methods for epidataCS and twinstim

Revision 482 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jan 24 14:05:06 2013 UTC (6 years ago) by wastl
File length: 24586 byte(s)
Diff to previous 478
bugfix: addSeason2formula() now also works for long formulae

Revision 478 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Dec 21 13:35:49 2012 UTC (6 years, 1 month ago) by wastl
File length: 24381 byte(s)
Diff to previous 477
- version 1.5-1 was published on CRAN @ 2012-12-14 -> now developing on 1.5-2
- plot.epidataCS_time now understands an "add"-argument

Revision 477 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Dec 13 13:26:23 2012 UTC (6 years, 2 months ago) by wastl
File length: 24014 byte(s)
Diff to previous 474
updated NEWS

Revision 474 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Dec 12 10:24:10 2012 UTC (6 years, 2 months ago) by wastl
File length: 23746 byte(s)
Diff to previous 473
- published surveillance version 1.5-0 on CRAN as at 2012-12-12
  -> now developing on 1.5-1
- added line breaks in NEWS.Rd to circumvent PR #15134

Revision 473 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Dec 10 23:47:45 2012 UTC (6 years, 2 months ago) by wastl
File length: 23738 byte(s)
Diff to previous 465
tidy; updated NEWS and TODO

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Modified Fri Dec 7 15:53:25 2012 UTC (6 years, 2 months ago) by wastl
File length: 23616 byte(s)
Diff to previous 463
implemented surveillance.options(), currently we have "allExamples" (TRUE)
and "gpclib" (FALSE, replacing the global option)

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Modified Thu Dec 6 16:26:39 2012 UTC (6 years, 2 months ago) by wastl
File length: 23563 byte(s)
Diff to previous 457
- implemented a gpclib-barrier (gpclibCheck) to have the package
  in round terms under GPL-2 as requested by the CRAN team.
  The gpclib package is no longer imported, but only suggested.
  This required a lot of small adaptions in many places in the code.
- the scale.poly-method for gpc.poly is now available as scale.gpc.poly
- changed the default return class of discpoly() from "gpc.poly" to "Polygon"
- tidying: placed some helper functions from zzz.R into own R source files
- updated the NEWS file

Revision 457 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 16 00:03:33 2012 UTC (6 years, 3 months ago) by wastl
File length: 22738 byte(s)
Diff to previous 398
updated NEWS and TODO files

Revision 398 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Aug 23 20:19:21 2012 UTC (6 years, 5 months ago) by wastl
File length: 16922 byte(s)
Diff to previous 390
package links in NEWS file

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Modified Fri Aug 17 15:48:09 2012 UTC (6 years, 6 months ago) by wastl
File length: 16914 byte(s)
Diff to previous 387
- removed redundant coef-methods for twinSIR and twinstim (just use coef.default)
- new R0-method for "simEpidataCS"-objects (wrapper for R0.twinstim)
- added argument checks in discpoly()
- .tiafIntFUN()-generator
- fixed bug in the "counter" step function returned by summary.epidataCS(),
  which resulted in false (lagged) numbers of infectives.
- removed dimyx and eps arguments from R0.twinstim();
  now uses nCub and nCub.adaptive from the fitted model and
  applies the same (numerical) integration method (by the .siafIntFUN()-generator)
- simEpidataCS() received tiny bug fixes and is now able to simulate from
  epidemic-only models
- The coefficients returned by simEpidataCS() are now stored in a vector rather
  than a list for compatibility with twinstim-methods

Revision 387 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Aug 15 15:11:25 2012 UTC (6 years, 6 months ago) by wastl
File length: 16097 byte(s)
Diff to previous 381
updated NEWS file

Revision 381 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Aug 10 15:13:27 2012 UTC (6 years, 6 months ago) by wastl
File length: 15922 byte(s)
Diff to previous 362
- different error handling of spsample in simEpidataCS (using ntries to
  avoid a potentially infinite loop)
- removed the call to browser() in simEpidataCS if ntries >= 1000
  for the siaf$simulate call (now stop())
- included CAVE about truncated stgrid for simulate.twinstim with
  simplified=TRUE and nsim>1
- speed-up of simulation examples (shorter simulation period) and
  twinstim examples (better start value)
- and finally: updated NEWS file!

Revision 362 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 26 21:19:19 2012 UTC (6 years, 6 months ago) by wastl
File length: 12223 byte(s)
Diff to previous 355
fixed typos in NEWS and index.php

Revision 355 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 26 09:24:40 2012 UTC (6 years, 6 months ago) by wastl
File length: 12216 byte(s)
Diff to previous 317
published version 1.4-1 on CRAN, started working on patched version 1.4-2

Revision 317 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Jul 22 22:09:53 2012 UTC (6 years, 6 months ago) by wastl
File length: 12082 byte(s)
Diff to previous 316
- subset-method for epidataCS (documented)
- use tryCatch instead of try in polyCub.midpoint
- fixed bug in [.epidataCS: nCircle2Poly attribute of
  x$events$.influenceRegion got lost
- twinstim:
  + message if constant siaf / tiaf
  + score function now also uses nCub if not adaptive
- updated the NEWS file

Revision 316 - (view) (download) (as text) (annotate) - [select for diffs]
Added Wed Jul 18 21:17:48 2012 UTC (6 years, 7 months ago) by wastl
File length: 11071 byte(s)
converted NEWS file to the Rd format (now found in /inst/NEWS.Rd)

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