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More from @tomtom_m

29 Dec
As flagged last week there is NO excess deaths report released this week. There were not many days in which deaths in the week to 25/12 could have been reported. Deaths in the week to 25/12 should have been reported this week, and will be included in the report next week.
On the testing side, proportions testing positive fell in many provinces.. But a data problem in NW last week, which saw duplicate negative results being loaded, means that that province's decline is exaggerated, as is (to a limited extent) the national figure.
The report is here:… National PTP 'fell' to 35.3% (see previous tweet for caveat). Gauteng fell from 29% to 22.7%. The WC, EC, NC and KZN all increased. ImageImage
Read 6 tweets
22 Dec
Latest @MRCza and @UCT_news report on excess deaths in South Africa released, covering the period to 18Dec21. 280 000 excess natural deaths (471/100 000) since 3May2020.
Report available here:…
2/ Nationally, natural deaths were 33% above expected (the p-score), compared to 18% the previous week. 2 600 excess natural deaths in the most recent week (12-18Dec), up from 1500 the previous week.
70% of excess deaths were among those aged 60+.
3/ By province, excess deaths increased in Gauteng over the week (p-score up from 16 to 44%). Limpopo up from 19% to 47%. Deaths in Johannesburg was 53% above expected (last week 27%). But still FAR below the peaks in previous waves
Read 21 tweets
19 Dec
A series of mini-thoughts for a Sunday afternoon. South Africa vs. Rest of the World - the Omicron Edition.
1) We are pretty confident that Gauteng, the province at the South African Omicron epicentre is past its peak in terms of proportion of tests returning positive.
2) Despite massive number of cases (and incredibly high PTP: in the week to 11Dec, in Gauteng an ALL-TIME high of 38.7% - and an intra-week daily high of 41% when looking at PCR tests only), we have seen relatively few hospitalisations and deaths.
3) It really *does seem* as if South Africa, my country, will escape relatively unscathed in this wave.

None of that is particularly new. But other things gnaw at me.
Read 12 tweets
16 Dec
More on the turn in proportions testing positive in Gauteng (mentioned in last night's thread: ).
1. While we had suspected that the daily PTP had maxed out on 1 Dec, the clear periodicity in the data means that we had to wait to confirm
1b. We also had crashed into data problems of loaded data from public facilities, so had to split by public/private to be more certain that PTP in each had turned before calling it.
On top of that, the known issues with loading of Ag test results means focus must be on PCR tests.
1c. Weekly periodicity means that it's preferable to use a 7day centred moving average, and to wait until the daily peaks had moved out of the 7DCMA window to confirm. Adding another day's data (covering to 14/12) confirms the trend. NB! GAUTENG PCR ONLY
Read 9 tweets
15 Dec
Latest @MRCza and @UCT_news report on excess deaths in South Africa released, covering the period to 11Dec2021. A total of 277 700 excess natural deaths since 3May20. Full report available here:…
(2/) 1 887 excess natural deaths in the week to 11Dec, up from 1 726 in the preceding week. The p-score this week is 23%, up slightly from 21% the previous week.
(3/) Still no strong excess natural mortality signal from Gauteng or its metros. The p-score in Gauteng in the most recent week is 19% (the fourth lowest of the 9 provinces). Highest in the Eastern Cape (45%) and Mpumalanga (25%).
Read 21 tweets
12 Dec
Given the comedic misinterpretation of the South African testing data offered by @BallouxFrancois (and many others!) last night ... I offer some tips having contributed to the analysis of the testing data for the @nicd_sa since April last year. (1/6)
1. The daily tests announced are those that are LOADED that day. The test may have been conducted several days/weeks earlier. What those daily reports mean is pretty hard to interpret. (2/6)
2. The VOLUME of daily tests is highly periodic, low on weekends, for example. The count of CASES is also highly periodic. But the proportion testing positive is ALSO periodic - so it's not a case of the two periodicities in cases and tests cancelling each other out. (3/6)
Read 6 tweets

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